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1. The identification of the 3′terminus of the 70 S RNA of murine sarcoma virus (moloney) [1972]

  • Robin, Jacqueline, Larsen, Christian Jacques, Ravicovitch, Rodica Emanöil, Bazilier, Monique, Mauchauffe, Martine, and Boiron, Michel
  • FEBS Letters; October 1972, Vol. 27 Issue: 1 p58-62, 5p

2. Immunological Comparison of Muscle Actins from Mammal, Bird and Fish [1979]

  • Benyamin, Yves, Roger, Michel, Gabrion, Jacqueline, Robin, Yvonne, and Van Thoai, Nguyen
  • FEBS Letters; June 1979, Vol. 102 Issue: 1 p69-74, 6p

3. On Winning Friends and Influencing People: Action Identification and Self-Presentation Success [1992]

  • Vallacher, Robin R., Wegner, Daniel M., McMahan, Susan C., Cotter, Jacqueline, and Larsen, Kathleen A.
  • Social Cognition; Fall 1992, Vol. 10 Issue: 3 p335-355, 21p
Abstract
This study tested the performance optimality hypothesis of action identification theory in the context of self-presentation. Optimal performance is said to occur when a personally easy action is identified in relatively high level terms (i.e., the action's goals and likely effects) or a personally difficult action is identified in relatively low level terms (i.e., the action's mechanical details). To test this idea with respect to self-presentation, subjects were asked to describe themselves to either a difficult-to-impress or an easy-to-impress stranger in advance of a get-acquainted conversation with him or her. Subjects were induced to think about the self-description task in either high level terms (e.g., demonstrating their personality) or low level terms (e.g., smiling when appropriate). Support for the optimality hypothesis was obtained in subjects' self-reports of their self-presentation effectiveness and in observers' evaluations of subjects. Discussion centered on the manifestation of self-presentation nonoptimality in the early stages of relationship formation.

4. Characteristics Relating to Ovarian Cancer Risk Collaborative Analysis of 12 U.S. Case-Control Studies. VI. Nonepithelial Cancers among Adults [1992]

  • Horn-Ross, Pamela L., Whittemore, Alice S., Harris, Robin, and Itnyre, Jacqueline
  • Epidemiology; November 1992, Vol. 3 Issue: 6 p490-495, 6p
Abstract
Nonepithelial ovarian cancers are rare, and little is known about their etiology. Of particular interest are the effects of oral contraceptive use and pregnancy, both of which are associated with large decreases in risk for epithelial ovarian cancer. We examined the risk factors for nonepithelial ovarian tumors by combining data from four case-control studies conducted in the United States. We compared personal characteristics of 38 germ cell cases and 45 stromal cases, respectively, with 1,142 and 2,617 general population controls. All subjects were over age 18 years. For germ cell tumors, there was a weak negative association with parity but no consistent pattern of decreasing risk with increasing parity. In contrast, relative to nulligravid women, gravid nulliparous women were at increased risk of developing a germ cell cancer odds ratio (OR) 4.8, 95 confidence interval (CI) 1.2-18.61. The use of oral contraceptives was also associated with elevated risk (OR 2.0,95 CI 0.77- 5.1); however, no clear trends in risk were observed. For stromal tumors, oral contraceptive use was associated with decreased risk (OR 0.37, 95 CI 0.16-0.83), whereas pregnancy was associated with a small elevation in risk. A trend of increasing risk with increasing age at first term pregnancy was observed, with an odds ratio of 3.6 (95 CI 1.0-12.5) for a first birth after age 29 years. Risk factors for nonepithelial ovarian cancers do not appear to parallel each other or those for epithelial ovarian cancer. (Epidemiology 1992;3490-495)

5. Characteristics Relating to Ovarian Cancer Risk: Collaborative Analysis of 12 US Case-Control Studies: I. Methods [1992]

  • Whittemore, Alice S., Harris, Robin, Itnyre, Jacqueline, Halpern, Jerry, and Group, the Collaborative Ovarian Cancer
  • American Journal of Epidemiology; November 1992, Vol. 136 Issue: 10 p1175-1175, 1p
Abstract
Data from 12 US case-control studies of ovarian cancer, conducted during the period 1956–1986 and representing some 3, 000 cases and 10,000 controls, were pooled and reanalyzed. Separate analyses were conducted for four subgroups of the pooled data: invasive epithelial ovarian cancers in white women; epithelial ovarian cancers of low malignant potential in white women, epithelial ovarian cancers in black women, and nonepithelial ovarian cancers. This paper gives a brief description of the participating studies and describes the methods used in the collaborative analysis. Am J Epidemiol1992; 136: 1175–83

6. Characteristics Relating to Ovarian Cancer Risk: Collaborative Analysis of 12 US Case -Control Studies: II. Invasive Epithelial Ovarian Cancers in White Women [1992]

  • Whittmore, Alice S., Harris, Robin, Itnyre, Jacqueline, and Group, the Collaborative Ovarian Cancer
  • American Journal of Epidemiology; November 1992, Vol. 136 Issue: 10 p1184-1184, 1p
Abstract
Data collected from 2,197 white ovarian cancer patients and 8,893 white controls in 12 US case-control studies conducted in the period 1956–1986 were used to evaluate the relation of invasive epithelial ovarian cancer to reproductive and menstrual characteristics, exogenous estrogen use, and prior pelvic surgeries. Clear trends of decreasing risk were evident with increasing number of pregnancies (regardless of outcome) and increasing duration of breast feeding and oral contraceptive use. Ovarian dysfunction leading to both infertility and malignancy is an unlikely explanation for these trends for several reasons: 1) The trends were evident even among the highly parous; 2) risk among nulliparous women did not vary by marital status or gravidity; and 3) risk among ever-married women showed little relation to length of longest pregnancy attempt or history of clinically diagnosed infertility. Risk was increased among women who had used fertility drugs and among women with long total duration of premenopausal sexual activity without birth control; these associations were particularly strong among the nulligravid. No consistent trends in risk were seen with age at menarche, age at menopause, or duration of estrogen replacement therapy. A history of tubal ligation or of hystereclomy with ovarian conservation was associated with reduced ovarian cancer risk. These observations suggest that pregnancy, breast feeding, and oral contraceptive use induce biological changes that protect against ovarian malignancy, that, at most, a small fraction of the excess ovarian cancer risk among nulliparous women is due to infertility, and that any increased risk associated with infertility may be due to the use of fertility drugs. Am J Epidemiol 1992; 136: 1184–1203

7. Characteristics Relating to Ovarian Cancer Risk: Collaborative Analysis of 12 US Case-Control Studies: III. Epithelial Tumors of Low Malignant Potential in White Women [1992]

  • Harris, Robin, Whittemore, Alice S., Itnyre, Jacqueline, and Group, the Collaborative Ovarian Cancer
  • American Journal of Epidemiology; November 1992, Vol. 136 Issue: 10 p1204-1204, 1p
Abstract
Epithelial ovarian neoplasms of low malignant potential, also called borderline ovarian tumors, have various features of malignancy, but they do not invade the ovarian stroma. Women with these tumors usually are younger when diagnosed and have better prognoses than do women with invasive tumors. There have been few epidemiologic studies of borderline tumors, and it is unclear whether there are etiologic differences between the two types of tumor behavior. Combined data from nine case-control studies, conducted from 1974 to 1986 and representing 327 white women with tumors of low malignant potential and 4, 144 white controls, were used to evaluate the relation between these tumors and personal characteristics related to invasive ovarian cancer. The risk profile for tumors of low malignant potential was found to be similar to that for invasive tumors, with two exceptions: Compared with that of invasive tumors, risk of borderline tumors was less clearly reduced among women who had used oral contraceptives and more clearly elevated among women with a history of Infertility. Am J Epidemiol 1992; 136: 1204–11

8. Characteristics Relating to ovarian Cancer Risk: Collaborative Analysis of 12 US case-Control Studies: IV. The Pathogenesis of Epithlial Ovarian Cancer [1992]

  • Whittemore, Alice S., Harris, Robin, ltnyre, Jacqueline, and Group, the Collaborative Ovarian Cancer
  • American Journal of Epidemiology; November 1992, Vol. 136 Issue: 10 p1212-1212, 1p
Abstract
Two hypotheses have been proposed to explain the reduced risk of epithelial ovarian cancer associated with pregnancy and oral contraceptive use. The first states that some sequelae of ovulation increase the likelihood of malignancy and that pregnancies and oral contraceptives protect by suppressing ovulation. The second hypothesis states that circulating levels of pituitary gonadotropins increase the risk of malignancy and that pregnancies and oral contraceptives protect by suppressing secretion of these hormones. The authors evaluate the two hypotheses in light of combined data from 12 United States case-oxitrol studies of epithelial ovarian cancer in white women conducted from 1956 to 1986. While a number of observations support both hypotheses, there are exceptions. Differential risk reduction associated with pregnancy and oral contraceptive use (pregnancy being the more effective in young women and the less effective in older women) conflicts with the first “ovulation” hypothesis, while reduced risk associated with breast feeding and absence of altered risk associated with estrogen replacement therapy conflicts with the second “gonadotropin” hypothesis. Several findings would not have been predicted by either hypothesis, e.g., only weak trends relate cancer risk to age at menarche, and, among older women, no clear trends relate risk to age at menopause. Odds ratio attenuation due to errors in reporting personal characteristics may be responsible for some of these inconsistencies. Multidisciplinary research is needed to clarify the etkrfogic roles of ovulation and gonadotropin stimulation, both of which may enhance carcinogenesis in the ovarian epithelium. Am J Epidemiol 1992: 136: 1212–20

9. Characteristics Relating to Ovarian Cancer Risk: Collaborative Analysis of Seven U.S. Case-Control Studies. Epithelial Ovarian Cancer in Black Women [1993]

  • John, Esther M., Whittemore, Alice S., Harris, Robin, Itnyre, Jacqueline, and Group, Collaborative Ovarian Cancer
  • JNCI Journal of the National Cancer Institute; January 1993, Vol. 85 Issue: 2 p142-142, 1p
Abstract
Background Previous epidemiologic studies of ovarian cancer have focused chiefly on White women, who have a higher incidence of ovarian cancer than Black women. No study has previously examined risk factors for ovarian cancer among Black women. Purpose This study was designed to evaluate the risk of epithelial ovarian cancer in Black women in relation to reproductive characteristics such as pregnancy, oral contraceptive use, and breast-feeding, and to determine whether differences in reproductive factors between Black and White women account for differences in ovarian cancer incidence. Methods Combining interview data from seven case-control studies, we compared reproductive characteristics of 110 Black case subjects with a diagnosis of epithelial ovarian cancer between 1971 and 1986 with characteristics of 251 Black population control subjects and 114 Black hospital control subjects. We also compared the prevalence of reproductive factors in 246 Black population control subjects and 4378 White population control subjects and estimated the fraction of Black-White differences in ovarian cancer incidence attributable to racial differences in prevalence of these characteristics. Results Decreased risks of epithelial ovarian cancer in Black women were associated with parity of four or higher (odds ratio [OR]=0.53; 95% confidence interval [CI]=0.25–1.1), breast-feeding for 6 months or longer (OR=0.85; 95% CI=0.36–2.0), and use of oral contraceptives for 6 years or longer (OR=0.62; 95% CI=0.24–1.6). A greater proportion of Black women (48%) than White women (27%) reported four or more term pregnancies, and Black women (62%) were more likely than White women (53%) to have breast-fed their children. Oral contraceptive use was more common among White women (59%) than Black women (51%). Conclusions Differences in the prevalence of other factors related to ovarian cancer risk or differences in genetic susceptibility must explain most of the Black-White differences in incidence of ovarian cancer. [J Natl Cancer Inst 85:142–147, 1993]

10. New barriers to ventricular invasion in paraglottic laryngeal cancer [1994]

  • Beitler, Jonathan J., Mahadevia, Panna S., Silver, Carl E., Wadler, Scott, Rubin, John S., Bello, Jacqueline A., Mitnick, Robin J., and Vikram, Bhadrasain
  • Cancer. May 15, 1994, Vol. 73 Issue 10, p2648, 5 p.
Subjects
Physiological aspects, Development and progression, Cancer invasiveness -- Physiological aspects, and Laryngeal cancer -- Development and progression
Abstract
Background. Anatomic barriers to the spread of laryngeal cancer include the conus elasticus, the quadrangular membrane, and the thyroid cartilage. It has been speculated that an elastic barrier surrounds and protects the ventricle. Methods. The authors studied the microanatomic patterns of spread of 17 cases of patients who had laryngeal cancer with paraglottic disease and confirmed their findings by examining normal autopsy specimens. Results. Five patients of the seventeen cases showed no ventricular mucosal involvement despite extensive paraglottic disease. Both an inner, central, subepithelial periventricular elastic barrier, and a more peripheral periventricular elastic membrane barrier were identified; the latter was in continuity with the conus elasticus and quadrangular membrane. Conclusions. Two weak fibroelastic barriers surround the ventricle. The outer, peripheral, fibroelastic membrane is contiguous with the conus elasticus and the quadrangular membrane. Therefore, ventricular involvement is not a sensitive indicator of paraglottic spread. Squamous cell cancer may grow around the periventricular barriers to involve both the true and false cords but may spare the ventricle. The prognostic significance of the violation or preservation of the periventricular elastic barriers is unknown.

11. Developmental Expression of the Sea Urchin Egg Receptor for Sperm [1994]

  • Ohlendieck, Kay, Partin, Jacqueline S., Stears, Robin L., and Lennarz, William J.
  • Developmental Biology; September 1994, Vol. 165 Issue: 1 p53-62, 10p
Abstract
Little is known about the biochemical changes underlying the morphological differentiation of the sea urchin egg during oogenesis. Because of this and the essential role of gamete recognition in fertilization, we studied the developmental expression of the recently identified egg surface receptor for sperm during oogenesis. Consecutive stages of ovaries undergoing oogenesis over a 4-month time course were examined morphologically and assessed with respect to content of sperm receptor mRNA, as well as the content and subcellular distribution of the sperm receptor glycoprotein. Although in early oocyte stages neither mRNA encoding for the receptor nor receptor glycoprotein was detectable, at the last two stages of development the level of receptor mRNA accumulation increased dramatically. This finding correlated well with immunoblot analyses which established that sperm receptor protein was only detectable at the last two stages of egg maturation. Interestingly, immunocytochemistry showed that the formation of the receptor correlated temporally and spatially with the formation of cortical granules. In the earlier of these two stages of maturation, the receptor population identified by immunoblotting was found by immunocytochemistry to be restricted to the cortical granules and small vesicles in the cytoplasm. In contrast, at the last stage of egg maturation, sperm receptor was also detected at the surface of the oocyte, localized predominantly to the microvilli. Two receptor populations appear to exist, one in cortical granules and a second at the cell surface that may be formed via secretory vesicles. The late appearance of the receptor on the plasma membrane during oogenesis is consistent with its biological role in binding sperm to the mature egg cell surface.

12. The Use of Magnetic Resonance Angiography prior to Pharyngeal Flap Surgery in Patients with Velocardiofacial Syndrome [1996]

  • Mitnick, Robin J., Bello, Jacqueline A., GoldingKushner, Karen J., Argamaso, Ravelo V., and Shprintzen, Robert J.
  • Plastic and Reconstructive Surgery; April 1996, Vol. 97 Issue: 5 p908-919, 12p
Abstract
Twenty consecutive patients with velocardiofacial syndrome underwent magnetic resonance angiography MRA to determine if abnormalities of the neck arteries would contraindicate pharyngeal flap surgery. All 20 patients were found to have anomalies of the carotid arteries, vertebral arteries, or both. Anomalies included tortuous or kinked vertebral arteries, medially placed internal carotids, low carotid bifurcations, and tortuous or kinked internal carotids. The internal carotids were found to be almost directly under the mucous membrane of the pharynx in two patients. In these two patients, the arteries were close to the pharyngeal midline at the base of the first cervical vertebra and might easily be severed during the raising of a pharyngeal flap. Hypoplastic vertebral arteries also were found. One patient had an extra neck vessel. The anomalies of the internal carotids did not have a strong correlation with endoscopically observed pulsations in the posterior pharyngeal wall. It also was found that head position affected the location of the internal carotid arteries when they were located close to the pharyngeal mucous membrane. The information provided in the MRA studies allowed assessment of the arterial anomalies in relation to the flap donor site so that the patients in the sample who underwent pharyngeal flap surgery using a short superiorly based flap had no major bleeding complications. Plast. Reconstr. Surg. 97 908, 1996.

13. Internal medicine student clubs in U.S. medical schools [1996]

  • Albritton, T., Fincher, Ruth-Marie, Mutha, Sunita, Womeodu, Robin, Kirk, Lynne, Peterson, Jacqueline, and Carson, Jeffrey
  • Journal of General Internal Medicine; July 1996, Vol. 11 Issue: 7 p440-440, 1p

14. Uncertainties in field-line tracing in the magnetosphere. Part I: the axisymmetric part of the internal geomagnetic field [1997]

  • Willis, D. M., Singh, J. Robin, and Comer, Jacqueline
  • Annales Geophysicae; February 1997, Vol. 15 Issue: 2 p165-180, 16p
Abstract
The technique of tracing along magnetic field lines is widely used in magnetospheric physics to provide a “magnetic frame of reference” that facilitates both the planning of experiments and the interpretation of observations. The precision of any such magnetic frame of reference depends critically on the accurate representation of the various sources of magnetic field in the magnetosphere. In order to consider this important problem systematically, a study is initiated to estimate first the uncertainties in magnetic-field-line tracing in the magnetosphere that arise solely from the published (standard) errors in the specification of the geomagnetic field of internal origin. Because of the complexity in computing these uncertainties for the complete geomagnetic field of internal origin, attention is focused in this preliminary paper on the uncertainties in magnetic-field-line tracing that result from the standard errors in just the axisymmetric part of the internal geomagnetic field. An exact analytic equation exists for the magnetic field lines of an arbitrary linear combination of axisymmetric multipoles. This equation is used to derive numerical estimates of the uncertainties in magnetic-field-line tracing that are due to the published standard errors in the axisymmetric spherical harmonic coefficients (i.e. gn0 ± dgn0). Numerical results determined from the analytic equation are compared with computational results based on stepwise numerical integration along magnetic field lines. Excellent agreement is obtained between the analytical and computational methods in the axisymmetric case, which provides great confidence in the accuracy of the computer program used for stepwise numerical integration along magnetic field lines. This computer program is then used in the following paper to estimate the uncertainties in magnetic-field-line tracing in the magnetosphere that arise from the published standard errors in the full set of spherical harmonic coefficients, which define the complete (non-axisymmetric) geomagnetic field of internal origin. Numerical estimates of the uncertainties in magnetic-field-line tracing in the magnetosphere, calculated here for the axisymmetric part of the internal geomagnetic filed, should be regarded as “first approximations” in the sense that such estimates are only as accurate as the published standard errors in the set of axisymmetric spherical harmonic coefficients. However, all procedures developed in this preliminary paper can be applied to the derivation of more realistic estimates of the uncertainties in magnetic-field-line tracing in the magnetosphere, following further progress in the determination of more accurate standard errors in the spherical harmonic coefficients.

15. Ki-67 Antigen Staining as an Adjunct to Identifying Cervical Intraepithelial Neoplasia [1997]

  • Dunton, Charles J., van Hoeven, Karen H., Kovatich, Al J., Oliver, Robin E., Scacheri, Robert Q., Cater, Jacqueline R., and Carlson, John A.
  • Gynecologic Oncology; March 1997, Vol. 64 Issue: 3 p451-455, 5p
Abstract
The purpose of the work was to determine the feasibility and predictive value of Ki-67 immunostaining of cervical cytology and the detection of cervical dysplasia. Air-dried cervical smears were stained with MIB-1 antibody to identify the Ki-67 antigen. Nuclear decoration in abnormal squamous nuclei determined immunoreactivity. One hundred twenty-four nonpregnant patients underwent colposcopy and directed biopsies for abnormal cytology. Sensitivity (0.89), specificity (0.65), positive predictive value (0.60), and negative predictive value (0.91) were found for Ki-67 immunostaining in detection of high-grade cervical intraepithelial neoplasia (CIN) in 124 patients and positive Ki-67 staining was a significant predictor of high-grade CIN in both univariate (odds ratio 15.5 (95% CI 5.5–43.8) and multivariable (odds ratio 21.5 (95% CI 5.0–92.0) analysis. In 101 patients with ASCUS and LGSIL, Ki-67 immunostaining demonstrated the following in detection of high-grade CIN: sensitivity (0.96), specificity (0.67), positive predictive value (0.49), and negative predictive value (0.98). Ki-67 immunostaining of cervical cytology is a predictor of significant cervical pathology with high sensitivity and negative predictive value. Ki-67 immunostaining of cervical cytology may represent a new and cost-effective triage tool for patients with minor abnormalities on cytology.

16. The Efficacy and Effectiveness of Process Consultation in Improving Staff Morale and Absenteeism [1997]

  • Weir*, Robin, †, Stewart*, Larry, †, ‡, Browne*, Gina, †, §, ¶, Roberts*, Jacqueline, §, ¶, Gafni§, Amiram, ¶, Easton*, Sandra, †, ‡, and Seymour‡, Louise
  • Medical Care; April 1997, Vol. 35 Issue: 4 p334-353, 20p
Abstract
The purpose of this randomized controlled trial was to test the efficacy and effectiveness of process consultation consisting of a series of nurse manager-consultant problem-solving meetings for leadership development that would lead to their staff's improved morale, quality of care, and reduced absenteeism.

17. CD4-Independent Infection by HIV-2 (ROD/B): Use of the 7-Transmembrane Receptors CXCR-4, CCR-3, and V28 for Entry [1997]

  • Reeves, Jacqueline D., McKnight, ÁINE, Potempa, Sandra, Simmons, Graham, Gray, Patrick W., Power, Christine A., Wells, Timothy, Weiss, Robin A., and Talbot, Simon J.
  • Virology; April 1997, Vol. 231 Issue: 1 p130-134, 5p
Abstract
We have assayed a variety of 7tm chemokine receptors (CCR-2b, CCR-3, CCR-4, CCR-5, CXCR-1, CXCR-4) and two orphan 7tm receptors (V28 and EBI.1) for their ability to allow infection of CD4-negative feline kidney CCC cells by the HIV-2 strains ROD/A and ROD/B. We found that ROD/B was able to use CXCR-4 transiently expressed in CCC cells, and infection by ROD/A was enhanced 15-fold in the presence of sCD4. Feline CCC cells also became permissive to ROD/B and ROD/A entry when transiently transfected with the chemokine receptor CCR-3 or the orphan 7tm receptor V28, when cultured in the presence of sCD4. Entry of ROD/A into CCC cells expressing CCR-3 could be blocked by 800 ng/ml eotaxin, the natural ligand for CCR-3.

18. An evaluation of peer and professional trainers in a union-based occupational health and safety training program [1997]

  • Kurtz, Jacqueline R., Robins, Thomas G., and Schork, M. Anthony
  • Journal of Occupational and Environmental Medicine. July 1997, Vol. 39 Issue 7, p661, 11 p.
Subjects
Training, Evaluation, Occupational safety and health -- Training, Employee trainers -- Evaluation, and Occupational health and safety -- Training
Abstract
Social cognitive theory posits that behavior can be changed by observing others perform or describe performance of behaviors. This framework was applied to understanding health behavior change associated with workplace health and safety training. Questionnaires were developed and administered to 426 workers at a United Automobile Worker's Union health and safety training program. Participants received training from one of three trainers: (1) local union discussion leaders (LUDLs), (2) professional staff trainers, or (3) LUDLs with professional staff trainers. Data were collected in three phases: before, after, and three months post-training. Findings show that subjects trained by LUDLs identify most closely with their instructors, whereas subjects trained by staff trainers identify least closely with them. In addition, workers trained by LUDLs reported changing behavior as a result of training more often than workers trained by others.

19. Reactivity of carbanions of Fischer-type carbene complexes with pyrylium salts. Synthesis of new γ-methylenepyran carbene complexes via an addition-oxidation-deprotonation process [1998]

  • Caro, Bertrand, Le Poul, Pascal, Robin-Le Guen, Françoise, Sénéchal-Tocquer, Marie-Claude, and Vaisserman, Jacqueline
  • Tetrahedron Letters; January 1998, Vol. 39 Issue: 7 p557-560, 4p
Abstract
The condensation reaction between γ-unsubstituted pyrylium salts and carbanions of Fischer-type carbene complexes allowed the synthesis of new γ-methylenepyran carbene complexes. 13C NMR data and single cristal X-ray analysis suggest a delocalisation of the oxygene lone pair of the heterocycle.

20. Randomised trial of isoniazid versus rifampicin and pyrazinamide for prevention of tuberculosis in HIV-1 infection [1998]

  • Halsey, Neal A, Coberly, Jacqueline S, Desormeaux, Julio, Losikoff, Phyllis, Atkinson, Joan, Moulton, Lawrence H, Contave, Mireil, Johnson, Michael, Davis, Homer, Geiter, Lawrence, Johnson, Erica, Huebner, Robin, Boulos, Reginald, and Chaisson, Richard E
  • The Lancet; March 1998, Vol. 351 Issue: 9105 p786-792, 7p

21. Latanoprost treatment for glaucoma: effects of treating for 1 year and of switching from timolol [1998]

  • Camras, Carl B., Wax, Martin B., Ritch, Robert, Weinreb, Robert, Robin, Alan L., Higginbotham, Eve J., Lustgarten, Jacqueline, Stewart, William C., Sherwood, Mark, Krupin, Theodore, Wilensky, Jacob, Cioffi, George A., Katz, L. Jay, Schumer, Robert A., Kaufman, Paul L., Minckler, Don, Zimmerman, Thom, and Stjernschantz, Johan
  • American Journal of Ophthalmology. Sept 1998, Vol. 126 Issue 3, p390, 10 p.

22. Enterocytic differentiation of the human Caco-2 cell line correlates with alterations in integrin signaling [1998]

  • Lévy, Peggy, Robin, Hélène, Kornprobst, Michel, Capeau, Jacqueline, and Cherqui, Gisèle
  • Journal of Cellular Physiology; December 1998, Vol. 177 Issue: 4 p618-627, 10p
Abstract
We previously reported that the enterocytic differentiation of human colonic Caco-2 cells correlated with down-regulation of fibronectin (FN) and laminin (LN), two extracellular matrix components interacting with cell surface integrin receptors. We now investigated whether Caco-2 cell differentiation was associated with alterations in integrin signaling with special interest in the expression and activity of focal adhesion kinase (FAK) and mitogen-activated protein (MAP) kinase. The differentiation of Caco-2 cells was associated with: 1) down-regulation of β1 integrin expression at the mRNA and protein levels; 2) increased FAK expression together with decreased FAK autophosphorylation; 3) decreased FAK's ability to associate with PI3-kinase and pp60c-src; and 4) increased MAP kinase expression along with decreased MAP activity. In addition, we show that FAK and MAP kinase belong to distinct integrin signaling pathways and that both pathways remain functional during Caco-2 cell differentiation since the coating of differentiating cells on FN and LN but not on polylysine increased the tyrosine phosphorylation of FAK and of its endogenous substrate paxillin, and stimulated MAP kinase activity. In conclusion, our results provide evidence that FAK and MAP kinase, two signaling molecules activated independently by β1 integrins in Caco-2 cells, undergo alterations of both expression and activity during the enterocytic differentiation of this cell line. J Cell Physiol 177:618627, 1998. © 1998 Wiley-Liss, Inc.

23. LETTERS. [1999]

  • Brand, William, Rudnick, David, Dunphy, Brendan, Moen, Gerald, Rutelli, Francesco, Fadiman, Jeffrey, Sivasubramanian, M. N., Desmond, Marc, Harris, Robin, Lamont, Lord, Talekar, N. S., Mounteer, Carl, Fitzpatrick, Maurice, Richards, Ian, Teo, Jacqueline, Sass, Edgar, and Dussolier, Maurice
  • Economist. 2/13/1999, Vol. 350 Issue 8106, p6-8. 2p.
Subjects
LETTERS to the editor, DAY trading (Securities), BUBBLE gum, ECONOMICS, and ECONOMIC policy
Abstract
Several letters to the editor are presented in response to articles in previous issues including "When the Bubble Bursts," in the January 30, 1999 issue, "Blame It on the Bubbles," in the January 23, 1999 issue, and "A Nervous Shuffle in Malaysia," in the January 16, 1999 issue.

24. Insulin Antiapoptotic Signaling Involves Insulin Activation of the Nuclear Factor κB-dependent Survival Genes Encoding Tumor Necrosis Factor Receptor-associated Factor 2 and Manganese-superoxide Dismutase* [1999]

  • Bertrand, France, Desbois-Mouthon, Christèle, Cadoret, Axelle, Prunier, Céline, Robin, Hélène, Capeau, Jacqueline, Atfi, Azeddine, and Cherqui, Gisèle
  • Journal of Biological Chemistry; October 1999, Vol. 274 Issue: 43 p30596-30602, 7p
Abstract
We recently showed that the antiapoptotic function of insulin requires nuclear factor κB (NF-κB) activation (Bertrand, F., Atfi, A., Cadoret, A., L'Allemain, G., Robin, H., Lascols, O., Capeau, J., and Cherqui, G. (1998) J. Biol. Chem.273, 2931–2938). Here we sought to identify the NF-κB-dependent survival genes that are activated by insulin to mediate this function. Insulin increased the expression of tumor necrosis factor receptor-associated factor 2 (TRAF2) mRNA and protein in Chinese hamster ovary cells overexpressing insulin receptors (IRs). This effect required (i) IR activation since it was abrogated by IR mutation at tyrosines 1162 and 1163 and (ii) NF-κB activation since it was abolished by overexpression of dominant-negative IκB-α(A32/36) and mimicked by overexpression of the NF-κB c-Rel subunit. TRAF2 contributed to insulin protection against serum withdrawal-induced apoptosis since TRAF2 overexpression mimicked insulin protection, whereas overexpression of dominant-negative TRAF2-(87–501) reduced this process. Along with its protective effect, overexpressed TRAF2 increased basal and insulin-stimulated NF-κB activities. All effects were inhibited by IκB-α(A32/36), suggesting that an amplification loop involving TRAF2 activation of NF-κB is implicated in insulin antiapoptotic signaling. We also show that insulin increased manganese-superoxide dismutase (Mn-SOD) mRNA expression through NF-κB activation and that Mn-SOD contributed to insulin antiapoptotic signaling since expression of antisense Mn-SOD RNA decreased this process. This study provides the first evidence that insulin activates the NF-κB-dependent survival genes encoding TRAF2 and Mn-SOD and thereby clarifies the role of NF-κB in the antiapoptotic function of insulin.

25. Book reviews and notices [2000]

  • Trasi, Nitin, Clooney, Francis, Hibbets, Maria, Cronk, George, Hatcher, Brian, Rinehart, Robin, Prentiss, Karen, French, Hal, Clooney, Francis, Bellantoni, Lisa, Korom, Frank, Menzies, Robert, Bailly, Constantina, Flood, Gavin, Manring, Rebecca, Biernacki, Loriliai, Pennington, Brian, Grimes, John, MacPhail, Richard, Wallis, Glenn, Thatamanil, John, Grimes, John, Forsthoefel, Thomas, Cush, Denise, Saikia, Yasmin, Bracken, Joseph, Vail, Lise, Hirst, Jacqueline, Trapnell, Judson, Findly, Ellison, Waldau, Paul, Johnson, D., and Grimes, John
  • International Journal of Hindu Studies; April 2000, Vol. 4 Issue: 1 p61-107, 47p

26. Telangiectasia macularis eruptiva perstans and multiple myeloma [2000]

  • Bachmeyer, Claude, Guillemette, Jacqueline, Blum, Laurent, Turc, Yves, Dhôte, Robin, Fermand, Jean-Paul, and Aractingi, Selim
  • Journal of the American Academy of Dermatology; November 2000, Vol. 43 Issue: 5 p972-974, 3p
Abstract
The association of mast cell diseases and some hematologic malignancies, usually myeloproliferative disorders, myelodysplastic syndromes, and acute leukemia is well recognized. We report the case of a patient with telangiectasia macularis eruptiva perstans, a rare form of cutaneous mastocytosis, and multiple myeloma, an association that has been described only twice in the literature. Parallel improvement of both conditions was observed under chemotherapy regimens for multiple myeloma. Pathogenesis remains unclear, although the abnormalities in the c-kitpathway may play a role in the proliferation of cells from both lineages. (J Am Acad Dermatol 2000;43:972-4.)

27. Linkage and association analysis of chromosome 19q13 in multiple sclerosis [2001]

  • Pericak-Vance, Margaret, Rimmler, Jacqueline, Martin, Eden, Haines, Jonathan, Garcia, Melissa, Oksenberg, Jorge, Barcellos, Lisa, Lincoln, Robin, Goodkin, Donald, and Hauser, Stephen
  • neurogenetics; 20011001, Vol. 3 Issue: 4 p195-201, 7p
Abstract
Abstract.: Multiple sclerosis (MS) is an autoimmune neurological disorder with a complex etiology. Sibling risk, twin, and adoption studies have demonstrated that genes play a vital role in susceptibility to MS. Numerous association and linkage studies have implicated the major histocompatibility complex (MHC) as one component of the genetic etiology, but additional loci remain to be identified. Genomic screens have suggested over 50 regions that might harbor these genes, but there has been little agreement between studies. The one region suggested by all four screens resides within chromosome 19q13. Allelic associations with several markers in this region have also been described. This region has now been examined in detail in an expanded dataset of MS families from the United States. Genetic linkage and association were tested with multiple markers in this region using both parametric and non-parametric analyses. Additional support for an MS susceptibility locus was observed, primarily in families with the MS-associated HLA-DR2 allele. While consistent, this effect appears to be modest with a maximum λS=1.47, probably representing no more than 10% of the overall genetic effect in MS.

28. Toxic equivalency factors for PAH and their applicability in shellfish pollution monitoring studies [2002]

  • Law, Robin J., Kelly, Carole, Baker, Kerry, Jones, Jacqueline, McIntosh, Alistair D., and Moffat, Colin F.
  • Journal of Environmental Monitoring; May 24, 2002, Vol. 4 Issue: 3 p383-388, 6p
Abstract
Fish and shellfish are exposed to a wide range of polycyclic aromatic hydrocarbons (PAH) following oil spills at sea, and can become contaminated as a result. Finfish have a more effective mixed-function oxidase enzyme system than shellfish, and are therefore able to metabolise and excrete PAH more effectively than the invertebrates. Thus, contamination by high-molecular weight PAH, including those with carcinogenic potential and so of concern with regard to human consumers, is therefore usually observed in shellfish, and particularly in bivalve molluscs. Oil spills are not the sole source of PAH, however, as parent compounds are also generated by a wide range of combustion processes. In this paper, consideration is given to monitoring data gathered following recent oil spills (both of crude oil and diesel fuel), alongside data from other studies. These include studies conducted around a former gasworks site and downstream of an aluminium smelter in the UK, and from mussel monitoring studies undertaken in the UK and the USA (including the Exxon Valdez oil spill and the National Status and Trends programme), and in other countries in Europe. For comparative purposes the PAH concentrations are summed and also expressed as benzo[a]pyrene equivalents, their relative concentrations being weighted in relation to the carcinogenic potential of individual PAH compounds using toxic equivalency factors (TEF). Our aim was to assess the utility of this approach in fishery resource monitoring and control following oil spills. Certainly this approach seems useful from the data assessed in this study, and the relative ranking of the various studies seems to reflect the relative degree of concern for human consumers due to the differing contamination sources. As a simple tool for control purposes it is equally applicable to PAH derived from oil spills, and from industrial and combustion sources.

29. Health effects of World Trade Center site workers [2002]

  • Levin, Stephen, Herbert, Robin, Skloot, Gwen, Szeinuk, Jaime, Teirstein, Alvin, Fischler, David, Milek, Debra, Piligian, George, Wilk‐Rivard, Elizabeth, and Moline, Jacqueline
  • American Journal of Industrial Medicine; December 2002, Vol. 42 Issue: 6 p545-547, 3p

30. A Case of "Ifufunyane" A Xhosa Culture-Bound Syndrome [2005]

  • NIEHAUS, DANA J. H., STEIN, DAN J., KOEN, LIEZL, LOCHNER, CHRISTINE, MULLER, JACQUELINE E., MBANGA, N. IRENE, EMSLEY, ROBIN A., and GORMAN, JACK M.
  • Journal of Psychiatric Practice; November 2005, Vol. 11 Issue: 6 p411-413, 3p

31. Community-Associated Methicillin-Resistant Staphylococcus aureusEpidemic Clone USA300 in Isolates from Florida and Washington [2006]

  • Roberts, Jill C., Krueger, Robin L., Peak, K. Kealy, Veguilla, William, Cannons, Andrew C., Amuso, Philip T., and Cattani, Jacqueline
  • Journal of Clinical Microbiology; January 2006, Vol. 44 Issue: 1 p225-226, 2p
Abstract
ABSTRACTWe examined 299 methicillin-resistant, community-associated Staphylococcus aureusisolates from Florida and Washington State for the presence of the USA300 epidemic clone. Pulsed-field gel electrophoresis demonstrated the epidemic clone in 43% of our S. aureusstrains and in isolates from both states. The majority of the USA300 isolates (88%) were from wound infections.

32. Letters. [2007]

  • Fisher, Trevor, Karp, Jacqueline, Addington, Jim, Arrand, Peter, Cowley, George, Green, Colin, Hamel, Noel, Clark, Roy, Wendt, Robin, Sturgeon, Nicola, Reed, Jamie, Burns-Cox, Chris, and McKenna, Peter
  • New Statesman. 5/21/2007, Vol. 136 Issue 4845, p6-7. 2p. 1 Illustration.
Subjects
LETTERS to the editor
Abstract
Several letters to the editor are presented in response to articles in previous issues including an editorial, a column by John Pilger concerning Robert F. Kennedy and Gordon Brown and the article "Inside Track" by Philip Gould. All of these items appeared in the May 14, 2007 issue.

33. Reducing Fall Risk for Frail Older Home-Care Clients Using a Multifactorial and Interdisciplinary Team Approach [2007]

  • Markle-Reid, Maureen, Henderson, Sandra, Hecimovich, Catherine, Baxter, Pamela, Anderson, Malcolm, Browne, Gina, Weir, Robin, Gafni, Amiram, and Roberts, Jacqueline
  • Journal of Patient Safety; September 2007, Vol. 3 Issue: 3 p149-157, 9p
Abstract
This article describes the background and design of a study that is currently in progress. The objective of the study is to evaluate the 6-month effects and costs of a multifactorial and interdisciplinary team approach to fall prevention compared with usual home care for frail older people at risk for falls. The barriers and facilitators to implementing an interdisciplinary team approach in home care will also be discussed.

34. Additional EFNB1mutations in craniofrontonasal syndromeThis article is a US Government work and, as such, is in the public domain in the United States of America.How to cite this article: Wallis D, Lacbawan F, Jain M, Der Kaloustian VM, Steiner CE, Moeschler JB, Losken HW, Kaitila II, Cantrell S, Proud VK, Carey JC, Day DW, Lev D, Teebi AS, Robinson LK, Hoyme HE, AlTorki N, SiegelBartelt J, Mulliken JB, Robin NH, Saavedra D, Zackai EH, Muenke M. 2008. Additional EFNB1mutations in craniofrontonasal syndrome. Am J Med Genet Part A 146A:2008–2012. [2008]

  • Wallis, Deeann, Lacbawan, Felicitas, Jain, Mahim, Der Kaloustian, Vazken M., Steiner, Carlos E., Moeschler, John B., Losken, H. Wolfgang, Kaitila, Ilkka I., Cantrell, Stephen, Proud, Virginia K., Carey, John C., Day, Donald W., Lev, Dorit, Teebi, Ahmad S., Robinson, Luther K., Hoyme, H. Eugene, AlTorki, Nadia, SiegelBartelt, Jacqueline, Mulliken, John B., Robin, Nathaniel H., Saavedra, Dolores, Zackai, Elaine H., and Muenke, Maximilian
  • American Journal of Medical Genetics. Part A; August 2008, Vol. 146 Issue: 15 p2008-2012, 5p
Abstract
No Abstract.

35. Ovarian status in healthy postmenopausal women [2008]

  • Healy, David L., Bell, Robin, Robertson, David M., Jobling, Tom, Oehler, Martin K., Edwards, Andrew, Shekleton, Paul, Oldham, Jacqueline, Piessens, Sofie, Teoh, Mark, Mamers, Pamela, Taylor, Nancy, and Walker, Frances
  • Menopause; December 2008, Vol. 15 Issue: 6 p1109-1114, 6p
Abstract
There are currently no programs to assess ovarian health in postmenopausal women. The aim of this study was to describe the ovaries in healthy women at least 5 years after menopause by questionnaire, transvaginal ultrasonography, and blood ovarian cancer markers.

36. Longitudinal assessment of spirometry in the World Trade Center Medical Monitoring Program [2009]

  • Skloot, Gwen S., Schechter, Clyde B., Herbert, Robin, Moline, Jacqueline M., Levin, Stephen M., Crowley, Laura E., Luft, Benjamin J., Udasin, Iris G., and Enright, Paul L.
  • Chest. Feb 2009, Vol. 135 Issue 2, p492, 7 p.
Subjects
World Trade Center and Pentagon Attacks, 2001, Usage, Abnormalities, Health aspects, Diagnosis, Spirometry -- Usage, Health screening -- Abnormalities, Volunteers -- Health aspects, Lung diseases -- Diagnosis, and Medical screening -- Abnormalities

37. Use of a Nisin-Producing Starter Culture of Lactococcus lactissubsp. lactisTo Improve Traditional Fish Fermentation in Senegal [2009]

  • Diop, Michel Bakar, Dubois-Dauphin, Robin, Destain, Jacqueline, Tine, Emmanuel, and Thonart, Philippe
  • Journal of Food Protection; September 2009, Vol. 72 Issue: 9 p1930-1934, 5p
Abstract
Lactococcus lactissubsp. lactisstrain CWBI B1410, which produces various antibacterial compounds including organic acids and nisin, was used as a starter culture to improve the traditional Senegalese fish fermentation in which fish are mostly transformed to guedj by spontaneous fermentation for 24 to 48 h at ambient temperatures near 30°C followed by salting (with NaCl) and sun drying. Assays were performed on lean fish (Podamasys jubelini) and fat fish (Arius heudelotii) purchased at a local market. The total viable microbial counts in raw fillets of P. jubeliniand A. heudelotiiwere 5.78 and 5.39 log CFU/g, respectively. Populations of enteric bacteria (which can include pathogenic bacteria) in P. jubeliniand A. heudelotiiwere 4.08 and 4.12 log CFU/g, respectively. Spontaneous fermentation of raw fillets at 30°C led to the proliferation of enteric bacteria to 9 log CFU/g after 24 h in fermented P. jubeliniand A. heudelotiifillets with pH values of 6.83 and 7.50, respectively. When raw fish fillets were supplemented with glucose (1%, wt/wt) and inoculated with Lactococcus lactis(107CFU/g), the pH decreased to about 4.60 after 10 h at 30°C, and nisin activity was detected in juice from the fillets. Traditionally fermented fillets of P. jubeliniand A. heudelotiicontained enteric bacteria at higher levels of 4 and 2 log CFU/g, respectively, than did fillets of the same fish supplemented with glucose and fermented with the starter culture. These data suggest that this new fish fermentation strategy combined with salting and drying can be used to enhance the safety of guedj.

38. THE PREVALENCE OF ASTHMA AMONG 20193 WORLD TRADE CENTER RESPONDERS [2009]

  • Kim, Hyun, Herbert, Robin, Moline, Jacqueline, Markowitz, Steven, Udasin, Iris, Crowley, Laura, and Enright, Paul
  • Chest; October 2009, Vol. 136 Issue: 4, Number 4 Supplement 1 p25S-25S, 1p

39. Ovarian status in healthy postmenopausal women [2009]

  • Bell, Robin J., Healy, David L., Robertson, David M., Jobling, Tom, Oehler, Martin K., Edwards, Andrew, Shekleton, Paul, Oldham, Jacqueline, Piessens, Sofie, Teoh, Mark, Mamers, Pamela, Taylor, Nancy, and Walker, Frances
  • Menopause; November 2009, Vol. 16 Issue: 6 p1149-1155, 7p
Abstract
We have previously reported on the point prevalence of ovarian lesions detected by transvaginal ultrasound (TVU) in 515 asymptomatic women at least 5 years postmenopause. The aims of this study were to report, in the same women, on the repeatability of visualization of the ovaries (TVU) and the natural history of ovarian lesions seen at baseline but not treated surgically and to assess whether any women developed new ovarian abnormalities 12 months later.

40. Base-Pair Resolution of Somatic and Germline-Derived Genome Rearrangement Breakpoints in Follicular Lymphoma. [2009]

  • Mungall, Andrew J., Chu, Andy, Chiu, Readman, Corbett, Richard, Field, Matthew A., Jackman, Shaun D., Mungall, Karen L., Wong, Kim, Boyle, Merrill, Carlsen, Rebecca, Chan, Susanna Y., Coope, Robin J.N., Hirst, Carrie A., Hirst, Martin, Johnson, Nathalie, Krzywinski, Martin, Lee, Darlene, Lin, Jasmine BingXue, Moore, Richard, Severson, Tesa, Simpson, Jared T., Steidl, Christian, Zeng, Thomas, Zhao, Yongjun, Birol, Inanc, Holt, Robert A., Jones, Steven J., Gascoyne, Randy D., Horsman, Douglas E., Connors, Joseph M., Schein, Jacqueline E., and Marra, Marco A.
  • Blood; November 2009, Vol. 114 Issue: 22 p439-439, 1p
Abstract
Abstract 439

41. World Trade Center multiple myeloma: police responders only? [2009]

  • Miller, Albert, Moline, Jacqueline M., Herbert, Robin, Crowley, Laura, Troy, Kevin, Hodgman, Erica, Shukla, Gauri, Udasin, Iris, Luft, Benjamin, and Wallenstein, Sylvan
  • Journal of Occupational and Environmental Medicine. Dec 2009, Vol. 51 Issue 12, p1357, 2 p.
Subjects
World Trade Center and Pentagon Attacks, 2001, Risk factors, Demographic aspects, Health aspects, Multiple myeloma -- Risk factors, Multiple myeloma -- Demographic aspects, and First responders -- Health aspects

42. A Cross-Sectional Study of the Prevalence, Correlates, and Costs of Falls in Older Home Care Clients ?At Risk? for Falling* [2010]

  • Markle-Reid, Maureen, Browne, Gina, Gafni, Amiram, Roberts, Jacqueline, Weir, Robin, Thabane, Lehana, Miles, Melody, Vaitonis, Vida, Hecimovich, Catherine, Baxter, Pamela, and Henderson, Sandra
  • Canadian Journal on Aging; March 2010, Vol. 29 Issue: 1 p119-137, 19p
Abstract
R?SUM?Cette ?tude a examin? la pr?valence pendant 6 mois, ? l?aide des services de soutien ? domicile, des facteurs de risque et des co?ts de chutes de personnes ?g?es qui sont ? risque de chute. Des 109 participants, 70,6 pour cent ont indiqu? une chute dans les six mois pr?c?dents et 27,5 pour cent ont ?prouv? plusieurs chutes. Bien qu?il n?y avait aucune diff?rence statistiquement significative dans n?importe quel facteur de risque li? ? la chute parmi ceux qui sont tomb?s (1+ chutes) et ceux qui ne sont pas tomb?s (0 chutes), ceux qui sont tomb?s ont montr?s des tendances de plus en plus ?videntes de fonctionnement r?duit sur le plan physique, social et psychologique. Dans le co?t total par personne d?utilisation des services de sant? au cours des 6 derniers mois, il n?y avait aucune diff?rence statistiquement significative entre ceux qui sont tomb?s et ceux qui ne sont pas tomb?s; toutefois, il y avait des diff?rences significatives entre les groupes dans certains types de services de sant?. L?analyse multivariable a r?v?l? la pr?sence de cinq facteurs de risques de chutes: troubles neurologiques (p. ex., diminution cognitive, maladie de Parkinson), l??ge ?85 ans, risques environnementaux, glissade ou tr?buchant pr?c?dente et d?ficience visuelle.

43. The Effects and Costs of a Multifactorial and Interdisciplinary Team Approach to Falls Prevention for Older Home Care Clients ?At Risk? for Falling: A Randomized Controlled Trial* [2010]

  • Markle-Reid, Maureen, Browne, Gina, Gafni, Amiram, Roberts, Jacqueline, Weir, Robin, Thabane, Lehana, Miles, Melody, Vaitonis, Vida, Hecimovich, Catherine, Baxter, Pamela, and Henderson, Sandra
  • Canadian Journal on Aging; March 2010, Vol. 29 Issue: 1 p139-161, 23p
Abstract
R?SUM?Cette ?tude a d?termin? les effets et les co?ts d?une approche d??quipe multifactoriel et interdisciplinaire ? la pr?vention des chutes. Essai contr?l? al?atoire de 109 adultes plus ?g?s qui sont ? risque de chutes. Ce fut une strat?gie de pr?vention multifactoriel fond?e sur des donn?es probantes de 6 mois, impliquant une ?quipe interdisciplinaire. Le r?sultat principal a ?t? le nombre des chutes suivi pendant 6 mois. ? 6 mois, il n?y a aucune diff?rence dans le nombre moyen de chutes entre groupes. Des analyses des sous-groupes ont montr?s que l?intervention r?duit efficacement les chutes chez les hommes (75?84 ans) qui ont peur de tomber ou une histoire n?gative de chutes. Le nombre de glissades et de tr?buch?s a ?t? consid?rablement r?duit, et la sant? ?motionnelle a montr? une am?lioration plus importante dans le fonctionnement li? ? la sant? ?motionnelle dans le groupe d?intervention. La qualit? de vie a ?t? am?lior?e, glissades et tr?buch?s ont ?t? r?duits, comme l??taient les chutes chez les hommes qui avaient peur de tomber ou une histoire de chutes n?gative.

44. Persistence of multiple illnesses in World Trade Center rescue and recovery workers: a cohort study [2011]

  • Wisnivesky, Juan P, Teitelbaum, Susan L, Todd, Andrew C, Boffetta, Paolo, Crane, Michael, Crowley, Laura, de la Hoz, Rafael E, Dellenbaugh, Cornelia, Harrison, Denise, Herbert, Robin, Kim, Hyun, Jeon, Yunho, Kaplan, Julia, Katz, Craig, Levin, Stephen, Luft, Ben, Markowitz, Steven, Moline, Jacqueline M, Ozbay, Fatih, Pietrzak, Robert H, Shapiro, Moshe, Sharma, Vansh, Skloot, Gwen, Southwick, Steven, Stevenson, Lori A, Udasin, Iris, Wallenstein, Sylvan, and Landrigan, Philip J
  • The Lancet; September 2011, Vol. 378 Issue: 9794 p888-897, 10p
Abstract
More than 50 000 people participated in the rescue and recovery work that followed the Sept 11, 2001 (9/11) attacks on the World Trade Center (WTC). Multiple health problems in these workers were reported in the early years after the disaster. We report incidence and prevalence rates of physical and mental health disorders during the 9 years since the attacks, examine their associations with occupational exposures, and quantify physical and mental health comorbidities.

45. Work-Related Injuries and Illnesses Reported by World Trade Center Response Workers and Volunteers [2011]

  • Perritt, Kara R., Herbert, Robin, Levin, Stephen M., and Moline, Jacqueline
  • Prehospital and Disaster Medicine; December 2011, Vol. 26 Issue: 6 p401-407, 7p
Abstract
AbstractIntroduction:In 2002, the Mount Sinai Center for Occupational and Environmental Medicine, with support from the National Institute for Occupational Safety and Health (NIOSH), began coordinating the World Trade Center (WTC) Worker and Volunteer Medical Screening Program (MSP) to monitor the health of qualified WTC responders. Enrolled participants were offered a clinical examination; interviewed to collect medical, mental health, and exposure information; and requested to complete a self-administered medical questionnaire. The objective of this study was to better understand work-related injuries and illnesses sustained on-site by WTC responders.Methods:A descriptive analysis of select data from the MSP self-administered medical questionnaire was conducted. Data collected July 2002 through April 2004 from MSP participants enrolled at the Mount Sinai clinic were reviewed using univariate statistical techniques.Results:Records from 7,810 participants were analyzed, with most participants associated with either the construction industry (n = 2,623, 34%) or law enforcement (n = 2,036, 26%). Approximately a third of the participants (n = 2,486, 32%) reported at least one injury or illness requiring medical treatment that was sustained during WTC work/volunteer activities. Of the total 4,768 injuries/illnesses reported by these participants, respiratory complaints were most common (n = 1,350, 28%), followed by traumatic injuries excluding eye injuries (n = 961, 20%), eye injuries/ailments (n = 709, 15%), chest pain (n = 375, 8%), headaches (n = 359, 8%), skin conditions (n = 178, 4%), and digestive system conditions (n = 163, 3%). Participants reported that 36% of injuries/illnesses were treated off-site and 29% were treated on-site, with the remaining not specifying treatment location. Off-site treatment was prevalent for respiratory complaints, psychological stress, and chest pain. On-site treatment was predominate for eye injuries/ailments and traumatic injuries excluding eye injuries.Conclusion:Study results underscore the need for rapid deployment of personal protective equipment for disaster responders and medical care stations mobilized near disaster worksites. Additionally, the results, many of which are comparable to findings from previous WTC studies where data were collected in real-time, indicate that a screening program such as the MSP may be effective in retrospectively providing general information on disaster responder demographics and work-related injuries and illnesses.

46. Thesis Abstracts [2012]

  • Adamson, Mike, Deverson, Katherine, Dibden, Julie, Forde, Kieran, Hamacher, Duane W., Joannes-Boyau, Renaud, Ralph, Jordan, Stannard, Georgia, Stone, Robert M., Thomas, David C., Tumney, Jacqueline N., Twaddle, Robin, and Wilcox, Morgan Kae
  • Australian archaeology. 75(1):128-133

47. Inhibition of autophagy impairs tumor cell invasion in an organotypic model [2012]

  • Macintosh, Robin L., Timpson, Paul, Thorburn, Jacqueline, Anderson, Kurt I., Thorburn, Andrew, and Ryan, Kevin M.
  • Cell cycle. 11(10):2022-2029

48. Total Synthesis of Homogeneous Antifreeze Glycopeptides and Glycoproteins [2012]

  • Wilkinson, Brendan L., Stone, Robin S., Capicciotti, Chantelle J., Thaysen‐Andersen, Morten, Matthews, Jacqueline M., Packer, Nicolle H., Ben, Robert N., and Payne, Richard J.
  • Angewandte Chemie. International Edition; April 2012, Vol. 51 Issue: 15 p3606-3610, 5p
Abstract
Don't freeze!A native chemical ligation–desulfurization strategy has been employed for the convergent synthesis of a library of defined antifreeze glycopeptides and glycoproteins (AFGPs) ranging in size from 1.2 to 19.5 kDa (see picture). These AFGPs possessed the secondary structure of a polyproline type II helix and exhibited significant ice recrystallization inhibition and thermal hysteresis activity.

49. Perceived Benefits of a Transplant Surgery Experience to General Surgery Residency Training [2012]

  • Schwartz, Jason J., Thiesset, Heather F., Bohn, Jacqueline A., Sloat, Benjamin, Carricaburu, Martin, Hatch, Jenny, Sorensen, John B., Kim, Robin D., Vargo, Daniel, and Fryer, Jonathan P.
  • Journal of Surgical Education; May 2012, Vol. 69 Issue: 3 p371-384, 14p
Abstract
The benefit of a solid-organ transplant experience during general surgical training has been questioned recently. In 2008, in response to an American Board of Surgery (ABS) directive, a survey was conducted by the Association of Program Directors in Surgery (APDS) in coordination with the American Society of Transplant Surgeons (ASTS) to determine the perceived value of a transplant surgery rotation to program directors and residents. With the aim of providing additional insight, we conducted a separate study, independent of the ABS and ASTS, to ascertain resident perceptions regarding the specific skill sets that they acquire during their transplant surgery rotations and their applicability to other surgical subspecialties.

50. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010 [2012]

  • Lozano, Rafael, Naghavi, Mohsen, Foreman, Kyle, Lim, Stephen, Shibuya, Kenji, Aboyans, Victor, Abraham, Jerry, Adair, Timothy, Aggarwal, Rakesh, Ahn, Stephanie Y, AlMazroa, Mohammad A, Alvarado, Miriam, Anderson, H Ross, Anderson, Laurie M, Andrews, Kathryn G, Atkinson, Charles, Baddour, Larry M, Barker-Collo, Suzanne, Bartels, David H, Bell, Michelle L, Benjamin, Emelia J, Bennett, Derrick, Bhalla, Kavi, Bikbov, Boris, Abdulhak, Aref Bin, Birbeck, Gretchen, Blyth, Fiona, Bolliger, Ian, Boufous, Soufiane, Bucello, Chiara, Burch, Michael, Burney, Peter, Carapetis, Jonathan, Chen, Honglei, Chou, David, Chugh, Sumeet S, Coffeng, Luc E, Colan, Steven D, Colquhoun, Samantha, Colson, K Ellicott, Condon, John, Connor, Myles D, Cooper, Leslie T, Corriere, Matthew, Cortinovis, Monica, de Vaccaro, Karen Courville, Couser, William, Cowie, Benjamin C, Criqui, Michael H, Cross, Marita, Dabhadkar, Kaustubh C, Dahodwala, Nabila, De Leo, Diego, Degenhardt, Louisa, Delossantos, Allyne, Denenberg, Julie, Des Jarlais, Don C, Dharmaratne, Samath D, Dorsey, E Ray, Driscoll, Tim, Duber, Herbert, Ebel, Beth, Erwin, Patricia J, Espindola, Patricia, Ezzati, Majid, Feigin, Valery, Flaxman, Abraham D, Forouzanfar, Mohammad H, Fowkes, Francis Gerry R, Franklin, Richard, Fransen, Marlene, Freeman, Michael K, Gabriel, Sherine E, Gakidou, Emmanuela, Gaspari, Flavio, Gillum, Richard F, Gonzalez-Medina, Diego, Halasa, Yara A, Haring, Diana, Harrison, James E, Havmoeller, Rasmus, Hay, Roderick J, Hoen, Bruno, Hotez, Peter J, Hoy, Damian, Jacobsen, Kathryn H, James, Spencer L, Jasrasaria, Rashmi, Jayaraman, Sudha, Johns, Nicole, Karthikeyan, Ganesan, Kassebaum, Nicholas, Keren, Andre, Khoo, Jon-Paul, Knowlton, Lisa Marie, Kobusingye, Olive, Koranteng, Adofo, Krishnamurthi, Rita, Lipnick, Michael, Lipshultz, Steven E, Ohno, Summer Lockett, Mabweijano, Jacqueline, MacIntyre, Michael F, Mallinger, Leslie, March, Lyn, Marks, Guy B, Marks, Robin, Matsumori, Akira, Matzopoulos, Richard, Mayosi, Bongani M, McAnulty, John H, McDermott, Mary M, McGrath, John, Memish, Ziad A, Mensah, George A, Merriman, Tony R, Michaud, Catherine, Miller, Matthew, Miller, Ted R, Mock, Charles, Mocumbi, Ana Olga, Mokdad, Ali A, Moran, Andrew, Mulholland, Kim, Nair, M Nathan, Naldi, Luigi, Narayan, K M Venkat, Nasseri, Kiumarss, Norman, Paul, O'Donnell, Martin, Omer, Saad B, Ortblad, Katrina, Osborne, Richard, Ozgediz, Doruk, Pahari, Bishnu, Pandian, Jeyaraj Durai, Rivero, Andrea Panozo, Padilla, Rogelio Perez, Perez-Ruiz, Fernando, Perico, Norberto, Phillips, David, Pierce, Kelsey, Pope, C Arden, Porrini, Esteban, Pourmalek, Farshad, Raju, Murugesan, Ranganathan, Dharani, Rehm, Jürgen T, Rein, David B, Remuzzi, Guiseppe, Rivara, Frederick P, Roberts, Thomas, De León, Felipe Rodriguez, Rosenfeld, Lisa C, Rushton, Lesley, Sacco, Ralph L, Salomon, Joshua A, Sampson, Uchechukwu, Sanman, Ella, Schwebel, David C, Segui-Gomez, Maria, Shepard, Donald S, Singh, David, Singleton, Jessica, Sliwa, Karen, Smith, Emma, Steer, Andrew, Taylor, Jennifer A, Thomas, Bernadette, Tleyjeh, Imad M, Towbin, Jeffrey A, Truelsen, Thomas, Undurraga, Eduardo A, Venketasubramanian, N, Vijayakumar, Lakshmi, Vos, Theo, Wagner, Gregory R, Wang, Mengru, Wang, Wenzhi, Watt, Kerrianne, Weinstock, Martin A, Weintraub, Robert, Wilkinson, James D, Woolf, Anthony D, Wulf, Sarah, Yeh, Pon-Hsiu, Yip, Paul, Zabetian, Azadeh, Zheng, Zhi-Jie, Lopez, Alan D, and Murray, Christopher JL
  • The Lancet; December-January 2012, Vol. 380 Issue: 9859 p2095-2128, 34p
Abstract
Reliable and timely information on the leading causes of death in populations, and how these are changing, is a crucial input into health policy debates. In the Global Burden of Diseases, Injuries, and Risk Factors Study 2010 (GBD 2010), we aimed to estimate annual deaths for the world and 21 regions between 1980 and 2010 for 235 causes, with uncertainty intervals (UIs), separately by age and sex.

51. Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010 [2012]

  • Vos, Theo, Flaxman, Abraham D, Naghavi, Mohsen, Lozano, Rafael, Michaud, Catherine, Ezzati, Majid, Shibuya, Kenji, Salomon, Joshua A, Abdalla, Safa, Aboyans, Victor, Abraham, Jerry, Ackerman, Ilana, Aggarwal, Rakesh, Ahn, Stephanie Y, Ali, Mohammed K, AlMazroa, Mohammad A, Alvarado, Miriam, Anderson, H Ross, Anderson, Laurie M, Andrews, Kathryn G, Atkinson, Charles, Baddour, Larry M, Bahalim, Adil N, Barker-Collo, Suzanne, Barrero, Lope H, Bartels, David H, Basáñez, Maria-Gloria, Baxter, Amanda, Bell, Michelle L, Benjamin, Emelia J, Bennett, Derrick, Bernabé, Eduardo, Bhalla, Kavi, Bhandari, Bishal, Bikbov, Boris, Abdulhak, Aref Bin, Birbeck, Gretchen, Black, James A, Blencowe, Hannah, Blore, Jed D, Blyth, Fiona, Bolliger, Ian, Bonaventure, Audrey, Boufous, Soufiane, Bourne, Rupert, Boussinesq, Michel, Braithwaite, Tasanee, Brayne, Carol, Bridgett, Lisa, Brooker, Simon, Brooks, Peter, Brugha, Traolach S, Bryan-Hancock, Claire, Bucello, Chiara, Buchbinder, Rachelle, Buckle, Geoffrey, Budke, Christine M, Burch, Michael, Burney, Peter, Burstein, Roy, Calabria, Bianca, Campbell, Benjamin, Canter, Charles E, Carabin, Hélène, Carapetis, Jonathan, Carmona, Loreto, Cella, Claudia, Charlson, Fiona, Chen, Honglei, Cheng, Andrew Tai-Ann, Chou, David, Chugh, Sumeet S, Coffeng, Luc E, Colan, Steven D, Colquhoun, Samantha, Colson, K Ellicott, Condon, John, Connor, Myles D, Cooper, Leslie T, Corriere, Matthew, Cortinovis, Monica, de Vaccaro, Karen Courville, Couser, William, Cowie, Benjamin C, Criqui, Michael H, Cross, Marita, Dabhadkar, Kaustubh C, Dahiya, Manu, Dahodwala, Nabila, Damsere-Derry, James, Danaei, Goodarz, Davis, Adrian, De Leo, Diego, Degenhardt, Louisa, Dellavalle, Robert, Delossantos, Allyne, Denenberg, Julie, Derrett, Sarah, Des Jarlais, Don C, Dharmaratne, Samath D, Dherani, Mukesh, Diaz-Torne, Cesar, Dolk, Helen, Dorsey, E Ray, Driscoll, Tim, Duber, Herbert, Ebel, Beth, Edmond, Karen, Elbaz, Alexis, Ali, Suad Eltahir, Erskine, Holly, Erwin, Patricia J, Espindola, Patricia, Ewoigbokhan, Stalin E, Farzadfar, Farshad, Feigin, Valery, Felson, David T, Ferrari, Alize, Ferri, Cleusa P, Fèvre, Eric M, Finucane, Mariel M, Flaxman, Seth, Flood, Louise, Foreman, Kyle, Forouzanfar, Mohammad H, Fowkes, Francis Gerry R, Franklin, Richard, Fransen, Marlene, Freeman, Michael K, Gabbe, Belinda J, Gabriel, Sherine E, Gakidou, Emmanuela, Ganatra, Hammad A, Garcia, Bianca, Gaspari, Flavio, Gillum, Richard F, Gmel, Gerhard, Gosselin, Richard, Grainger, Rebecca, Groeger, Justina, Guillemin, Francis, Gunnell, David, Gupta, Ramyani, Haagsma, Juanita, Hagan, Holly, Halasa, Yara A, Hall, Wayne, Haring, Diana, Haro, Josep Maria, Harrison, James E, Havmoeller, Rasmus, Hay, Roderick J, Higashi, Hideki, Hill, Catherine, Hoen, Bruno, Hoffman, Howard, Hotez, Peter J, Hoy, Damian, Huang, John J, Ibeanusi, Sydney E, Jacobsen, Kathryn H, James, Spencer L, Jarvis, Deborah, Jasrasaria, Rashmi, Jayaraman, Sudha, Johns, Nicole, Jonas, Jost B, Karthikeyan, Ganesan, Kassebaum, Nicholas, Kawakami, Norito, Keren, Andre, Khoo, Jon-Paul, King, Charles H, Knowlton, Lisa Marie, Kobusingye, Olive, Koranteng, Adofo, Krishnamurthi, Rita, Lalloo, Ratilal, Laslett, Laura L, Lathlean, Tim, Leasher, Janet L, Lee, Yong Yi, Leigh, James, Lim, Stephen S, Limb, Elizabeth, Lin, John Kent, Lipnick, Michael, Lipshultz, Steven E, Liu, Wei, Loane, Maria, Ohno, Summer Lockett, Lyons, Ronan, Ma, Jixiang, Mabweijano, Jacqueline, MacIntyre, Michael F, Malekzadeh, Reza, Mallinger, Leslie, Manivannan, Sivabalan, Marcenes, Wagner, March, Lyn, Margolis, David J, Marks, Guy B, Marks, Robin, Matsumori, Akira, Matzopoulos, Richard, Mayosi, Bongani M, McAnulty, John H, McDermott, Mary M, McGill, Neil, McGrath, John, Medina-Mora, Maria Elena, Meltzer, Michele, Memish, Ziad A, Mensah, George A, Merriman, Tony R, Meyer, Ana-Claire, Miglioli, Valeria, Miller, Matthew, Miller, Ted R, Mitchell, Philip B, Mocumbi, Ana Olga, Moffitt, Terrie E, Mokdad, Ali A, Monasta, Lorenzo, Montico, Marcella, Moradi-Lakeh, Maziar, Moran, Andrew, Morawska, Lidia, Mori, Rintaro, Murdoch, Michele E, Mwaniki, Michael K, Naidoo, Kovin, Nair, M Nathan, Naldi, Luigi, Narayan, KM Venkat, Nelson, Paul K, Nelson, Robert G, Nevitt, Michael C, Newton, Charles R, Nolte, Sandra, Norman, Paul, Norman, Rosana, O'Donnell, Martin, O'Hanlon, Simon, Olives, Casey, Omer, Saad B, Ortblad, Katrina, Osborne, Richard, Ozgediz, Doruk, Page, Andrew, Pahari, Bishnu, Pandian, Jeyaraj Durai, Rivero, Andrea Panozo, Patten, Scott B, Pearce, Neil, Padilla, Rogelio Perez, Perez-Ruiz, Fernando, Perico, Norberto, Pesudovs, Konrad, Phillips, David, Phillips, Michael R, Pierce, Kelsey, Pion, Sébastien, Polanczyk, Guilherme V, Polinder, Suzanne, Pope, C Arden, Popova, Svetlana, Porrini, Esteban, Pourmalek, Farshad, Prince, Martin, Pullan, Rachel L, Ramaiah, Kapa D, Ranganathan, Dharani, Razavi, Homie, Regan, Mathilda, Rehm, Jürgen T, Rein, David B, Remuzzi, Guiseppe, Richardson, Kathryn, Rivara, Frederick P, Roberts, Thomas, Robinson, Carolyn, De Leòn, Felipe Rodriguez, Ronfani, Luca, Room, Robin, Rosenfeld, Lisa C, Rushton, Lesley, Sacco, Ralph L, Saha, Sukanta, Sampson, Uchechukwu, Sanchez-Riera, Lidia, Sanman, Ella, Schwebel, David C, Scott, James Graham, Segui-Gomez, Maria, Shahraz, Saeid, Shepard, Donald S, Shin, Hwashin, Shivakoti, Rupak, Silberberg, Donald, Singh, David, Singh, Gitanjali M, Singh, Jasvinder A, Singleton, Jessica, Sleet, David A, Sliwa, Karen, Smith, Emma, Smith, Jennifer L, Stapelberg, Nicolas JC, Steer, Andrew, Steiner, Timothy, Stolk, Wilma A, Stovner, Lars Jacob, Sudfeld, Christopher, Syed, Sana, Tamburlini, Giorgio, Tavakkoli, Mohammad, Taylor, Hugh R, Taylor, Jennifer A, Taylor, William J, Thomas, Bernadette, Thomson, W Murray, Thurston, George D, Tleyjeh, Imad M, Tonelli, Marcello, Towbin, Jeffrey A, Truelsen, Thomas, Tsilimbaris, Miltiadis K, Ubeda, Clotilde, Undurraga, Eduardo A, van der Werf, Marieke J, van Os, Jim, Vavilala, Monica S, Venketasubramanian, N, Wang, Mengru, Wang, Wenzhi, Watt, Kerrianne, Weatherall, David J, Weinstock, Martin A, Weintraub, Robert, Weisskopf, Marc G, Weissman, Myrna M, White, Richard A, Whiteford, Harvey, Wiersma, Steven T, Wilkinson, James D, Williams, Hywel C, Williams, Sean RM, Witt, Emma, Wolfe, Frederick, Woolf, Anthony D, Wulf, Sarah, Yeh, Pon-Hsiu, Zaidi, Anita KM, Zheng, Zhi-Jie, Zonies, David, Lopez, Alan D, and Murray, Christopher JL
  • The Lancet; December-January 2012, Vol. 380 Issue: 9859 p2163-2196, 34p
Abstract
Non-fatal health outcomes from diseases and injuries are a crucial consideration in the promotion and monitoring of individual and population health. The Global Burden of Disease (GBD) studies done in 1990 and 2000 have been the only studies to quantify non-fatal health outcomes across an exhaustive set of disorders at the global and regional level. Neither effort quantified uncertainty in prevalence or years lived with disability (YLDs).

52. Disability-adjusted life years (DALYs) for 291 diseases and injuries in 21 regions, 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010 [2012]

  • Murray, Christopher J L, Vos, Theo, Lozano, Rafael, Naghavi, Mohsen, Flaxman, Abraham D, Michaud, Catherine, Ezzati, Majid, Shibuya, Kenji, Salomon, Joshua A, Abdalla, Safa, Aboyans, Victor, Abraham, Jerry, Ackerman, Ilana, Aggarwal, Rakesh, Ahn, Stephanie Y, Ali, Mohammed K, AlMazroa, Mohammad A, Alvarado, Miriam, Anderson, H Ross, Anderson, Laurie M, Andrews, Kathryn G, Atkinson, Charles, Baddour, Larry M, Bahalim, Adil N, Barker-Collo, Suzanne, Barrero, Lope H, Bartels, David H, Basáñez, Maria-Gloria, Baxter, Amanda, Bell, Michelle L, Benjamin, Emelia J, Bennett, Derrick, Bernabé, Eduardo, Bhalla, Kavi, Bhandari, Bishal, Bikbov, Boris, Abdulhak, Aref Bin, Birbeck, Gretchen, Black, James A, Blencowe, Hannah, Blore, Jed D, Blyth, Fiona, Bolliger, Ian, Bonaventure, Audrey, Boufous, Soufiane, Bourne, Rupert, Boussinesq, Michel, Braithwaite, Tasanee, Brayne, Carol, Bridgett, Lisa, Brooker, Simon, Brooks, Peter, Brugha, Traolach S, Bryan-Hancock, Claire, Bucello, Chiara, Buchbinder, Rachelle, Buckle, Geoffrey, Budke, Christine M, Burch, Michael, Burney, Peter, Burstein, Roy, Calabria, Bianca, Campbell, Benjamin, Canter, Charles E, Carabin, Hélène, Carapetis, Jonathan, Carmona, Loreto, Cella, Claudia, Charlson, Fiona, Chen, Honglei, Cheng, Andrew Tai-Ann, Chou, David, Chugh, Sumeet S, Coffeng, Luc E, Colan, Steven D, Colquhoun, Samantha, Colson, K Ellicott, Condon, John, Connor, Myles D, Cooper, Leslie T, Corriere, Matthew, Cortinovis, Monica, de Vaccaro, Karen Courville, Couser, William, Cowie, Benjamin C, Criqui, Michael H, Cross, Marita, Dabhadkar, Kaustubh C, Dahiya, Manu, Dahodwala, Nabila, Damsere-Derry, James, Danaei, Goodarz, Davis, Adrian, Leo, Diego De, Degenhardt, Louisa, Dellavalle, Robert, Delossantos, Allyne, Denenberg, Julie, Derrett, Sarah, Des Jarlais, Don C, Dharmaratne, Samath D, Dherani, Mukesh, Diaz-Torne, Cesar, Dolk, Helen, Dorsey, E Ray, Driscoll, Tim, Duber, Herbert, Ebel, Beth, Edmond, Karen, Elbaz, Alexis, Ali, Suad Eltahir, Erskine, Holly, Erwin, Patricia J, Espindola, Patricia, Ewoigbokhan, Stalin E, Farzadfar, Farshad, Feigin, Valery, Felson, David T, Ferrari, Alize, Ferri, Cleusa P, Fèvre, Eric M, Finucane, Mariel M, Flaxman, Seth, Flood, Louise, Foreman, Kyle, Forouzanfar, Mohammad H, Fowkes, Francis Gerry R, Fransen, Marlene, Freeman, Michael K, Gabbe, Belinda J, Gabriel, Sherine E, Gakidou, Emmanuela, Ganatra, Hammad A, Garcia, Bianca, Gaspari, Flavio, Gillum, Richard F, Gmel, Gerhard, Gonzalez-Medina, Diego, Gosselin, Richard, Grainger, Rebecca, Grant, Bridget, Groeger, Justina, Guillemin, Francis, Gunnell, David, Gupta, Ramyani, Haagsma, Juanita, Hagan, Holly, Halasa, Yara A, Hall, Wayne, Haring, Diana, Haro, Josep Maria, Harrison, James E, Havmoeller, Rasmus, Hay, Roderick J, Higashi, Hideki, Hill, Catherine, Hoen, Bruno, Hoffman, Howard, Hotez, Peter J, Hoy, Damian, Huang, John J, Ibeanusi, Sydney E, Jacobsen, Kathryn H, James, Spencer L, Jarvis, Deborah, Jasrasaria, Rashmi, Jayaraman, Sudha, Johns, Nicole, Jonas, Jost B, Karthikeyan, Ganesan, Kassebaum, Nicholas, Kawakami, Norito, Keren, Andre, Khoo, Jon-Paul, King, Charles H, Knowlton, Lisa Marie, Kobusingye, Olive, Koranteng, Adofo, Krishnamurthi, Rita, Laden, Francine, Lalloo, Ratilal, Laslett, Laura L, Lathlean, Tim, Leasher, Janet L, Lee, Yong Yi, Leigh, James, Levinson, Daphna, Lim, Stephen S, Limb, Elizabeth, Lin, John Kent, Lipnick, Michael, Lipshultz, Steven E, Liu, Wei, Loane, Maria, Ohno, Summer Lockett, Lyons, Ronan, Mabweijano, Jacqueline, MacIntyre, Michael F, Malekzadeh, Reza, Mallinger, Leslie, Manivannan, Sivabalan, Marcenes, Wagner, March, Lyn, Margolis, David J, Marks, Guy B, Marks, Robin, Matsumori, Akira, Matzopoulos, Richard, Mayosi, Bongani M, McAnulty, John H, McDermott, Mary M, McGill, Neil, McGrath, John, Medina-Mora, Maria Elena, Meltzer, Michele, Memish, Ziad A, Mensah, George A, Merriman, Tony R, Meyer, Ana-Claire, Miglioli, Valeria, Miller, Matthew, Miller, Ted R, Mitchell, Philip B, Mock, Charles, Mocumbi, Ana Olga, Moffitt, Terrie E, Mokdad, Ali A, Monasta, Lorenzo, Montico, Marcella, Moradi-Lakeh, Maziar, Moran, Andrew, Morawska, Lidia, Mori, Rintaro, Murdoch, Michele E, Mwaniki, Michael K, Naidoo, Kovin, Nair, M Nathan, Naldi, Luigi, Narayan, K M Venkat, Nelson, Paul K, Nelson, Robert G, Nevitt, Michael C, Newton, Charles R, Nolte, Sandra, Norman, Paul, Norman, Rosana, O'Donnell, Martin, O'Hanlon, Simon, Olives, Casey, Omer, Saad B, Ortblad, Katrina, Osborne, Richard, Ozgediz, Doruk, Page, Andrew, Pahari, Bishnu, Pandian, Jeyaraj Durai, Rivero, Andrea Panozo, Patten, Scott B, Pearce, Neil, Padilla, Rogelio Perez, Perez-Ruiz, Fernando, Perico, Norberto, Pesudovs, Konrad, Phillips, David, Phillips, Michael R, Pierce, Kelsey, Pion, Sébastien, Polanczyk, Guilherme V, Polinder, Suzanne, Pope, C Arden, Popova, Svetlana, Porrini, Esteban, Pourmalek, Farshad, Prince, Martin, Pullan, Rachel L, Ramaiah, Kapa D, Ranganathan, Dharani, Razavi, Homie, Regan, Mathilda, Rehm, Jürgen T, Rein, David B, Remuzzi, Guiseppe, Richardson, Kathryn, Rivara, Frederick P, Roberts, Thomas, Robinson, Carolyn, De Leòn, Felipe Rodriguez, Ronfani, Luca, Room, Robin, Rosenfeld, Lisa C, Rushton, Lesley, Sacco, Ralph L, Saha, Sukanta, Sampson, Uchechukwu, Sanchez-Riera, Lidia, Sanman, Ella, Schwebel, David C, Scott, James Graham, Segui-Gomez, Maria, Shahraz, Saeid, Shepard, Donald S, Shin, Hwashin, Shivakoti, Rupak, Silberberg, Donald, Singh, David, Singh, Gitanjali M, Singh, Jasvinder A, Singleton, Jessica, Sleet, David A, Sliwa, Karen, Smith, Emma, Smith, Jennifer L, Stapelberg, Nicolas JC, Steer, Andrew, Steiner, Timothy, Stolk, Wilma A, Stovner, Lars Jacob, Sudfeld, Christopher, Syed, Sana, Tamburlini, Giorgio, Tavakkoli, Mohammad, Taylor, Hugh R, Taylor, Jennifer A, Taylor, William J, Thomas, Bernadette, Thomson, W Murray, Thurston, George D, Tleyjeh, Imad M, Tonelli, Marcello, Towbin, Jeffrey A, Truelsen, Thomas, Tsilimbaris, Miltiadis K, Ubeda, Clotilde, Undurraga, Eduardo A, van der Werf, Marieke J, van Os, Jim, Vavilala, Monica S, Venketasubramanian, N, Wang, Mengru, Wang, Wenzhi, Watt, Kerrianne, Weatherall, David J, Weinstock, Martin A, Weintraub, Robert, Weisskopf, Marc G, Weissman, Myrna M, White, Richard A, Whiteford, Harvey, Wiebe, Natasha, Wiersma, Steven T, Wilkinson, James D, Williams, Hywel C, Williams, Sean RM, Witt, Emma, Wolfe, Frederick, Woolf, Anthony D, Wulf, Sarah, Yeh, Pon-Hsiu, Zaidi, Anita KM, Zheng, Zhi-Jie, Zonies, David, and Lopez, Alan D
  • The Lancet; December-January 2012, Vol. 380 Issue: 9859 p2197-2223, 27p
Abstract
Measuring disease and injury burden in populations requires a composite metric that captures both premature mortality and the prevalence and severity of ill-health. The 1990 Global Burden of Disease study proposed disability-adjusted life years (DALYs) to measure disease burden. No comprehensive update of disease burden worldwide incorporating a systematic reassessment of disease and injury-specific epidemiology has been done since the 1990 study. We aimed to calculate disease burden worldwide and for 21 regions for 1990, 2005, and 2010 with methods to enable meaningful comparisons over time.

53. Geospatial and contextual approaches to energy balance and health [2015]

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  • Annals of GIS. 21(2):157-168

54. Vaccination attitudes and mobile readiness: A survey of expectant and new mothers [2015]

  • Atkinson, Katherine M, Ducharme, Robin, Westeinde, Jacqueline, Wilson, Sarah E, Deeks, Shelley L, Pascali, Dante, and Wilson, Kumanan
  • Human vaccines & immunotherapeutics. 11(4):1039-1045

55. Using mobile technologies for immunization: Predictors of uptake of a pan-Canadian immunization app (ImmunizeCA) [2015]

  • Atkinson, Katherine M., Westeinde, Jacqueline, Hawken, Steven, Ducharme, Robin, Barnhardt, Kim, and Wilson, Kumanan
  • Paediatrics & child health. 20(7):351-352

56. Dissecting the Mechanism of Type VI Secretion System Effector Delivery by Fluorescence Cross-Correlation Microscopy [2015]

  • Corbitt, Jacqueline, LeRoux, Michele, Kirkpatrick, Robin, Mougous, Joseph, and Wiggins, Paul A.
  • Biophysical Journal; January 2015, Vol. 108 Issue: 2, Number 2 Supplement 1 p600a-600a, 1p

57. Severe Thrombocytopenia in Adults with Severe Acute Respiratory Distress Syndrome: Impact of Extracorporeal Membrane Oxygenation Use [2016]

  • Dzierba, Amy L., Roberts, Russel, Muir, Justin, Alhammad, Abdullah, Schumaker, Greg, Clark, Jacqueline, Ruthazer, Robin, and Devlin, John W.
  • ASAIO journal. 62(6):710-714

58. Can mobile technologies improve on-time vaccination? A study piloting maternal use of ImmunizeCA, a Pan-Canadian immunization app [2016]

  • Atkinson, Katherine M., Westeinde, Jacqueline, Ducharme, Robin, Wilson, Sarah E., Deeks, Shelley L., Crowcroft, Natasha, Hawken, Steven, and Wilson, Kumanan
  • Human vaccines & immunotherapeutics. 12(10):2654-2661

59. Risk, coping and PTSD symptom trajectories in World Trade Center responders [2016]

  • Feder, Adriana, Mota, Natalie, Salim, Ryan, Rodriguez, Janice, Singh, Ritika, Schaffer, Jamie, Schechter, Clyde B., Cancelmo, Leo M., Bromet, Evelyn J., Katz, Craig L., Reissman, Dori B., Ozbay, Fatih, Kotov, Roman, Crane, Michael, Harrison, Denise J., Herbert, Robin, Levin, Stephen M., Luft, Benjamin J., Moline, Jacqueline M., Stellman, Jeanne M., Udasin, Iris G., Landrigan, Philip J., Zvolensky, Michael J., Yehuda, Rachel, Southwick, Steven M., and Pietrzak, Robert H.
  • Journal of psychiatric research. 82:68-79

60. Latent typologies of posttraumatic stress disorder in World Trade Center responders [2016]

  • Horn, Sarah R., Pietrzak, Robert H., Schechter, Clyde, Bromet, Evelyn J., Katz, Craig L., Reissman, Dori B., Kotov, Roman, Crane, Michael, Harrison, Denise J., Herbert, Robin, Luft, Benjamin J., Moline, Jacqueline M., Stellman, Jeanne M., Udasin, Iris G., Landrigan, Philip J., Zvolensky, Michael J., Southwick, Steven M., and Feder, Adriana
  • Journal of psychiatric research. 83:151-159

61. Carbene-Catalyzed Dynamic Kinetic Resolution of Carboxylic Esters [2016]

  • Chen, Xingkuan, Fong, Jacqueline Zi Mei, Xu, Jianfeng, Mou, Chengli, Lu, Yunpeng, Yang, Song, Song, Bao-An, and Chi, Yonggui Robin
  • Journal of the American Chemical Society. 138(23):7212-7215

62. Galactic cosmic ray simulation at the NASA Space Radiation Laboratory [2016]

  • Norbury, John W., Schimmerling, Walter, Slaba, Tony C., Azzam, Edouard I., Badavi, Francis F., Baiocco, Giorgio, Benton, Eric, Bindi, Veronica, Blakely, Eleanor A., Blattnig, Steve R., Boothman, David A., Borak, Thomas B., Britten, Richard A., Curtis, Stan, Dingfelder, Michael, Durante, Marco, Dynan, William S., Eisch, Amelia J., Robin Elgart, S., Goodhead, Dudley T., Guida, Peter M., Heilbronn, Lawrence H., Hellweg, Christine E., Huff, Janice L., Kronenberg, Amy, La Tessa, Chiara, Lowenstein, Derek I., Miller, Jack, Morita, Takashi, Narici, Livio, Nelson, Gregory A., Norman, Ryan B., Ottolenghi, Andrea, Patel, Zarana S., Reitz, Guenther, Rusek, Adam, Schreurs, Ann-Sofie, Scott-Carnell, Lisa A., Semones, Edward, Shay, Jerry W., Shurshakov, Vyacheslav A., Sihver, Lembit, Simonsen, Lisa C., Story, Michael D., Turker, Mitchell S., Uchihori, Yukio, Williams, Jacqueline, and Zeitlin, Cary J.
  • Life Sciences in Space Research; February 2016, Vol. 8 Issue: 1 p38-51, 14p
Abstract
Most accelerator-based space radiation experiments have been performed with single ion beams at fixed energies. However, the space radiation environment consists of a wide variety of ion species with a continuous range of energies. Due to recent developments in beam switching technology implemented at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (BNL), it is now possible to rapidly switch ion species and energies, allowing for the possibility to more realistically simulate the actual radiation environment found in space. The present paper discusses a variety of issues related to implementation of galactic cosmic ray (GCR) simulation at NSRL, especially for experiments in radiobiology. Advantages and disadvantages of different approaches to developing a GCR simulator are presented. In addition, issues common to both GCR simulation and single beam experiments are compared to issues unique to GCR simulation studies. A set of conclusions is presented as well as a discussion of the technical implementation of GCR simulation.

63. Personal Burden of Isotretinoin Therapy and Willingness to Pay for Electronic Follow-up Visits [2016]

  • Mori, Westley S., Houston, Neil, Moreau, Jacqueline F., Prevost, Noel, Gehris, Robin P., Ferris, Laura Korb, and Patton, Timothy J.
  • JAMA Dermatology; March 2016, Vol. 152 Issue: 3 p338-340, 3p

64. The 5As Team Program: Improving patient-centered obesity assessment and management in primary care [2017]

  • Campbell-Scherer, Denise L., Luig, Thea, Asselin, Jodie, Anderson, Robin, Fielding, Sheri, Heatherington, Melanie, Borrowitz, Michelle, Torti, Jacqueline, Cave, Andrew, Johnson, Jeffrey A., and Sharma, Arya M.
  • Canadian journal of diabetes. 41(5):S54-S54

65. Hypothyroidism [2017]

  • Chaker, Layal, Bianco, Antonio C, Jonklaas, Jacqueline, and Peeters, Robin P
  • Lancet. 390(10101):1550-1562

66. A parallel group randomised open blinded evaluation of Acceptance and Commitment Therapy for depression after psychosis: Pilot trial outcomes (ADAPT) [2017]

  • Gumley, Andrew, White, Ross, Briggs, Andy, Ford, Ian, Barry, Sarah, Stewart, Corinna, Beedie, Sara, McTaggart, Jacqueline, Clarke, Caoimhe, MacLeod, Rachel, Lidstone, Emma, Riveros, Bruno Salgado, Young, Robin, and McLeod, Hamish
  • Schizophrenia research. 183:143-150

67. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles [2017]

  • Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A. Gordon, Hinoue, Toshinori, Hoadley, Katherine A., Gibb, Ewan A., Roszik, Jason, Covington, Kyle R., Wu, Chia-Chin, Shinbrot, Eve, Stransky, Nicolas, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Hess, Julian M., Auman, J. Todd, Rhie, Suhn K., Bowlby, Reanne, Borad, Mitesh J., Akbani, Rehan, Allotey, Loretta K., Ally, Adrian, Alvaro, Domenico, Andersen, Jesper B., Appelbaum, Elizabeth L., Arora, Arshi, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Bardeesy, Nabeel, Bathe, Oliver F., Baylin, Stephen B., Beroukhim, Rameen, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Borad, Mitesh J., Bowen, Jay, Bowlby, Reanne, Bragazzi, Maria Consiglia, Brooks, Denise, Cardinale, Vincenzo, Carlsen, Rebecca, Carpino, Guido, Carvalho, Andre L., Chaiteerakij, Roongruedee, Chandan, Vishal C., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cordes, Matthew G., Covington, Kyle R., Crain, Daniel, Curley, Erin, De Rose, Agostino Maria, Defreitas, Timothy, Demchok, John A., Deshpande, Vikram, Dhalla, Noreen, Ding, Li, Evason, Kimberley, Farshidfar, Farshad, Felau, Ina, Ferguson, Martin L., Foo, Wai Chin, Franchitto, Antonio, Frazer, Scott, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Gabriel, Stacey B., Gardner, Johanna, Gastier-Foster, Julie M., Gaudio, Eugenio, Gehlenborg, Nils, Genovese, Giannicola, Gerken, Mark, Getz, Gad, Giama, Nasra H., Gibbs, Richard A., Gingras, Marie-Claude, Giuliante, Felice, Grazi, Gian Luca, Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Hess, Julian M., Hinoue, Toshinori, Hoadley, Katherine A., Holbrook, Andrea, Holt, Robert A., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J.M., Jones, Corbin D., Kasaian, Katayoon, Kelley, Robin K., Kim, Jaegil, Kleiner, David E., Kocher, Jean-Pierre A., Kwong, Lawrence N., Lai, Phillip H., Laird, Peter W., Lawrence, Michael S., Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Wenbin, Liu, Jia, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Mallery, David, Mardis, Elaine R., Marra, Marco A., Matsushita, Marcus M., Mayo, Michael, McLellan, Michael D., McRee, Autumn J., Meier, Sam, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Christopher A., Mills, Gordon B., Moore, Richard A., Morris, Scott, Mose, Lisle E., Moser, Catherine D., Mounajjed, Taofic, Mungall, Andrew J., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Newton, Yulia, Noble, Michael S., O’Brien, Daniel R., Ojesina, Akinyemi I., Parker, Joel S., Patel, Tushar C., Paulauskis, Joseph, Pedamallu, Chandra Sekhar, Penny, Robert, Perou, Charles M., Perou, Amy H., Pihl, Todd, Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Reznik, Ed, Rhie, Suhn K., Roach, Jeffrey, Roberts, Lewis R., Robertson, A. Gordon, Sadeghi, Sara, Saksena, Gordon, Sander, Chris, Schein, Jacqueline E., Schmidt, Heather K., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Shen, Ronglai, Sheth, Margi, Shi, Yan, Shih, Juliann, Shinbrot, Eve, Shroff, Rachna, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Stoppler, Hubert, Stransky, Nicolas, Stuart, Josh, Sun, Qiang, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh B., Torbenson, Michael S., Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel G.W., Voet, Doug, Wan, Yunhu, Wang, Zhining, Weinstein, John N., Weisenberger, Daniel J., Wheeler, David A., Wilson, Richard K., Wise, Lisa, Wong, Tina, Wu, Chia-Chin, Wu, Ye, Xi, Liu, Yang, Ju Dong, Yang, Liming, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jiashan (Julia), Zheng, Siyuan, Zmuda, Erik, Zhu, Andrew X., Stuart, Josh M., Sander, Chris, Akbani, Rehan, Cherniack, Andrew D., Deshpande, Vikram, Mounajjed, Taofic, Foo, Wai Chin, Torbenson, Michael S., Kleiner, David E., Laird, Peter W., Wheeler, David A., McRee, Autumn J., Bathe, Oliver F., Andersen, Jesper B., Bardeesy, Nabeel, Roberts, Lewis R., and Kwong, Lawrence N.
  • Cell Reports; March 2017, Vol. 18 Issue: 11 p2780-2794, 15p
Abstract
Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDHmutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDHmutant subtype. More broadly, we found that IDHmutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

68. MUC1-mediated induction of myeloid-derived suppressor cells in patients with acute myeloid leukemia [2017]

  • Pyzer, Athalia Rachel, Stroopinsky, Dina, Rajabi, Hasan, Washington, Abigail, Tagde, Ashujit, Coll, Maxwell, Fung, Jacqueline, Bryant, Mary Paty, Cole, Leandra, Palmer, Kristen, Somaiya, Poorvi, Karp Leaf, Rebecca, Nahas, Myrna, Apel, Arie, Jain, Salvia, McMasters, Malgorzata, Mendez, Lourdes, Levine, James, Joyce, Robin, Arnason, Jon, Pandolfi, Pier Paolo, Kufe, Donald, Rosenblatt, Jacalyn, and Avigan, David
  • Blood; March 2017, Vol. 129 Issue: 13 p1791-1801, 11p
Abstract
Myeloid-derived suppressor cells (MDSCs) play a critical role in promoting immune tolerance and disease growth. The mechanism by which tumor cells evoke the expansion of MDSCs in acute myeloid leukemia (AML) has not been well described. We have demonstrated that patients with AML exhibit increased presence of MDSCs in their peripheral blood, in comparison with normal controls. Cytogenetic studies demonstrated that MDSCs in patients with AML may be derived from leukemic or apparently normal progenitors. Engraftment of C57BL/6 mice with TIB-49 AML led to an expansion of CD11b+Gr1+MDSCs in bone marrow and spleen. Coculture of the AML cell lines MOLM-4, THP-1 or primary AML cells with donor peripheral blood mononuclear cells elicited a cell contact–dependent expansion of MDSCs. MDSCs were suppressive of autologous T-cell responses as evidenced by reduced T-cell proliferation and a switch from a Th1 to a Th2 phenotype. We hypothesized that the expansion of MDSCs in AML is accomplished by tumor-derived extracellular vesicles (EVs). Using tracking studies, we demonstrated that AML EVs are taken-up myeloid progenitor cells, resulting in the selective proliferation of MDSCs in comparison with functionally competent antigen-presenting cells. The MUC1 oncoprotein was subsequently identified as the critical driver of EV-mediated MDSC expansion. MUC1 induces increased expression of c-myc in EVs that induces proliferation in the target MDSC population via downstream effects on cell cycle proteins. Moreover, we demonstrate that the microRNA miR34a acts as the regulatory mechanism by which MUC1 drives c-myc expression in AML cells and EVs.

69. Seek, test, treat: substance-using women in the HIV treatment cascade in South Africa [2017]

  • Wechsberg, Wendee, Horst, Charles, Ndirangu, Jacqueline, Doherty, Irene, Kline, Tracy, Browne, Felicia, Belus, Jennifer, Nance, Robin, and Zule, William
  • Addiction Science & Clinical Practice; December 2017, Vol. 12 Issue: 1 p1-11, 11p
Abstract
Women in South Africa who use alcohol and other drugs face multiple barriers to HIV care. These barriers make it difficult for women to progress through each step in the HIV treatment cascade from diagnosis to treatment initiation and adherence. This paper examines correlates of HIV status, newly diagnosed HIV status, and use of antiretroviral therapy (ART). Outreach workers recruited sexually active Black African women who used substances in Pretoria as part of a U.S. National Institutes of Health-funded geographically clustered randomized trial examining the effect of an intervention to reduce alcohol and drug use as well as sexual risk behaviors. To address the question of interest in the current investigation, cross-sectional baseline data were used. At study enrollment, all participants (N = 641) completed an interview, and underwent rapid HIV testing and biological drug screening. Those who tested positive for HIV and were eligible for ART were asked about their barriers to initiating or adhering to ART. Bivariate and multivariable logistic regression analyses were conducted to determine correlates of HIV status, newly diagnosed HIV, and ART use. At enrollment, 55% of participants tested positive for HIV, and 36% of these women were newly diagnosed. In multivariable analyses of the entire sample, women who had completed 10th grade were less likely to be living with HIV (OR 0.69; CI 0.48, 0.99) and those from the inner city were more likely to be living with HIV (OR 1.83; CI 1.26, 2.67). Among HIV-positive participants, women were less likely to be newly diagnosed if they had ever been in substance abuse treatment (OR 0.15; CI 0.03, 0.69) or used a condom at last sex (OR 0.58; CI 0.34, 0.98) and more likely to be newly diagnosed if they were physically assaulted in the past year (OR 1.97; CI 1.01, 3.84). Among women eligible for ART, fewer were likely to be on treatment (by self-report) if they had a positive urine test for opiates or cocaine (OR 0.27; CI 0.09, 0.80). These results, although cross-sectional, provide some guidance for provincial authorities to address barriers to HIV care for sexually active, substance-using vulnerable women in Pretoria. Targeting the inner city with prevention campaigns, expanding and improving substance abuse treatment programs, linking clients with simultaneous HIV testing and treatment, and targeting women who have experienced sexual assault and violence may help the government achieve the UNAIDS 90-90-90 treatment target. Clinical Trials.gov NCT01497405 registered on December 1, 2011.

70. Phase I/Ib Trial of the MUC1 Inhibitor GO-203-2C Alone and in Combination with Decitabine for Acute Myeloid Leukemia [2017]

  • Liegel, Jessica, Rosenblatt, Jacalyn, Stone, Richard M., McMasters, Malgorzata, Levine, James D., Nahas, Myrna, Joyce, Robin M., Jain, Salvia, DeAngelo, Daniel J., Garcia, Jacqueline S., Bazemore, Josie, Galinsky, Ilene, Neuberg, Donna S., Werner, Lillian, Logan, Emma, Mikami, Kaleb, Bryant, Mary Paty, Allen, Victoria, Stroopinsky, Dina, Cole, Leandra, Washington, Abigail J., Ephraim, Adam, and Avigan, David E.
  • Blood; December 2017, Vol. 130 Issue: 1, Number 1 Supplement 1 p2659-2659, 1p
Abstract
MUC1, an oncogenic protein aberrantly expressed on AML and leukemic stem cells, supports critical aspects of the malignant phenotype including resistance to apoptosis, cell proliferation and autonomous self renewal. GO-203-2C is a novel cell-penetrating peptide that blocks homodimerization of the MUC1-C subunit required for nuclear translocation and downstream signaling. In murine AML models, treatment with GO-203-2C resulted in specific eradication of myeloid leukemia. GO-203-2C is synergistic with hypomethylating agents in pre-clinical models of AML. Based on these findings, we are conducting a phase I/Ib study of GO-203-2C alone and in combination with decitabine in patients with AML.

71. Breakfast food health and acute exercise: Effects on state body image [2018]

  • Hayes, Jacqueline F., Giles, Grace E., Mahoney, Caroline R., and Kanarek, Robin B.
  • Eating behaviors. 30:22-27

72. Hypothyroidism and hypertension: fact or myth? – Authors' reply [2018]

  • Chaker, Layal, Bianco, Antonio C, Jonklaas, Jacqueline, and Peeters, Robin P
  • lancet. 391(10115):30-30

73. Cellular immunotherapy on primary multiple myeloma expanded in a 3D bone marrow niche model [2018]

  • Braham, Maaike V. J., Minnema, Monique C., Aarts, Tineke, Sebestyen, Zsolt, Straetemans, Trudy, Vyborova, Anna, Kuball, Jurgen, Öner, F. Cumhur, Robin, Catherine, and Alblas, Jacqueline
  • Oncoimmunology. 7(6)

74. Using Teacher Ratings to Investigate Developmental Regression as a Potential Indicator of School-Age Symptoms in Students with Autism Spectrum Disorder [2018]

  • Mire, Sarah S., Anderson, Jacqueline R., Manis, Jamie K., Hughes, K. R., Raff, Natalie S., and Goin-Kochel, Robin P.
  • School mental health. 10(1):77-90

75. The effect of probiotics and zinc supplementation on the immune response to oral rotavirus vaccine: A randomized, factorial design, placebo-controlled study among Indian infants [2018]

  • Lazarus, Robin P., John, Jacob, Shanmugasundaram, E., Rajan, Anand K., Thiagarajan, S., Giri, Sidhartha, Babji, Sudhir, Sarkar, Rajiv, Kaliappan, P. Saravankumar, Venugopal, Srinivasan, Praharaj, Ira, Raman, Uma, Paranjpe, Meghana, Grassly, Nicholas C., Parker, Edward P.K., Parashar, Umesh D., Tate, Jacqueline E., Fleming, Jessica A., Steele, A. Duncan, Muliyil, Jayaprakash, Abraham, Asha M., and Kang, Gagandeep
  • Vaccine. 36(2):273-279

76. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas [2018]

  • Way, Gregory P., Sanchez-Vega, Francisco, La, Konnor, Armenia, Joshua, Chatila, Walid K., Luna, Augustin, Sander, Chris, Cherniack, Andrew D., Mina, Marco, Ciriello, Giovanni, Schultz, Nikolaus, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, Jonathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. Mora, Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Sanchez, Yolanda, and Greene, Casey S.
  • Cell Reports; April 2018, Vol. 23 Issue: 1 p172-180.e3
Abstract
Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may respond. The transcriptome of these “hidden responders” may reveal responsive molecular states. We describe and evaluate a machine-learning approach to classify aberrant pathway activity in tumors, which may aid in hidden responder identification. The algorithm integrates RNA-seq, copy number, and mutations from 33 different cancer types across The Cancer Genome Atlas (TCGA) PanCanAtlas project to predict aberrant molecular states in tumors. Applied to the Ras pathway, the method detects Ras activation across cancer types and identifies phenocopying variants. The model, trained on human tumors, can predict response to MEK inhibitors in wild-type Ras cell lines. We also present data that suggest that multiple hits in the Ras pathway confer increased Ras activity. The transcriptome is underused in precision oncology and, combined with machine learning, can aid in the identification of hidden responders.

77. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images [2018]

  • Saltz, Joel, Gupta, Rajarsi, Hou, Le, Kurc, Tahsin, Singh, Pankaj, Nguyen, Vu, Samaras, Dimitris, Shroyer, Kenneth R., Zhao, Tianhao, Batiste, Rebecca, Van Arnam, John, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, onathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. Mora, Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Shmulevich, Ilya, Rao, Arvind U.K., Lazar, Alexander J., Sharma, Ashish, and Thorsson, Vésteinn
  • Cell Reports; April 2018, Vol. 23 Issue: 1 p181-193.e7
Abstract
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumor-infiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment.

78. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas [2018]

  • Campbell, Joshua D., Yau, Christina, Bowlby, Reanne, Liu, Yuexin, Brennan, Kevin, Fan, Huihui, Taylor, Alison M., Wang, Chen, Walter, Vonn, Akbani, Rehan, Byers, Lauren Averett, Creighton, Chad J., Coarfa, Cristian, Shih, Juliann, Cherniack, Andrew D., Gevaert, Olivier, Prunello, Marcos, Shen, Hui, Anur, Pavana, Chen, Jianhong, Cheng, Hui, Hayes, D. Neil, Bullman, Susan, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Sadeghi, Sara, Mungall, Karen L., Robertson, A. Gordon, Benz, Christopher, Schultz, Andre, Kanchi, Rupa S., Gay, Carl M., Hegde, Apurva, Diao, Lixia, Wang, Jing, Ma, Wencai, Sumazin, Pavel, Chiu, Hua-Sheng, Chen, Ting-Wen, Gunaratne, Preethi, Donehower, Larry, Rader, Janet S., Zuna, Rosemary, Al-Ahmadie, Hikmat, Lazar, Alexander J., Flores, Elsa R., Tsai, Kenneth Y., Zhou, Jane H., Rustgi, Anil K., Drill, Esther, Shen, Ronglei, Wong, Christopher K., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, onathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. 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  • Cell Reports; April 2018, Vol. 23 Issue: 1 p194-212.e6
Abstract
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches.

79. Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types [2018]

  • Ge, Zhongqi, Leighton, Jake S., Wang, Yumeng, Peng, Xinxin, Chen, Zhongyuan, Chen, Hu, Sun, Yutong, Yao, Fan, Li, Jun, Zhang, Huiwen, Liu, Jianfang, Shriver, Craig D., Hu, Hai, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. 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Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, Jonathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. Mora, Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Piwnica-Worms, Helen, Ma, Li, and Liang, Han
  • Cell Reports; April 2018, Vol. 23 Issue: 1 p213-226.e3
Abstract
Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atlas, we perform comprehensive molecular characterization of 929 ubiquitin-related genes and 95 deubiquitinase genes. Among them, we systematically identify top somatic driver candidates, including mutated FBXW7with cancer-type-specific patterns and amplified MDM2showing a mutually exclusive pattern with BRAFmutations. Ubiquitin pathway genes tend to be upregulated in cancer mediated by diverse mechanisms. By integrating pan-cancer multiomic data, we identify a group of tumor samples that exhibit worse prognosis. These samples are consistently associated with the upregulation of cell-cycle and DNA repair pathways, characterized by mutated TP53, MYC/TERTamplification, and APC/PTENdeletion. Our analysis highlights the importance of the ubiquitin pathway in cancer development and lays a foundation for developing relevant therapeutic strategies.

80. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers [2018]

  • Gao, Qingsong, Liang, Wen-Wei, Foltz, Steven M., Mutharasu, Gnanavel, Jayasinghe, Reyka G., Cao, Song, Liao, Wen-Wei, Reynolds, Sheila M., Wyczalkowski, Matthew A., Yao, Lijun, Yu, Lihua, Sun, Sam Q., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, Jonathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. Mora, Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Chen, Ken, Lazar, Alexander J., Fields, Ryan C., Wendl, Michael C., Van Tine, Brian A., Vij, Ravi, Chen, Feng, Nykter, Matti, Shmulevich, Ilya, and Ding, Li
  • Cell Reports; April 2018, Vol. 23 Issue: 1 p227-238.e3
Abstract
Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy.

81. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas [2018]

  • Knijnenburg, Theo A., Wang, Linghua, Zimmermann, Michael T., Chambwe, Nyasha, Gao, Galen F., Cherniack, Andrew D., Fan, Huihui, Shen, Hui, Way, Gregory P., Greene, Casey S., Liu, Yuexin, Akbani, Rehan, Feng, Bin, Donehower, Lawrence A., Miller, Chase, Shen, Yang, Karimi, Mostafa, Chen, Haoran, Kim, Pora, Jia, Peilin, Shinbrot, Eve, Zhang, Shaojun, Liu, Jianfang, Hu, Hai, Bailey, Matthew H., Yau, Christina, Wolf, Denise, Zhao, Zhongming, Weinstein, John N., Li, Lei, Ding, Li, Mills, Gordon B., Laird, Peter W., Wheeler, David A., Shmulevich, Ilya, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. 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  • Cell Reports; April 2018, Vol. 23 Issue: 1 p239-254.e6
Abstract
DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 cancer types. Mutations with accompanying loss of heterozygosity were observed in over 1/3 of DDR genes, including TP53and BRCA1/2. Other prevalent alterations included epigenetic silencing of the direct repair genes EXO5, MGMT, and ALKBH3in ∼20% of samples. Homologous recombination deficiency (HRD) was present at varying frequency in many cancer types, most notably ovarian cancer. However, in contrast to ovarian cancer, HRD was associated with worse outcomes in several other cancers. Protein structure-based analyses allowed us to predict functional consequences of rare, recurrent DDR mutations. A new machine-learning-based classifier developed from gene expression data allowed us to identify alterations that phenocopy deleterious TP53mutations. These frequent DDR gene alterations in many human cancers have functional consequences that may determine cancer progression and guide therapy.

82. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers [2018]

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Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, Jonathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. Mora, Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Bathe, Oliver F., and Liang, Han
  • Cell Reports; April 2018, Vol. 23 Issue: 1 p255-269.e4
Abstract
Metabolic reprogramming provides critical information for clinical oncology. Using molecular data of 9,125 patient samples from The Cancer Genome Atlas, we identified tumor subtypes in 33 cancer types based on mRNA expression patterns of seven major metabolic processes and assessed their clinical relevance. Our metabolic expression subtypes correlated extensively with clinical outcome: subtypes with upregulated carbohydrate, nucleotide, and vitamin/cofactor metabolism most consistently correlated with worse prognosis, whereas subtypes with upregulated lipid metabolism showed the opposite. Metabolic subtypes correlated with diverse somatic drivers but exhibited effects convergent on cancer hallmark pathways and were modulated by highly recurrent master regulators across cancer types. As a proof-of-concept example, we demonstrated that knockdown of SNAI1or RUNX1—master regulators of carbohydrate metabolic subtypes—modulates metabolic activity and drug sensitivity. Our study provides a system-level view of metabolic heterogeneity within and across cancer types and identifies pathway cross-talk, suggesting related prognostic, therapeutic, and predictive utility.

83. Systematic Analysis of Splice-Site-Creating Mutations in Cancer [2018]

  • Jayasinghe, Reyka G., Cao, Song, Gao, Qingsong, Wendl, Michael C., Vo, Nam Sy, Reynolds, Sheila M., Zhao, Yanyan, Climente-González, Héctor, Chai, Shengjie, Wang, Fang, Varghese, Rajees, Huang, Mo, Liang, Wen-Wei, Wyczalkowski, Matthew A., Sengupta, Sohini, Li, Zhi, Payne, Samuel H., Fenyö, David, Miner, Jeffrey H., Walter, Matthew J., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, Jonathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. Mora, Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Vincent, Benjamin, Eyras, Eduardo, Chen, Ken, Shmulevich, Ilya, Chen, Feng, and Ding, Li
  • Cell Reports; April 2018, Vol. 23 Issue: 1 p270-281.e3
Abstract
For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53and GATA3have 26 and 18 SCMs, respectively, and ATRXhas 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.

84. Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types [2018]

  • Seiler, Michael, Peng, Shouyong, Agrawal, Anant A., Palacino, James, Teng, Teng, Zhu, Ping, Smith, Peter G., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Angulo Gonzalez, Ana Maria, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, Jonathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Mora Pinero, Edna M., Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Buonamici, Silvia, and Yu, Lihua
  • Cell Reports; April 2018, Vol. 23 Issue: 1 p282-296.e4
Abstract
Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA), and we identified 119 splicing factor genes with significant non-silent mutation patterns, including mutation over-representation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). Furthermore, RNA sequencing analysis revealed altered splicing events associated with selected splicing factor mutations. In addition, we were able to identify common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of genes involved in the RNA-splicing process is common in cancer and may represent an underappreciated hallmark of tumorigenesis.

85. Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context [2018]

  • Chiu, Hua-Sheng, Somvanshi, Sonal, Patel, Ektaben, Chen, Ting-Wen, Singh, Vivek P., Zorman, Barry, Patil, Sagar L., Pan, Yinghong, Chatterjee, Sujash S., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. 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Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, Jonathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. Mora, Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Sood, Anil K., Gunaratne, Preethi H., and Sumazin, Pavel
  • Cell Reports; April 2018, Vol. 23 Issue: 1 p297-312.e12
Abstract
Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, and microRNAs in 5,185 TCGA tumors and 1,019 ENCODE assays. Our predictions included hundreds of candidate onco- and tumor-suppressor lncRNAs (cancer lncRNAs) whose somatic alterations account for the dysregulation of dozens of cancer genes and pathways in each of 14 tumor contexts. To demonstrate proof of concept, we showed that perturbations targeting OIP5-AS1 (an inferred tumor suppressor) and TUG1 and WT1-AS (inferred onco-lncRNAs) dysregulated cancer genes and altered proliferation of breast and gynecologic cancer cells. Our analysis indicates that, although most lncRNAs are dysregulated in a tumor-specific manner, some, including OIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergistically dysregulate cancer pathways in multiple tumor contexts.

86. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma [2018]

  • Ricketts, Christopher J., De Cubas, Aguirre A., Fan, Huihui, Smith, Christof C., Lang, Martin, Reznik, Ed, Bowlby, Reanne, Gibb, Ewan A., Akbani, Rehan, Beroukhim, Rameen, Bottaro, Donald P., Choueiri, Toni K., Gibbs, Richard A., Godwin, Andrew K., Haake, Scott, Hakimi, A. Ari, Henske, Elizabeth P., Hsieh, James J., Ho, Thai H., Kanchi, Rupa S., Krishnan, Bhavani, Kwiatkowski, David J., Lui, Wembin, Merino, Maria J., Mills, Gordon B., Myers, Jerome, Nickerson, Michael L., Reuter, Victor E., Schmidt, Laura S., Shelley, C. Simon, Shen, Hui, Shuch, Brian, Signoretti, Sabina, Srinivasan, Ramaprasad, Tamboli, Pheroze, Thomas, George, Vincent, Benjamin G., Vocke, Cathy D., Wheeler, David A., Yang, Lixing, Kim, William Y., Robertson, A. Gordon, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, onathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. Mora, Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Spellman, Paul T., Rathmell, W. Kimryn, and Linehan, W. Marston
  • Cell Reports; April 2018, Vol. 23 Issue: 1 p313-326.e5
Abstract
Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTENand altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2Aalteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival.

87. Endosteal and Perivascular Subniches in a 3D Bone Marrow Model for Multiple Myeloma [2018]

  • Braham, Maaike V.J., Ahlfeld, Tilman, Akkineni, A. Rahul, Minnema, Monique C., Dhert, Wouter J.A., Öner, F. Cumhur, Robin, Catherine, Lode, Anja, Gelinsky, Michael, and Alblas, Jacqueline
  • Tissue Engineering Part C: Methods; May 2018, Vol. 24 Issue: 5 p300-312, 13p
Abstract
The bone marrow microenvironment is the preferred location of multiple myeloma, supporting tumor growth and development. It is composed of a collection of interacting subniches, including the endosteal and perivascular niche. Current in vitromodels mimic either of these subniches. By developing a model combining both niches, this study aims to further enhance the ability to culture primary myeloma cells in vitro. Also, the dependency of myeloma cells on each niche was studied. A 3D bone marrow model containing two subniches was created using 3D bioprinting technology. We used a bioprintable pasty calcium phosphate cement (CPC) scaffold with seeded osteogenic multipotent mesenchymal stromal cells (O-MSCs) to model the endosteal niche, and Matrigel containing both endothelial progenitor cells (EPCs) and MSCs to model the perivascular niche. Within the model containing one or both of the niches, primary CD138+myeloma cells were cultured and analyzed for both survival and proliferation. The 3D bone marrow model with combined subniches significantly increasing the proliferation of CD138+myeloma cells compared to both environments separately. The developed model showed an essential role of the perivascular niche over the endosteal niche in supporting myeloma cells. The developed model can be used to study the expansion of primary myeloma cells and their interactions with varying bone marrow subniches.

88. Registered Replication Report on Mazar, Amir, and Ariely (2008) [2018]

  • Verschuere, Bruno, Meijer, Ewout H., Jim, Ariane, Hoogesteyn, Katherine, Orthey, Robin, McCarthy, Randy J., Skowronski, John J., Acar, Oguz A., Aczel, Balazs, Bakos, Bence E., Barbosa, Fernando, Baskin, Ernest, Bègue, Laurent, Ben-Shakhar, Gershon, Birt, Angie R., Blatz, Lisa, Charman, Steve D., Claesen, Aline, Clay, Samuel L., Coary, Sean P., Crusius, Jan, Evans, Jacqueline R., Feldman, Noa, Ferreira-Santos, Fernando, Gamer, Matthias, Gomes, Sara, González-Iraizoz, Marta, Holzmeister, Felix, Huber, Juergen, Isoni, Andrea, Jessup, Ryan K., Kirchler, Michael, klein Selle, Nathalie, Koppel, Lina, Kovacs, Marton, Laine, Tei, Lentz, Frank, Loschelder, David D., Ludvig, Elliot A., Lynn, Monty L., Martin, Scott D., McLatchie, Neil M., Mechtel, Mario, Nahari, Galit, Özdoğru, Asil Ali, Pasion, Rita, Pennington, Charlotte R., Roets, Arne, Rozmann, Nir, Scopelliti, Irene, Spiegelman, Eli, Suchotzki, Kristina, Sutan, Angela, Szecsi, Peter, Tinghög, Gustav, Tisserand, Jean-Christian, Tran, Ulrich S., Van Hiel, Alain, Vanpaemel, Wolf, Västfjäll, Daniel, Verliefde, Thomas, Vezirian, Kévin, Voracek, Martin, Warmelink, Lara, Wick, Katherine, Wiggins, Bradford J., Wylie, Keith, and Yıldız, Ezgi
  • Advances in Methods and Practices in Psychological Science; September 2018, Vol. 1 Issue: 3 p299-317, 19p
Abstract
The self-concept maintenance theory holds that many people will cheat in order to maximize self-profit, but only to the extent that they can do so while maintaining a positive self-concept. Mazar, Amir, and Ariely (2008, Experiment 1) gave participants an opportunity and incentive to cheat on a problem-solving task. Prior to that task, participants either recalled the Ten Commandments (a moral reminder) or recalled 10 books they had read in high school (a neutral task). Results were consistent with the self-concept maintenance theory. When given the opportunity to cheat, participants given the moral-reminder priming task reported solving 1.45 fewer matrices than did those given a neutral prime (Cohen’s d= 0.48); moral reminders reduced cheating. Mazar et al.’s article is among the most cited in deception research, but their Experiment 1 has not been replicated directly. This Registered Replication Report describes the aggregated result of 25 direct replications (total N= 5,786), all of which followed the same preregistered protocol. In the primary meta-analysis (19 replications, total n= 4,674), participants who were given an opportunity to cheat reported solving 0.11 more matrices if they were given a moral reminder than if they were given a neutral reminder (95% confidence interval = [−0.09, 0.31]). This small effect was numerically in the opposite direction of the effect observed in the original study (Cohen’s d= −0.04).

89. Registered Replication Report on Srull and Wyer (1979) [2018]

  • McCarthy, Randy J., Skowronski, John J., Verschuere, Bruno, Meijer, Ewout H., Jim, Ariane, Hoogesteyn, Katherine, Orthey, Robin, Acar, Oguz A., Aczel, Balazs, Bakos, Bence E., Barbosa, Fernando, Baskin, Ernest, Bègue, Laurent, Ben-Shakhar, Gershon, Birt, Angie R., Blatz, Lisa, Charman, Steve D., Claesen, Aline, Clay, Samuel L., Coary, Sean P., Crusius, Jan, Evans, Jacqueline R., Feldman, Noa, Ferreira-Santos, Fernando, Gamer, Matthias, Gerlsma, Coby, Gomes, Sara, González-Iraizoz, Marta, Holzmeister, Felix, Huber, Juergen, Huntjens, Rafaele J. C., Isoni, Andrea, Jessup, Ryan K., Kirchler, Michael, klein Selle, Nathalie, Koppel, Lina, Kovacs, Marton, Laine, Tei, Lentz, Frank, Loschelder, David D., Ludvig, Elliot A., Lynn, Monty L., Martin, Scott D., McLatchie, Neil M., Mechtel, Mario, Nahari, Galit, Özdoğru, Asil Ali, Pasion, Rita, Pennington, Charlotte R., Roets, Arne, Rozmann, Nir, Scopelliti, Irene, Spiegelman, Eli, Suchotzki, Kristina, Sutan, Angela, Szecsi, Peter, Tinghög, Gustav, Tisserand, Jean-Christian, Tran, Ulrich S., Van Hiel, Alain, Vanpaemel, Wolf, Västfjäll, Daniel, Verliefde, Thomas, Vezirian, Kévin, Voracek, Martin, Warmelink, Lara, Wick, Katherine, Wiggins, Bradford J., Wylie, Keith, and Yıldız, Ezgi
  • Advances in Methods and Practices in Psychological Science; September 2018, Vol. 1 Issue: 3 p321-336, 16p
Abstract
Srull and Wyer (1979) demonstrated that exposing participants to more hostility-related stimuli caused them subsequently to interpret ambiguous behaviors as more hostile. In their Experiment 1, participants descrambled sets of words to form sentences. In one condition, 80% of the descrambled sentences described hostile behaviors, and in another condition, 20% described hostile behaviors. Following the descrambling task, all participants read a vignette about a man named Donald who behaved in an ambiguously hostile manner and then rated him on a set of personality traits. Next, participants rated the hostility of various ambiguously hostile behaviors (all ratings on scales from 0 to 10). Participants who descrambled mostly hostile sentences rated Donald and the ambiguous behaviors as approximately 3 scale points more hostile than did those who descrambled mostly neutral sentences. This Registered Replication Report describes the results of 26 independent replications (N= 7,373 in the total sample; k= 22 labs and N= 5,610 in the primary analyses) of Srull and Wyer’s Experiment 1, each of which followed a preregistered and vetted protocol. A random-effects meta-analysis showed that the protagonist was seen as 0.08 scale points more hostile when participants were primed with 80% hostile sentences than when they were primed with 20% hostile sentences (95% confidence interval, CI = [0.004, 0.16]). The ambiguously hostile behaviors were seen as 0.08 points less hostile when participants were primed with 80% hostile sentences than when they were primed with 20% hostile sentences (95% CI = [−0.18, 0.01]). Although the confidence interval for one outcome excluded zero and the observed effect was in the predicted direction, these results suggest that the currently used methods do not produce an assimilative priming effect that is practically and routinely detectable.

90. Alcohol use and burden for 195 countries and territories, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016 [2018]

  • Griswold, Max G, Fullman, Nancy, Hawley, Caitlin, Arian, Nicholas, Zimsen, Stephanie R M, Tymeson, Hayley D, Venkateswaran, Vidhya, Tapp, Austin Douglas, Forouzanfar, Mohammad H, Salama, Joseph S, Abate, Kalkidan Hassen, Abate, Degu, Abay, Solomon M, Abbafati, Cristiana, Abdulkader, Rizwan Suliankatchi, Abebe, Zegeye, Aboyans, Victor, Abrar, Mohammed Mehdi, Acharya, Pawan, Adetokunboh, Olatunji O, Adhikari, Tara Ballav, Adsuar, Jose C, Afarideh, Mohsen, Agardh, Emilie Elisabet, Agarwal, Gina, Aghayan, Sargis Aghasi, Agrawal, Sutapa, Ahmed, Muktar Beshir, Akibu, Mohammed, Akinyemiju, Tomi, Akseer, Nadia, Asfoor, Deena H Al, Al-Aly, Ziyad, Alahdab, Fares, Alam, Khurshid, Albujeer, Ammar, Alene, Kefyalew Addis, Ali, Raghib, Ali, Syed Danish, Alijanzadeh, Mehran, Aljunid, Syed Mohamed, Alkerwi, Ala'a, Allebeck, Peter, Alvis-Guzman, Nelson, Amare, Azmeraw T, Aminde, Leopold N, Ammar, Walid, Amoako, Yaw Ampem, Amul, Gianna Gayle Herrera, Andrei, Catalina Liliana, Angus, Colin, Ansha, Mustafa Geleto, Antonio, Carl Abelardo T, Aremu, Olatunde, Ärnlöv, Johan, Artaman, Al, Aryal, Krishna K, Assadi, Reza, Ausloos, Marcel, Avila-Burgos, Leticia, Avokpaho, Euripide F, Awasthi, Ashish, Ayele, Henok Tadesse, Ayer, Rakesh, Ayuk, Tambe B, Azzopardi, Peter S, Badali, Hamid, Badawi, Alaa, Banach, Maciej, Barker-Collo, Suzanne Lyn, Barrero, Lope H, Basaleem, Huda, Baye, Estifanos, Bazargan-Hejazi, Shahrzad, Bedi, Neeraj, Béjot, Yannick, Belachew, Abate Bekele, Belay, Saba Abraham, Bennett, Derrick A, Bensenor, Isabela M, Bernabe, Eduardo, Bernstein, Robert S, Beyene, Addisu Shunu, Beyranvand, Tina, Bhaumik, Soumyadeeep, Bhutta, Zulfiqar A, Biadgo, Belete, Bijani, Ali, Bililign, Nigus, Birlik, Sait Mentes, Birungi, Charles, Bizuneh, Hailemichael, Bjerregaard, Peter, Bjørge, Tone, Borges, Guilherme, Bosetti, Cristina, Boufous, Soufiane, Bragazzi, Nicola Luigi, Brenner, Hermann, Butt, Zahid A, Cahuana-Hurtado, Lucero, Calabria, Bianca, Campos-Nonato, Ismael R, Campuzano, Julio Cesar, Carreras, Giulia, Carrero, Juan J, Carvalho, Félix, Castañeda-Orjuela, Carlos A, Castillo Rivas, Jacqueline, Catalá-López, Ferrán, Chang, Jung-Chen, Charlson, Fiona J, Chattopadhyay, Aparajita, Chaturvedi, Pankaj, Chowdhury, Rajiv, Christopher, Devasahayam J, Chung, Sheng-Chia, Ciobanu, Liliana G, Claro, Rafael M, Conti, Sara, Cousin, Ewerton, Criqui, Michael H, Dachew, Berihun Assefa, Dargan, Paul I, Daryani, Ahmad, Das Neves, José, Davletov, Kairat, De Castro, Filipa, De Courten, Barbora, De Neve, Jan-Walter, Degenhardt, Louisa, Demoz, Gebre Teklemariam, Des Jarlais, Don C, Dey, Subhojit, Dhaliwal, Rupinder Singh, Dharmaratne, Samath Dhamminda, Dhimal, Meghnath, Doku, David Teye, Doyle, Kerrie E, Dubey, Manisha, Dubljanin, Eleonora, Duncan, Bruce B, Ebrahimi, Hedyeh, Edessa, Dumessa, El Sayed Zaki, Maysaa, Ermakov, Sergei Petrovich, Erskine, Holly E, Esteghamati, Alireza, Faramarzi, Mahbobeh, Farioli, Andrea, Faro, Andre, Farvid, Maryam S, Farzadfar, Farshad, Feigin, Valery L, Felisbino-Mendes, Mariana Santos, Fernandes, Eduarda, Ferrari, Alize J, Ferri, Cleusa P, Fijabi, Daniel Obadare, Filip, Irina, Finger, Jonas David, Fischer, Florian, Flaxman, Abraham D, Franklin, Richard Charles, Futran, Neal D, Gallus, Silvano, Ganji, Morsaleh, Gankpe, Fortune Gbetoho, Gebregergs, Gebremedhin Berhe, Gebrehiwot, Tsegaye Tewelde, Geleijnse, Johanna M, Ghadimi, Reza, Ghandour, Lilian A, Ghimire, Mamata, Gill, Paramjit Singh, Ginawi, Ibrahim Abdelmageed, Giref, Ababi Zergaw Z, Gona, Philimon N, Gopalani, Sameer Vali, Gotay, Carolyn C, Goulart, Alessandra C, Greaves, Felix, Grosso, Giuseppe, Guo, Yuming, Gupta, Rahul, Gupta, Rajeev, Gupta, Vipin, Gutiérrez, Reyna Alma, GVS, Murthy, Hafezi-Nejad, Nima, Hagos, Tekleberhan Beyene, Hailu, Gessessew Bugssa, Hamadeh, Randah R, Hamidi, Samer, Hankey, Graeme J, Harb, Hilda L, Harikrishnan, Sivadasanpillai, Haro, Josep Maria, Hassen, Hamid Yimam, Havmoeller, Rasmus, Hay, Simon I, Heibati, Behzad, Henok, Andualem, Heredia-Pi, Ileana, Hernández-Llanes, Norberto Francisco, Herteliu, Claudiu, Hibstu, Desalegn Ts Tsegaw, Hoogar, Praveen, Horita, Nobuyuki, Hosgood, H Dean, Hosseini, Mostafa, Hostiuc, Mihaela, Hu, Guoqing, Huang, Hsiang, Husseini, Abdullatif, Idrisov, Bulat, Ileanu, Bogdan Vasile, Ilesanmi, Olayinka Stephen, Irvani, Seyed Sina Naghibi, Islam, Sheikh Mohammed Shariful, Jackson, Maria D, Jakovljevic, Mihajlo, Jalu, Moti Tolera, Jayatilleke, Achala Upendra, Jha, Ravi Prakash, Jonas, Jost B, Jozwiak, Jacek Jerzy, Kabir, Zubair, Kadel, Rajendra, Kahsay, Amaha, Kapil, Umesh, Kasaeian, Amir, Kassa, Tesfaye D Dessale, Katikireddi, Srinivasa Vittal, Kawakami, Norito, Kebede, Seifu, Kefale, Adane Teshome, Keiyoro, Peter Njenga, Kengne, Andre Pascal, Khader, Yousef, Khafaie, Morteza Abdullatif, Khalil, Ibrahim A, Khan, Md Nuruzzaman, Khang, Young-Ho, Khater, Mona M, Khubchandani, Jagdish, Kim, Cho-Il, Kim, Daniel, Kim, Yun Jin, Kimokoti, Ruth W, Kisa, Adnan, Kivimäki, Mika, Kochhar, Sonali, Kosen, Soewarta, Koul, Parvaiz A, Koyanagi, Ai, Krishan, Kewal, Kuate Defo, Barthelemy, Kucuk Bicer, Burcu, Kulkarni, Veena S, Kumar, Pushpendra, Lafranconi, Alessandra, Lakshmana Balaji, Arjun, Lalloo, Ratilal, Lallukka, Tea, Lam, Hilton, Lami, Faris Hasan, Lan, Qing, Lang, Justin J, Lansky, Sonia, Larsson, Anders O, Latifi, Arman, Leasher, Janet L, Lee, Paul H, Leigh, James, Leinsalu, Mall, Leung, Janni, Levi, Miriam, Li, Yichong, Lim, Lee-Ling, Linn, Shai, Liu, Shiwei, Lobato-Cordero, Andrea, Lopez, Alan D, Lorkowski, Stefan, Lotufo, Paulo A, Macarayan, Erlyn Rachelle King, Machado, Isis Eloah, Madotto, Fabiana, Magdy Abd El Razek, Hassan, Magdy Abd El Razek, Muhammed, Majdan, Marek, Majdzadeh, Reza, Majeed, Azeem, Malekzadeh, Reza, Malta, Deborah Carvalho, Mapoma, Chabila Christopher, Martinez-Raga, Jose, Maulik, Pallab K, Mazidi, Mohsen, Mckee, Martin, Mehta, Varshil, Meier, Toni, Mekonen, Tesfa, Meles, Kidanu Gebremariam, Melese, Addisu, Memiah, Peter T N, Mendoza, Walter, Mengistu, Desalegn Tadese, Mensah, George A, Meretoja, Tuomo J, Mezgebe, Haftay Berhane, Miazgowski, Tomasz, Miller, Ted R, Mini, Gk, Mirica, Andreea, Mirrakhimov, Erkin M, Moazen, Babak, Mohammad, Karzan Abdulmuhsin, Mohammadifard, Noushin, Mohammed, Shafiu, Monasta, Lorenzo, Moraga, Paula, Morawska, Lidia, Mousavi, Seyyed Meysam, Mukhopadhyay, Satinath, Musa, Kamarul Imran, Naheed, Aliya, Naik, Gurudatta, Najafi, Farid, Nangia, Vinay, Nansseu, Jobert Richie, Nayak, Mudavath Siva Durga Prasad, Nejjari, Chakib, Neupane, Subas, Neupane, Sudan Prasad, Ngunjiri, Josephine W, Nguyen, Cuong Tat, Nguyen, Long Hoang, Nguyen, Trang Huyen, Ningrum, Dina Nur Anggraini, Nirayo, Yirga Legesse, Noubiap, Jean Jacques, Ofori-Asenso, Richard, Ogbo, Felix Akpojene, Oh, In-Hwan, Oladimeji, Olanrewaju, Olagunju, Andrew T, Olivares, Pedro R, Olusanya, Bolajoko Olubukunola, Olusanya, Jacob Olusegun, Oommen, Anu Mary, Oren, Eyal, Orpana, Heather M, Ortega-Altamirano, Doris D V, Ortiz, Justin R, Ota, Erika, Owolabi, Mayowa Ojo, Oyekale, Abayomi Samuel, P A, Mahesh, Pana, Adrian, Park, Eun-Kee, Parry, Charles D H, Parsian, Hadi, Patle, Ajay, Patton, George C, Paudel, Deepak, Petzold, Max, Phillips, Michael R, Pillay, Julian David, Postma, Maarten J, Pourmalek, Farshad, Prabhakaran, Dorairaj, Qorbani, Mostafa, Radfar, Amir, Rafay, Anwar, Rafiei, Alireza, Rahim, Fakher, Rahimi-Movaghar, Afarin, Rahman, Mahfuzar, Rahman, Muhammad Aziz, Rai, Rajesh Kumar, Rajsic, Sasa, Raju, Sree Bhushan, Ram, Usha, Rana, Saleem M, Ranabhat, Chhabi Lal, Rawaf, David Laith, Rawaf, Salman, Reiner, Robert C, Reis, Cesar, Renzaho, Andre M N, Rezai, Mohammad Sadegh, Roever, Leonardo, Ronfani, Luca, Room, Robin, Roshandel, Gholamreza, Rostami, Ali, Roth, Gregory A, Roy, Ambuj, Sabde, Yogesh Damodar, Saddik, Basema, Safiri, Saeid, Sahebkar, Amirhossein, Salama, Joseph S, Saleem, Zikria, Salomon, Joshua A, Salvi, Sundeep Santosh, Sanabria, Juan, Sanchez-Niño, Maria Dolores, Santomauro, Damian Francesco, Santos, Itamar S, Santric Milicevic, Milena M M, Sarker, Abdur Razzaque, Sarmiento-Suárez, Rodrigo, Sarrafzadegan, Nizal, Sartorius, Benn, Satpathy, Maheswar, Sawhney, Monika, Saxena, Sonia, Saylan, Mete, Schaub, Michael P, Schmidt, Maria Inês, Schneider, Ione J C, Schöttker, Ben, Schutte, Aletta Elisabeth, Schwendicke, Falk, Sepanlou, Sadaf G, Shaikh, Masood Ali, Sharif, Mehdi, She, Jun, Sheikh, Aziz, Shen, Jiabin, Shiferaw, Mekonnen Sisay, Shigematsu, Mika, Shiri, Rahman, Shishani, Kawkab, Shiue, Ivy, Shukla, Sharvari Rahul, Sigfusdottir, Inga Dora, Silva, Diego Augusto Santos, Silva, Natacha Torres Da, Silveira, Dayane Gabriele Alves, Sinha, Dhirendra Narain, Sitas, Freddy, Soares Filho, Adauto Martins, Soofi, Moslem, Sorensen, Reed J D, Soriano, Joan B, Sreeramareddy, Chandrashekhar T, Steckling, Nadine, Stein, Dan J, Sufiyan, Mu'awiyyah Babale, Sur, Patrick J, Sykes, Bryan L, Tabarés-Seisdedos, Rafael, Tabuchi, Takahiro, Tavakkoli, Mohammad, Tehrani-Banihashemi, Arash, Tekle, Merhawi Gebremedhin, Thapa, Subash, Thomas, Nihal, Topor-Madry, Roman, Topouzis, Fotis, Tran, Bach Xuan, Troeger, Christopher E, Truelsen, Thomas Clement, Tsilimparis, Nikolaos, Tyrovolas, Stefanos, Ukwaja, Kingsley Nnanna, Ullah, Irfan, Uthman, Olalekan A, Valdez, Pascual R, Van Boven, Job F M, Vasankari, Tommi Juhani, Venketasubramanian, Narayanaswamy, Violante, Francesco S, Vladimirov, Sergey Konstantinovitch, Vlassov, Vasily, Vollset, Stein Emil, Vos, Theo, Wagnew, Fasil Wagnew Shiferaw, Waheed, Yasir, Wang, Yuan-Pang, Weiderpass, Elisabete, Weldegebreal, Fitsum, Weldegwergs, Kidu Gidey, Werdecker, Andrea, Westerman, Ronny, Whiteford, Harvey A, Widecka, Justyna, Wijeratne, Tissa, Wyper, Grant M A, Xu, Gelin, Yamada, Tomohide, Yano, Yuichiro, Ye, Pengpeng, Yimer, Ebrahim M, Yip, Paul, Yirsaw, Biruck Desalegn, Yisma, Engida, Yonemoto, Naohiro, Yoon, Seok-Jun, Yotebieng, Marcel, Younis, Mustafa Z, Zachariah, Geevar, Zaidi, Zoubida, Zamani, Mohammad, Zhang, Xueying, Zodpey, Sanjay, Mokdad, Ali H, Naghavi, Mohsen, Murray, Christopher J L, and Gakidou, Emmanuela
  • The Lancet; September 2018, Vol. 392 Issue: 10152 p1015-1035, 21p
Abstract
Alcohol use is a leading risk factor for death and disability, but its overall association with health remains complex given the possible protective effects of moderate alcohol consumption on some conditions. With our comprehensive approach to health accounting within the Global Burden of Diseases, Injuries, and Risk Factors Study 2016, we generated improved estimates of alcohol use and alcohol-attributable deaths and disability-adjusted life-years (DALYs) for 195 locations from 1990 to 2016, for both sexes and for 5-year age groups between the ages of 15 years and 95 years and older.

91. A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily [2018]

  • Korkut, Anil, Zaidi, Sobia, Kanchi, Rupa S., Rao, Shuyun, Gough, Nancy R., Schultz, Andre, Li, Xubin, Lorenzi, Philip L., Berger, Ashton C., Robertson, Gordon, Kwong, Lawrence N., Datto, Mike, Roszik, Jason, Ling, Shiyun, Ravikumar, Visweswaran, Manyam, Ganiraju, Rao, Arvind, Shelley, Simon, Liu, Yuexin, Ju, Zhenlin, Hansel, Donna, de Velasco, Guillermo, Pennathur, Arjun, Andersen, Jesper B., O'Rourke, Colm J., Ohshiro, Kazufumi, Jogunoori, Wilma, Nguyen, Bao-Ngoc, Li, Shulin, Osmanbeyoglu, Hatice U., Ajani, Jaffer A., Mani, Sendurai A., Houseman, Andres, Wiznerowicz, Maciej, Chen, Jian, Gu, Shoujun, Ma, Wencai, Zhang, Jiexin, Tong, Pan, Cherniack, Andrew D., Deng, Chuxia, Resar, Linda, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. 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Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Angulo Gonzalez, Ana Maria, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, Jonathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Mora Pinero, Edna M., Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Weinstein, John N., Mishra, Lopa, and Akbani, Rehan
  • Cell Systems; October 2018, Vol. 7 Issue: 4 p422-437.e7
Abstract
We present an integromic analysis of gene alterations that modulate transforming growth factor β (TGF-β)-Smad-mediated signaling in 9,125 tumor samples across 33 cancer types in The Cancer Genome Atlas (TCGA). Focusing on genes that encode mediators and regulators of TGF-β signaling, we found at least one genomic alteration (mutation, homozygous deletion, or amplification) in 39% of samples, with highest frequencies in gastrointestinal cancers. We identified mutation hotspots in genes that encode TGF-β ligands (BMP5), receptors (TGFBR2, AVCR2A, and BMPR2), and Smads (SMAD2 and SMAD4). Alterations in the TGF-β superfamily correlated positively with expression of metastasis-associated genes and with decreased survival. Correlation analyses showed the contributions of mutation, amplification, deletion, DNA methylation, and miRNA expression to transcriptional activity of TGF-β signaling in each cancer type. This study provides a broad molecular perspective relevant for future functional and therapeutic studies of the diverse cancer pathways mediated by the TGF-β superfamily.

92. Effects of Genetic Variants Associated with Familial Hypercholesterolemia on Low-Density Lipoprotein-Cholesterol Levels and Cardiovascular Outcomes in the Million Veteran Program [2018]

  • Sun, Yan V., Damrauer, Scott M., Hui, Qin, Assimes, Themistocles L., Ho, Yuk-Lam, Natarajan, Pradeep, Klarin, Derek, Huang, Jie, Lynch, Julie, DuVall, Scott L., Pyarajan, Saiju, Honerlaw, Jacqueline P., Gaziano, J. Michael, Cho, Kelly, Rader, Daniel J., O’Donnell, Christopher J., Tsao, Philip S., Wilson, Peter W. F., Ramoni, Rachel, Breeling, Jim, Chang, Kyong-Mi, Huang, Grant, Muralidhar, Sumitra, Muralidhar, Sumitra, Moser, Jennifer, Whitbourne, Stacey B., Brewer, Jessica V., Concato, John, Warren, Stuart, Argyres, Dean P., Stephens, Brady, Brophy, Mary T., Humphries, Donald E., Do, Nhan, Shayan, Shahpoor, Nguyen, Xuan-Mai T., Hauser, Elizabeth, Sun, Yan, Zhao, Hongyu, Wilson, Peter, McArdle, Rachel, Dellitalia, Louis, Harley, John, Whittle, Jeffrey, Beckham, Jean, Wells, John, Gutierrez, Salvador, Gibson, Gretchen, Kaminsky, Laurence, Villareal, Gerardo, Kinlay, Scott, Xu, Junzhe, Hamner, Mark, Haddock, Kathlyn Sue, Bhushan, Sujata, Iruvanti, Pran, Godschalk, Michael, Ballas, Zuhair, Buford, Malcolm, Mastorides, Stephen, Klein, Jon, Ratcliffe, Nora, Florez, Hermes, Swann, Alan, Murdoch, Maureen, Sriram, Peruvemba, Yeh, Shing Shing, Washburn, Ronald, Jhala, Darshana, Aguayo, Samuel, Cohen, David, Sharma, Satish, Callaghan, John, Oursler, Kris Ann, Whooley, Mary, Ahuja, Sunil, Gutierrez, Amparo, Schifman, Ronald, Greco, Jennifer, Rauchman, Michael, Servatius, Richard, Oehlert, Mary, Wallbom, Agnes, Fernando, Ronald, Morgan, Timothy, Stapley, Todd, Sherman, Scott, Anderson, Gwenevere, Tsao, Philip, Sonel, Elif, Boyko, Edward, Meyer, Laurence, Gupta, Samir, Fayad, Joseph, Hung, Adriana, Lichy, Jack, Hurley, Robin, Robey, Brooks, and Striker, Robert
  • Circulation: Cardiovascular Genetics; December 2018, Vol. 11 Issue: 12 pe002192-e002192, 1p
Abstract
Supplemental Digital Content is available in the text.

93. A Human Hematopoietic Niche Model Supporting Hematopoietic Stem and Progenitor Cells In Vitro [2019]

  • Braham, Maaike V. J., Li Yim, Amélie S. P., Garcia Mateos, Jara, Minnema, Monique C., Dhert, Wouter J. A., Öner, F. Cumhur, Robin, Catherine, and Alblas, Jacqueline
  • Advanced healthcare materials. 8(10)

94. CORRELATION OF QUANTITATIVE SUSCEPTIBILITY MAPPING AND COGNITIVE DYSFUNCTION IN MIXED ALZHEIMER'S AND VASCULAR DEMENTIA [2019]

  • Lee, Hyunwoo, Wiggermann, Vanessa, Rauscher, Alexander, Kames, Christian, Beg, Mirza Faisal, Jacova, Claudia, Sossi, Vesna, Benavente, Oscar R., Pettersen, Jacqueline A., and Robin Hsiung, Ging-Yuek
  • Alzheimer's & dementia. 15(7):P74-P74

95. Population‐based identity‐by‐descent mapping combined with exome sequencing to detect rare risk variants for schizophrenia [2019]

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A., Band, Gavin, Bellenguez, Céline, Freeman, Colin, Hellenthal, Garrett, Giannoulatou, Eleni, Hopkins, Lucinda, Pirinen, Matti, Pearson, Richard, Strange, Amy, Su, Zhan, Vukcevic, Damjan, Langford, Cordelia, Hunt, Sarah E., Edkins, Sarah, Gwilliam, Rhian, Blackburn, Hannah, Bumpstead, Suzannah J., Dronov, Serge, Gillman, Matthew, Gray, Emma, Hammond, Naomi, Jayakumar, Alagurevathi, McCann, Owen T., Liddle, Jennifer, Potter, Simon C., Ravindrarajah, Radhi, Ricketts, Michelle, Waller, Matthew, Weston, Paul, Widaa, Sara, Whittaker, Pamela, Ripke, Stephan, Neale, Benjamin M., Walters, James T. R., Farh, Kai‐How, Holmans, Peter A., Lee, Phil, Bulik‐Sullivan, Brendan, Collier, David A., Huang, Hailiang, Pers, Tune H., Agartz, Ingrid, Agerbo, Esben, Albus, Margot, Alexander, Madeline, Amin, Farooq, Bacanu, Silviu A., Begemann, Martin, Belliveau, Richard A., Bene, Judit, Bergen, Sarah E., Bevilacqua, Elizabeth, Bigdeli, Tim B., Black, Donald W., Bruggeman, Richard, Buccola, Nancy G., Buckner, Randy L., Byerley, William, Cahn, Wiepke, Cai, Guiqing, Campion, Dominique, Cantor, Rita M., Carr, Vaughan J., Carrera, Noa, Catts, Stanley V., Chambert, Kimberley D., Chan, Raymond C. K., Chan, Ronald Y. L., Chen, Eric Y. H., Cheng, Wei, Cheung, Eric F. C., Chong, Siow Ann, Cloninger, C. Robert, Cohen, David, Cohen, Nadine, Cormican, Paul, Craddock, Nick, Crowley, James J., Curtis, David, Davidson, Michael, Davis, Kenneth L., Degenhardt, Franziska, Del Favero, Jurgen, Demontis, Ditte, Dikeos, Dimitris, Dinan, Timothy, Djurovic, Srdjan, Donohoe, Gary, Drapeau, Elodie, Duan, Jubao, Dudbridge, Frank, Durmishi, Naser, Eichhammer, Peter, Eriksson, Johan, Escott‐Price, Valentina, Essioux, Laurent, Fanous, Ayman H., Farrell, Martilias S., Frank, Josef, Franke, Lude, Freedman, Robert, Freimer, Nelson B., Friedl, Marion, Friedman, Joseph I., Fromer, Menachem, Genovese, Giulio, Georgieva, Lyudmila, Giegling, Ina, Giusti‐Rodríguez, Paola, Godard, Stephanie, Goldstein, Jacqueline I., Golimbet, Vera, Gopal, Srihari, Gratten, Jacob, Haan, Lieuwe, Hammer, Christian, Hamshere, Marian L., Hansen, Mark, Hansen, Thomas, Haroutunian, Vahram, Hartmann, Annette M., Henskens, Frans A., Herms, Stefan, Hirschhorn, Joel N., Hoffmann, Per, Hofman, Andrea, Hollegaard, Mads V., Hougaard, David M., Ikeda, Masashi, Joa, Inge, Julià, Antonio, Kalaydjieva, Luba, Karachanak‐Yankova, Sena, Karjalainen, Juha, Kavanagh, David, Keller, Matthew C., Kennedy, James L., Khrunin, Andrey, Kim, Yunjung, Klovins, Janis, Knowles, James A., Konte, Bettina, Kucinskas, Vaidutis, Kucinskiene, Zita Ausrele, Kuzelova‐Ptackova, Hana, Kähler, Anna K., Laurent, Claudine, Lee, Jimmy, Lee, S. Hong, Legge, Sophie E., Lerer, Bernard, Li, Miaoxin, Li, Tao, Liang, Kung‐Yee, Lieberman, Jeffrey, Limborska, Svetlana, Loughland, Carmel M., Lubinski, Jan, Lönnqvist, Jouko, Macek, Milan, Magnusson, Patrik K. E., Maher, Brion S., Maier, Wolfgang, Mallet, Jacques, Marsal, Sara, Mattheisen, Manuel, Mattingsdal, Morten, McCarley, Robert W., McDonald, Colm, McIntosh, Andrew M., Meier, Sandra, Meijer, Carin J., Melegh, Bela, Melle, Ingrid, Mesholam‐Gately, Raquelle I., Metspalu, Andres, Michie, Patricia T., Milani, Lili, Milanova, Vihra, Mokrab, Younes, Morris, Derek W., Mors, Ole, Murphy, Kieran C., Murray, Robin M., Myin‐Germeys, Inez, Müller‐Myhsok, Bertram, Nelis, Mari, Nenadic, Igor, Nertney, Deborah A., Nestadt, Gerald, Nicodemus, Kristin K., Nikitina‐Zake, Liene, Nisenbaum, Laura, Nordin, Annelie, O'Callaghan, Eadbhard, O'Dushlaine, Colm, O'Neill, F. Anthony, Oh, Sang‐Yun, Olincy, Ann, Olsen, Line, Van Os, Jim, Pantelis, Christos, Papadimitriou, George N., Papiol, Sergi, Parkhomenko, Elena, Pato, Michele T., Paunio, Tiina, Pejovic‐Milovancevic, Milica, Perkins, Diana O., Pietiläinen, Olli, Pimm, Jonathan, Pocklington, Andrew J., Price, Alkes, Pulver, Ann E., Purcell, Shaun M., Quested, Digby, Rasmussen, Henrik B., Reichenberg, Abraham, Reimers, Mark A., Richards, Alexander L., Roffman, Joshua L., Roussos, Panos, Ruderfer, Douglas M., Salomaa, Veikko, Sanders, Alan R., Schall, Ulrich, Schubert, Christian R., Schulze, Thomas G., Schwab, Sibylle G., Scolnick, Edward M., Scott, Rodney J., Seidman, Larry J., Shi, Jianxin, Sigurdsson, Engilbert, Silagadze, Teimuraz, Silverman, Jeremy M., Sim, Kang, Slominsky, Petr, Smoller, Jordan W., So, Hon‐Cheong, Stahl, Eli A., Stefansson, Hreinn, Steinberg, Stacy, Stogmann, Elisabeth, Straub, Richard E., Strengman, Eric, Strohmaier, Jana, Stroup, T. Scott, Subramaniam, Mythily, Suvisaari, Jaana, Svrakic, Dragan M., Szatkiewicz, Jin P., Söderman, Erik, Thirumalai, Srinivas, Toncheva, Draga, Tosato, Sarah, Veijola, Juha, Waddington, John, Walsh, Dermot, Wang, Dai, Wang, Qiang, Webb, Bradley T., Weiser, Mark, Wildenauer, Dieter B., Williams, Nigel M., Williams, Stephanie, Witt, Stephanie H., Wolen, Aaron R., Wong, Emily H. M., Wormley, Brandon K., Xi, Hualin Simon, Zai, Clement C., Zheng, Xuebin, Zimprich, Fritz, Wray, Naomi R., Stefansson, Kari, Visscher, Peter M., Adolfsson, Rolf, Andreassen, Ole A., Blackwood, Douglas H. R., Buxbaum, Joseph D., Børglum, Anders D., Darvasi, Ariel, Domenici, Enrico, Ehrenreich, Hannelore, Esko, Tõnu, Gejman, Pablo V., Gill, Michael, Gurling, Hugh, Hultman, Christina M., Iwata, Nakao, Jablensky, Assen V., Jönsson, Erik G., Kirov, George, Knight, Jo, Lencz, Todd, Levinson, Douglas F., Li, Qingqin S., Liu, Jianjun, Malhotra, Anil K., McCarroll, Steven A., McQuillin, Andrew, Moran, Jennifer L., Mortensen, Preben B., Mowry, Bryan J., Palotie, Aarno, Pato, Carlos N., Petryshen, Tracey L., Posthuma, Danielle, Rujescu, Dan, Sham, Pak C., Sklar, Pamela, Clair, David St, Weinberger, Daniel R., Wendland, Jens R., Werge, Thomas, Daly, Mark J., and Sullivan, Patrick F.
  • American journal of medical genetics.Part B.Neuropsychiatric genetics. 180(3):223-231

96. Intersectionality and sex and gender-based analyses as promising approaches in addressing intimate partner violence treatment programs among LGBT couples: A scoping review [2019]

  • Subirana-Malaret, Montse, Gahagan, Jacqueline, and Parker, Robin
  • Cogent social sciences. 5(1)

97. Aligning evidence generation and use across health, development, and environment [2019]

  • Tallis, Heather, Kreis, Katharine, Olander, Lydia, Ringler, Claudia, Ameyaw, David, Borsuk, Mark E, Fletschner, Diana, Game, Edward, Gilligan, Daniel O, Jeuland, Marc, Kennedy, Gina, Masuda, Yuta J, Mehta, Sumi, Miller, Nicholas, Parker, Megan, Pollino, Carmel, Rajaratnam, Julie, Wilkie, David, Zhang, Wei, Ahmed, Selena, Ajayi, Oluyede C, Alderman, Harold, Arhonditsis, George, Azevedo, Ines, Badola, Ruchi, Bailis, Rob, Balvanera, Patricia, Barbour, Emily, Bardini, Mark, Barton, David N, Baumgartner, Jill, Benton, Tim G, Bobrow, Emily, Bossio, Deborah, Bostrom, Ann, Braimoh, Ademola, Brondizio, Eduardo, Brown, Joe, Bryant, Benjamin P, Calder, Ryan SD, Chaplin-Kramer, Becky, Cullen, Alison, DeMello, Nicole, Dickinson, Katherine L, Ebi, Kristie L, Eves, Heather E, Fanzo, Jessica, Ferraro, Paul J, Fisher, Brendan, Frongillo, Edward A, Galford, Gillian, Garrity, Dennis, Gatere, Lydiah, Grieshop, Andrew P, Grigg, Nicola J, Groves, Craig, Gugerty, Mary Kay, Hamm, Michael, Hou, Xiaoyue, Huang, Cindy, Imhoff, Marc, Jack, Darby, Jones, Andrew D, Kelsey, Rodd, Kothari, Monica, Kumar, Ritesh, Lachat, Carl, Larsen, Ashley, Lawrence, Mark, DeClerck, Fabrice, Levin, Phillip S, Mabaya, Edward, Gibson, Jacqueline MacDonald, McDonald, Robert I, Mace, Georgina, Maertens, Ricardo, Mangale, Dorothy I, Martino, Robin, Mason, Sara, Mehta, Lyla, Meinzen-Dick, Ruth, Merz, Barbara, Msangi, Siwa, Murray, Grant, Murray, Kris A, Naude, Celeste E, Newlands, Nathaniel K, Nkonya, Ephraim, Peterman, Amber, Petruney, Tricia, Possingham, Hugh, Puri, Jyotsna, Remans, Roseline, Remlinger, Lisa, Ricketts, Taylor H, Reta, Bedilu, Robinson, Brian E, Roe, Dilys, Rosenthal, Joshua, Shen, Guofeng, Shindell, Drew, Stewart-Koster, Ben, Sunderland, Terry, Sutherland, William J, Tewksbury, Josh, Wasser, Heather, Wear, Stephanie, Webb, Chris, Whittington, Dale, Wilkerson, Marit, Wittmer, Heidi, Wood, Benjamin DK, Wood, Stephen, Wu, Joyce, Yadama, Gautam, and Zobrist, Stephanie
  • Current opinion in environmental sustainability. 39:81-93

98. Parental drinking in Australia: Does the age of children in the home matter? [2019]

  • Bowden, Jacqueline A., Delfabbro, Paul, Room, Robin, Miller, Caroline, and Wilson, Carlene
  • Drug and alcohol review. 38(3):306-315

99. Proficiency Testing to Evaluate Remote Telecytology Competency [2019]

  • Han, Min, Dietz, Robin, Monaco, Sara, Xing, Juan, Cuda, Jacqueline, and Pantanowitz, Liron
  • Journal. 8(5):S54-S54

100. Comparison Between the Performance of Panoptiq and RMT Dynamic Telecytology Platforms for Rapid On-site Evaluation [2019]

  • Dietz, Robin, Xing, Juan, Monaco, Sara, Cuda, Jacqueline, and Pantanowitz, Liron
  • Journal. 8(5):S63-S63

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