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51	Flower A, Lewith G, Liu J, Gibbs R, Hicks J. Applying the principles of the Five Phase (Wu Xing) model to inform good practice for studies of Chinese herbal medicine. Eur J Integr Med 2016. [DOI: 10.1016/j.eujim.2015.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Abstract Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
52	Srivastava AK, Wang Y, Huang R, Skinner C, Thompson T, Pollard L, Wood T, Luo F, Stevenson R, Polimanti R, Gelernter J, Lin X, Lim IY, Wu Y, Teh AL, Chen L, Aris IM, Soh SE, Tint MT, MacIsaac JL, Yap F, Kwek K, Saw SM, Kobor MS, Meaney MJ, Godfrey KM, Chong YS, Holbrook JD, Lee YS, Gluckman PD, Karnani N, Kapoor A, Lee D, Chakravarti A, Maercker C, Graf F, Boutros M, Stamoulis G, Santoni F, Makrythanasis P, Letourneau A, Guipponi M, Panousis N, Garieri M, Ribaux P, Falconnet E, Borel C, Antonarakis SE, Kumar S, Curran J, Blangero J, Chatterjee S, Kapoor A, Akiyama J, Auer D, Berrios C, Pennacchio L, Chakravarti A, Donti TR, Cappuccio G, Miller M, Atwal P, Kennedy A, Cardon A, Bacino C, Emrick L, Hertecant J, Baumer F, Porter B, Bainbridge M, Bonnen P, Graham B, Sutton R, Sun Q, Elsea S, Hu Z, Wang P, Zhu Y, Zhao J, Xiong M, Bennett DA, Hidalgo-Miranda A, Romero-Cordoba S, Rodriguez-Cuevas S, Rebollar-Vega R, Tagliabue E, Iorio M, D’Ippolito E, Baroni S, Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T, Hayashizaki Y, Carninci P, Forrest ARR, Semple CA, Rosenthal EA, Shirts B, Amendola L, Gallego C, Horike-Pyne M, Burt A, Robertson P, Beyers P, Nefcy C, Veenstra D, Hisama F, Bennett R, Dorschner M, Nickerson D, Smith J, Patterson K, Crosslin D, Nassir R, Zubair N, Harrison T, Peters U, Jarvik G, Menghi F, Inaki K, Woo X, Kumar P, Grzeda K, Malhotra A, Kim H, Ucar D, Shreckengast P, Karuturi K, Keck J, Chuang J, Liu ET, Ji B, Tyler A, Ananda G, Carter G, Nikbakht H, Montagne M, Zeinieh M, Harutyunyan A, Mcconechy M, Jabado N, Lavigne P, Majewski J, Goldstein JB, Overman M, Varadhachary G, Shroff R, Wolff R, Javle M, Futreal A, Fogelman D, Bravo L, Fajardo W, Gomez H, Castaneda C, Rolfo C, Pinto JA, Akdemir KC, Chin L, Futreal A, Patterson S, Statz C, Mockus S, Nikolaev SN, Bonilla XI, Parmentier L, King B, Bezrukov F, Kaya G, Zoete V, Seplyarskiy V, Sharpe H, McKee T, Letourneau A, Ribaux P, Popadin K, Basset-Seguin N, Chaabene RB, Santoni F, Andrianova M, Guipponi M, Garieri M, Verdan C, Grosdemange K, Sumara O, Eilers M, Aifantis I, Michielin O, de Sauvage F, Antonarakis S, Likhitrattanapisal S, Lincoln S, Kurian A, Desmond A, Yang S, Kobayashi Y, Ford J, Ellisen L, Peters TL, Alvarez KR, Hollingsworth EF, Lopez-Terrada DH, Hastie A, Dzakula Z, Pang AW, Lam ET, Anantharaman T, Saghbini M, Cao H, Gonzaga-Jauregui C, Ma L, King A, Rosenzweig EB, Krishnan U, Reid JG, Overton JD, Dewey F, Chung WK, Small K, DeLuca A, Cremers F, Lewis RA, Puech V, Bakall B, Silva-Garcia R, Rohrschneider K, Leys M, Shaya FS, Stone E, Sobreira NL, Schiettecatte F, Ling H, Pugh E, Witmer D, Hetrick K, Zhang P, Doheny K, Valle D, Hamosh A, Jhangiani SN, Akdemir ZC, Bainbridge MN, Charng W, Wiszniewski W, Gambin T, Karaca E, Bayram Y, Eldomery MK, Posey J, Doddapaneni H, Hu J, Sutton VR, Muzny DM, Boerwinkle EA, Valle D, Lupski JR, Gibbs RA, Shekar S, Salerno W, English A, Mangubat A, Bruestle J, Thorogood A, Knoppers BM, Takahashi H, Nitta KR, Kozhuharova A, Suzuki AM, Sharma H, Cotella D, Santoro C, Zucchelli S, Gustincich S, Carninci P, Mulvihill JJ, Baynam G, Gahl W, Groft SC, Kosaki K, Lasko P, Melegh B, Taruscio D, Ghosh R, Plon S, Scherer S, Qin X, Sanghvi R, Walker K, Chiang T, Muzny D, Wang L, Black J, Boerwinkle E, Weinshilboum R, Gibbs R, Karpinets T, Calderone T, Wani K, Yu X, Creasy C, Haymaker C, Forget M, Nanda V, Roszik J, Wargo J, Haydu L, Song X, Lazar A, Gershenwald J, Davies M, Bernatchez C, Zhang J, Futreal A, Woodman S, Chesler EJ, Reynolds T, Bubier JA, Phillips C, Langston MA, Baker EJ, Xiong M, Ma L, Lin N, Amos C, Lin N, Wang P, Zhu Y, Zhao J, Calhoun V, Xiong M, Dobretsberger O, Egger M, Leimgruber F, Sadedin S, Oshlack A, Antonio VAA, Ono N, Ahmed Z, Bolisetty M, Zeeshan S, Anguiano E, Ucar D, Sarkar A, Nandineni MR, Zeng C, Shao J, Cao H, Hastie A, Pang AW, Lam ET, Liang T, Pham K, Saghbini M, Dzakula Z, Chee-Wei Y, Dongsheng L, Lai-Ping W, Lian D, Hee ROT, Yunus Y, Aghakhanian F, Mokhtar SS, Lok-Yung CV, Bhak J, Phipps M, Shuhua X, Yik-Ying T, Kumar V, Boon-Peng H, Campbell I, Young MA, James P, Rain M, Mohammad G, Kukreti R, Pasha Q, Akilzhanova AR, Guelly C, Abilova Z, Rakhimova S, Akhmetova A, Kairov U, Trajanoski S, Zhumadilov Z, Bekbossynova M, Schumacher C, Sandhu S, Harkins T, Makarov V, Doddapaneni H, Glenn R, Momin Z, Dilrukshi B, Chao H, Meng Q, Gudenkauf B, Kshitij R, Jayaseelan J, Nessner C, Lee S, Blankenberg K, Lewis L, Hu J, Han Y, Dinh H, Jireh S, Walker K, Boerwinkle E, Muzny D, Gibbs R, Hu J, Walker K, Buhay C, Liu X, Wang Q, Sanghvi R, Doddapaneni H, Ding Y, Veeraraghavan N, Yang Y, Boerwinkle E, Beaudet AL, Eng CM, Muzny DM, Gibbs RA, Worley KCC, Liu Y, Hughes DST, Murali SC, Harris RA, English AC, Qin X, Hampton OA, Larsen P, Beck C, Han Y, Wang M, Doddapaneni H, Kovar CL, Salerno WJ, Yoder A, Richards S, Rogers J, Lupski JR, Muzny DM, Gibbs RA, Meng Q, Bainbridge M, Wang M, Doddapaneni H, Han Y, Muzny D, Gibbs R, Harris RA, Raveenedran M, Xue C, Dahdouli M, Cox L, Fan G, Ferguson B, Hovarth J, Johnson Z, Kanthaswamy S, Kubisch M, Platt M, Smith D, Vallender E, Wiseman R, Liu X, Below J, Muzny D, Gibbs R, Yu F, Rogers J, Lin J, Zhang Y, Ouyang Z, Moore A, Wang Z, Hofmann J, Purdue M, Stolzenberg-Solomon R, Weinstein S, Albanes D, Liu CS, Cheng WL, Lin TT, Lan Q, Rothman N, Berndt S, Chen ES, Bahrami H, Khoshzaban A, Keshal SH, Bahrami H, Khoshzaban A, Keshal SH, Alharbi KKR, Zhalbinova M, Akilzhanova A, Rakhimova S, Bekbosynova M, Myrzakhmetova S, Matar M, Mili N, Molinari R, Ma Y, Guerrier S, Elhawary N, Tayeb M, Bogari N, Qotb N, McClymont SA, Hook PW, Goff LA, McCallion A, Kong Y, Charette JR, Hicks WL, Naggert JK, Zhao L, Nishina PM, Edrees BM, Athar M, Al-Allaf FA, Taher MM, Khan W, Bouazzaoui A, Harbi NA, Safar R, Al-Edressi H, Anazi A, Altayeb N, Ahmed MA, Alansary K, Abduljaleel Z, Kratz A, Beguin P, Poulain S, Kaneko M, Takahiko C, Matsunaga A, Kato S, Suzuki AM, Bertin N, Lassmann T, Vigot R, Carninci P, Plessy C, Launey T, Graur D, Lee D, Kapoor A, Chakravarti A, Friis-Nielsen J, Izarzugaza JM, Brunak S, Chakraborty A, Basak J, Mukhopadhyay A, Soibam BS, Das D, Biswas N, Das S, Sarkar S, Maitra A, Panda C, Majumder P, Morsy H, Gaballah A, Samir M, Shamseya M, Mahrous H, Ghazal A, Arafat W, Hashish M, Gruber JJ, Jaeger N, Snyder M, Patel K, Bowman S, Davis T, Kraushaar D, Emerman A, Russello S, Henig N, Hendrickson C, Zhang K, Rodriguez-Dorantes M, Cruz-Hernandez CD, Garcia-Tobilla CDP, Solorzano-Rosales S, Jäger N, Chen J, Haile R, Hitchins M, Brooks JD, Snyder M, Jiménez-Morales S, Ramírez M, Nuñez J, Bekker V, Leal Y, Jiménez E, Medina A, Hidalgo A, Mejía J, Halytskiy V, Naggert J, Collin GB, DeMauro K, Hanusek R, Nishina PM, Belhassa K, Belhassan K, Bouguenouch L, Samri I, Sayel H, moufid FZ, El Bouchikhi I, Trhanint S, Hamdaoui H, Elotmani I, Khtiri I, Kettani O, Quibibo L, Ahagoud M, Abbassi M, Ouldim K, Marusin AV, Kornetov AN, Swarovskaya M, Vagaiceva K, Stepanov V, De La Paz EMC, Sy R, Nevado J, Reganit P, Santos L, Magno JD, Punzalan FE, Ona D, Llanes E, Santos-Cortes RL, Tiongco R, Aherrera J, Abrahan L, Pagauitan-Alan P, Morelli KH, Domire JS, Pyne N, Harper S, Burgess R, Zhalbinova M, Akilzhanova A, Rakhimova S, Bekbosynova M, Myrzakhmetova S, Gari MA, Dallol A, Alsehli H, Gari A, Gari M, Abuzenadah A, Thomas M, Sukhai M, Garg S, Misyura M, Zhang T, Schuh A, Stockley T, Kamel-Reid S, Sherry S, Xiao C, Slotta D, Rodarmer K, Feolo M, Kimelman M, Godynskiy G, O’Sullivan C, Yaschenko E, Xiao C, Yaschenko E, Sherry S, Rangel-Escareño C, Rueda-Zarate H, Tayubi IA, Mohammed R, Ahmed I, Ahmed T, Seth S, Amin S, Song X, Mao X, Sun H, Verhaak RG, Futreal A, Zhang J, Whiite SJ, Chiang T, English A, Farek J, Kahn Z, Salerno W, Veeraraghavan N, Boerwinkle E, Gibbs R, Kasukawa T, Lizio M, Harshbarger J, Hisashi S, Severin J, Imad A, Sahin S, Freeman TC, Baillie K, Sandelin A, Carninci P, Forrest ARR, Kawaji H, Salerno W, English A, Shekar SN, Mangubat A, Bruestle J, Boerwinkle E, Gibbs RA, Salem AH, Ali M, Ibrahim A, Ibrahim M, Barrera HA, Garza L, Torres JA, Barajas V, Ulloa-Aguirre A, Kershenobich D, Mortaji S, Guizar P, Loera E, Moreno K, De León A, Monsiváis D, Gómez J, Cardiel R, Fernandez-Lopez JC, Bonifaz-Peña V, Rangel-Escareño C, Hidalgo-Miranda A, Contreras AV, Polfus L, Wang X, Philip V, Carter G, Abuzenadah AA, Gari M, Turki R, Dallol A, Uyar A, Kaygun A, Zaman S, Marquez E, George J, Ucar D, Hendrickson CL, Emerman A, Kraushaar D, Bowman S, Henig N, Davis T, Russello S, Patel K, Starr DB, Baird M, Kirkpatrick B, Sheets K, Nitsche R, Prieto-Lafuente L, Landrum M, Lee J, Rubinstein W, Maglott D, Thavanati PKR, de Dios AE, Hernandez REN, Aldrate MEA, Mejia MRR, Kanala KRR, Abduljaleel Z, Khan W, Al-Allaf FA, Athar M, Taher MM, Shahzad N, Bouazzaoui A, Huber E, Dan A, Al-Allaf FA, Herr W, Sprotte G, Köstler J, Hiergeist A, Gessner A, Andreesen R, Holler E, Al-Allaf F, Alashwal A, Abduljaleel Z, Taher M, Bouazzaoui A, Abalkhail H, Al-Allaf A, Bamardadh R, Athar M, Filiptsova O, Kobets M, Kobets Y, Burlaka I, Timoshyna I, Filiptsova O, Kobets MN, Kobets Y, Burlaka I, Timoshyna I, Filiptsova O, Kobets MN, Kobets Y, Burlaka I, Timoshyna I, Al-allaf FA, Mohiuddin MT, Zainularifeen A, Mohammed A, Abalkhail H, Owaidah T, Bouazzaoui A. Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016. Hum Genomics 2016;10 Suppl 1:12. [PMID: 27294413 PMCID: PMC4896275 DOI: 10.1186/s40246-016-0063-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open Abstract O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A53 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR* gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
53	Norman E, Harling M, Skervin AL, Riga C, Khalifa M, Gibbs R, Hamady M. Modified use of thoracic and iliac branch endografts to treat an abdominal aortic aneurysm with an unusually narrow neck. BJR Case Rep 2016;2:20150402. [PMID: 30363651 PMCID: PMC6180878 DOI: 10.1259/bjrcr.20150402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/29/2015] [Accepted: 01/08/2016] [Indexed: 11/16/2022] Open Abstract Abdominal aortic aneurysms with hostile anatomy are a recognized hindrance to the continuing application of endovascular aortic interventions. Narrowed aneurysm necks pose technical difficulties, particularly in the absence of customized endografts. There are multiple suggested approaches to overcome shortened and angulated necks endovascularly; however, none of these address narrowed necks. We present a case where an endograft was used outside of its “instruction for use” by combining the thoracic and iliac branch technologies to overcome this problem. Expanding the use of commercially available endografts for aortic aneurysms with hostile anatomy could have significant practical and financial benefits. Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
54	Collison FT, Xie YA, Gambin T, Jhangiani S, Muzny D, Gibbs R, Lupski JR, Fishman GA, Allikmets R. Whole Exome Sequencing Identifies an Adult-Onset Case of Methylmalonic Aciduria and Homocystinuria Type C (cblC) with Non-Syndromic Bull's Eye Maculopathy. Ophthalmic Genet 2016;36:270-5. [PMID: 25687216 PMCID: PMC4539287 DOI: 10.3109/13816810.2015.1010736] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Abstract Background: Methylmalonic aciduria and homocystinuria type C (cblC), a disorder of vitamin B12 (cobalamin) metabolism caused by mutations in the MMACHC gene, presents with many systemic symptoms, including neurological, cognitive, psychiatric, and thromboembolic events. Retinal phenotypes, including maculopathy, pigmentary retinopathy, and optic atrophy are common in early onset form of the disease but are rare in adult onset forms. Materials and Methods: An adult Hispanic female presented with decreased central vision, bilateral pericentral ring scotomas and bull’s eye-appearing macular lesions at 28 years of age. Her medical history was otherwise unremarkable except for iron deficiency anemia and both urinary tract and kidney infections. Screening of the ABCA4 gene, mutations in which frequently cause bull’s eye maculopathy, was negative. Subsequently, analysis with whole exome sequencing was performed. Results: Whole exome sequencing discovered compound heterozygous mutations in MMACHC, c.G482A:p.Arg161Gln and c.270_271insA:p.Arg91Lysfs14, which segregated with the disease in the family. The genetic diagnosis was confirmed by biochemical laboratory testing, showing highly elevated urine methylmalonic acid/creatinine and homocysteine levels, and suggesting disease management with hydroxycobalamin injections and carnitine supplementation. Conclusions: In summary, a unique case of an adult patient with bull’s eye macular lesions and no clinically relevant systemic symptoms was diagnosed with cblC by genetic screening and follow-up biochemical laboratory tests. Collapse Key Words* Bull’s eye maculopathy methylmalonic aciduria and homocystinuria type C (MMACHC) whole-exome sequencing Collapse MESH Headings Collapse Grants Collapse
55	Herati A, Butler P, Cengiz C, Bainbridge M, Lupski J, Gibbs R, Lipshultz L, Lamb D. MP70-01 IFT140 IS A NOVEL CANDIDATE GENE FOR IMPAIRED SPERMATOGENESIS: IDENTIFICATION BY WHOLE EXOME SEQUENCING AND VALIDATION WITH SANGER SEQUENCING. J Urol 2016. [DOI: 10.1016/j.juro.2016.02.1426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Abstract Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
56	Liu X, White S, Peng B, Johnson AD, Brody JA, Li AH, Huang Z, Carroll A, Wei P, Gibbs R, Klein RJ, Boerwinkle E. WGSA: an annotation pipeline for human genome sequencing studies. J Med Genet 2015;53:111-2. [PMID: 26395054 DOI: 10.1136/jmedgenet-2015-103423] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/02/2015] [Indexed: 11/03/2022] Abstract Collapse Key Words Genetics Genome-wide Collapse MESH Headings Collapse Grants Collapse
57	Gingras MC, Johns A, Gill A, Overman M, Pilarsky C, Grimmond S, Biankin A, Wheeler D, Gibbs R. Abstract PR06: The ampullary adenocarcinoma, its molecular characterization and differentiation from the pancreatic ductal adenocarcinoma, duodenal adenocarcinoma, and cholangiocarcinoma. Cancer Res 2015. [DOI: 10.1158/1538-7445.panca2014-pr06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Abstract Abstract The ampulla of Vater is a region where the pancreatic duct, biliary duct, and intestinal duodenum converge creating a complex epithelial cellular environment from which the ampullary adenocarcinomas (AMPAC) arise to form a group of histopathologically heterogenous tumors. The confluence of three organs at the ampulla of Vater gives rise to complexity in diagnosis, treatment and outcomes. Previous studies have focused mainly on marker identification to differentiate between the AMPAC intestinal and pancreatobiliary subtypes. It is established by immunohistochemistry and expression analysis that the intestinal subtype correlates with better prognosis. However, no large scale genomic profiling has been untaken. To better understand the diverse make-up of the AMPAC subtypes and to potentially help guide treatment, we analyzed 94 AMPAC of intestinal, pancreatobiliary, and mixed subtypes; 33 cholangioadenocarcinomas (CAC); and 11 duodenal adenocarcinomas (DUOAC) and their normal matched samples by whole exome sequencing, SNP array and RNA seq. Whole exome revealed that AMPAC, DUOAC, and CAC shared in common with pancreatic ductal adenocarcinoma (PDAC) high mutation rate in KRAS and TP53, loss and mutation in CDKN2A and SMAD4. ATM, a key component of the DNA damage repair pathway significantly mutated in PDAC, was also mutated in AMPAC, but not in DUOA or CAC. In contrast, loss of function mutation in NF1, an important component of the KRAS pathway, rarely mutated in PDAC, was significantly mutated (12%) and exhibited allelic loss uniquely in AMPAC. Mutations in major gene components of the PIK and wnt signaling, observed in intestinal cancers were detected in DUOAC and AMPAC but not in CAC. The AMPAC, mutations in these genes were found in both intestinal and pancreatobiliary subtypes. We also observed microsatellite instability (MSI), a common feature of gastrointestinal cancers, in 5% AMPAC, 36% of DUOAC , and 3% CAC tumors. The MSI tumors showed mutation frequencies of 17 to 113 mutations per megabase compared to 0.1 to 9.3 mutations per megabase in non-MSI tumors. In our previous study of 94 PDAC, none were MSI. Copy number analysis by SNP array revealed frequent arm-level loss in chromosome 9p, 17p, and 18q in common with all cancers. The patters of copy number change differed most clearly between CAC and DUOAC; AMPAC shared characteristics of both. Gene expression by RNAseq revealed a strong intestinal signature, including high expression of the colon cancer biomarker KRT20, in the intestinal AMPAC but not in pancreatobiliary subtype. The theme that emerges from our study is that the AMPAC shares more similarity in molecular characteristics with gastrointestinal than pancreatic ductal cancers. Interestingly, the histological subtypes of intestinal (30), pancreatobilliary (43) or mixed (10) tumors recognized by pathologists is not strongly reflected in the molecular properties of the AMPAC tumors. Pancreatobiliary subtype shows mutations associated with intestinal tumors but not PDAC, for example 32% of pancreatobilary tumors harbor PIK3CA, PIK3R1, PTEN or wnt pathway members such as CTNNB1, and APC. Patient outcomes for these various mutation profiles are under investigation. From a clinical and therapeutic perspective, targets potentially include ERB-family, ALK and BRCA1/2, mutated tumors, which collectively represent 20% of the patients. An additional 5% of patients are MSI. MSI is a favorable prognostic marker in colorectal and endometrial cancers, and has therapeutic implications. In conclusion, future diagnosis and treatment decision may gain insight by including screening for specific mutations in the characterization of AMPAC. This abstract is also presented as Poster A1. Citation Format: Marie-Claude Gingras, Amber Johns, Anthony Gill, Michael Overman, Christian Pilarsky, Sean Grimmond, Andrew Biankin, David Wheeler, Richard Gibbs. The ampullary adenocarcinoma, its molecular characterization and differentiation from the pancreatic ductal adenocarcinoma, duodenal adenocarcinoma, and cholangiocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr PR06. Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
58	Brat DJ, Verhaak RGW, Aldape KD, Yung WKA, Salama SR, Cooper LAD, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DPC, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med 2015;372:2481-98. [PMID: 26061751 PMCID: PMC4530011 DOI: 10.1056/nejmoa1402121] [Citation(s) in RCA: 2144] [Impact Index Per Article: 238.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Abstract BACKGROUND Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas. METHODS We performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes. RESULTS Unsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma. CONCLUSIONS The integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastoma. (Funded by the National Institutes of Health.). Collapse Key Words Collapse MESH Headings Adolescent Adult Aged Chromosomes, Human, Pair 1 Chromosomes, Human, Pair 19 Cluster Analysis DNA, Neoplasm/analysis Female Genes, p53 Glioblastoma/genetics Glioma/genetics Glioma/metabolism Glioma/mortality Humans Kaplan-Meier Estimate Male Middle Aged Mutation Neoplasm Grading Proportional Hazards Models Sequence Analysis, DNA Signal Transduction Collapse Grants U24CA143840 NCI NIH HHS U24CA126561 NCI NIH HHS P30 CA016672 NCI NIH HHS U24 CA143882 NCI NIH HHS U54 HG003067 NHGRI NIH HHS U54HG003273 NHGRI NIH HHS U24 CA143835 NCI NIH HHS U24CA143731 NCI NIH HHS U24CA126551 NCI NIH HHS U24CA126543 NCI NIH HHS U24CA126554 NCI NIH HHS U24 CA143866 NCI NIH HHS U24CA143858 NCI NIH HHS U24CA126544 NCI NIH HHS P30CA016672 NCI NIH HHS U24CA143882 NCI NIH HHS U24 CA126551 NCI NIH HHS U24CA144025 NCI NIH HHS U54HG003067 NHGRI NIH HHS U24 CA143845 NCI NIH HHS U24 CA143799 NCI NIH HHS U01 CA168394 NCI NIH HHS U54 HG003273 NHGRI NIH HHS P30 CA008748 NCI NIH HHS U24 CA144025 NCI NIH HHS U24 CA194362 NCI NIH HHS U24CA143883 NCI NIH HHS U54HG003079 NHGRI NIH HHS U24 CA126554 NCI NIH HHS U24 CA180951 NCI NIH HHS U24 CA143840 NCI NIH HHS U24 CA143843 NCI NIH HHS U24CA143867 NCI NIH HHS U24CA143835 NCI NIH HHS U24 CA126561 NCI NIH HHS U24 CA143858 NCI NIH HHS U24CA143843 NCI NIH HHS R01 NS081125 NINDS NIH HHS U24 CA143848 NCI NIH HHS U24 CA126543 NCI NIH HHS U24CA143848 NCI NIH HHS U24CA126563 NCI NIH HHS U24CA126546 NCI NIH HHS U54 HG003079 NHGRI NIH HHS U24CA143799 NCI NIH HHS U54 HG007990 NHGRI NIH HHS U24 CA143883 NCI NIH HHS R01 CA163722 NCI NIH HHS U24CA143866 NCI NIH HHS U24CA143845 NCI NIH HHS U24 CA143867 NCI NIH HHS U24 CA126546 NCI NIH HHS U24 CA126563 NCI NIH HHS U24 CA126544 NCI NIH HHS Collapse
59	Lin FY, Bavle A, Wheeler D, Gibbs R, Lam S, Su J, Chintagumpala M, Adesina A, Roy A, Plon SE, Parsons DW. GE-06 * IDENTIFICATION OF TARGETABLE MUTATIONS IN RARE PEDIATRIC BRAIN TUMORS BY CLINICAL WHOLE EXOME SEQUENCING. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov061.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open Abstract Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
60	Westbrook TF, Nair A, Sun T, Karlin KL, Kessler J, Migliaccio I, Nguyen DX, Bernardi RJ, Renwick A, Creighton CJ, Dephoure N, Gygi SP, Shaw CA, Gibbs R, Wheeler D, Schiff R, Christensen JG, Shields DJ, Osborne CK, Elledge SJ, Hilsenbeck SG, Lewis MT. Abstract P6-11-01: A broad spectrum therapeutic strategy for TNBC revealed by a new pathway that coordinates oncogenic RTKs. Cancer Res 2015. [DOI: 10.1158/1538-7445.sabcs14-p6-11-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Abstract Abstract Triple-negative breast cancer (TNBC) is a collection of diseases with distinct clinical behaviors and heterogeneous molecular features. Such clinical and genetic heterogeneity has called into question whether there are common pathogenic mechanisms (and potential therapeutic targets) driving the TNBC subtype of breast cancer. Herein, we present evidence of a novel tumor suppressor network that is frequently compromised in TNBC, and a broadly-effective strategy to target this pathway for TNBC therapeutic intervention. Using an unbiased genetic screen, we identified a tumor suppressor network governing tumor survival of TNBCs in vitro and in vivo. We define the tyrosine phosphatase PTPN12 as a core component in this network. PTPN12 is a potent suppressor of mammary epithelial cell survival and transformation, and PTPN12 function is compromised in more than 70% of human TNBCs. Notably, the tumorigenic and metastatic potential of PTPN12-deficient TNBCs is severely impaired by restoring PTPN12, suggesting that strategies to mimic PTPN12 function have substantive therapeutic potential. Using integrative proteomic, genetic, and pharmacologic approaches, we demonstrate that PTPN12 suppresses TNBC survival by inhibiting multiple oncogenic receptor tyrosine kinases (TKs) including MET, PDGFRβ, and others. Frequent inactivation of PTPN12 in human TNBC unleashes these oncogenic TKs in a concerted manner. Importantly, combination inhibitors targeting these PTPN12-regulated TKs significantly impair TNBC cell survival and confer robust tumor regression across a panel of 18 patient-derived xenograft ("PDX") models of human TNBC. This suggests that TNBCs are broadly dependent on a distinct combination of proto-oncogenic tyrosine kinases constrained by PTPN12. Collectively, these data identify PTPN12 as a commonly inactivated tumor suppressor in TNBC and provide a rationale for combinatorially targeting select receptor tyrosine kinases in TNBC and other cancers based on their defects in tyrosine phosphatase activity. Citation Format: Thomas F Westbrook, Amritha Nair, Tingting Sun, Kristen L Karlin, Jessica Kessler, Ilenia Migliaccio, Don X Nguyen, Ronald J Bernardi, Alex Renwick, Chad J Creighton, Noah Dephoure, Steven P Gygi, Chad A Shaw, Richard Gibbs, David Wheeler, Rachel Schiff, James G Christensen, David J Shields, C Kent Osborne, Stephen J Elledge, Susan G Hilsenbeck, Michael T Lewis. A broad spectrum therapeutic strategy for TNBC revealed by a new pathway that coordinates oncogenic RTKs [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P6-11-01. Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
61	Riveiro-Álvarez R, Xie YA, López-Martínez MÁ, Gambin T, Pérez-Carro R, Ávila-Fernández A, López-Molina MI, Zernant J, Jhangiani S, Muzny D, Yuan B, Boerwinkle E, Gibbs R, Lupski JR, Ayuso C, Allikmets R. New mutations in the RAB28 gene in 2 Spanish families with cone-rod dystrophy. JAMA Ophthalmol 2015;133:133-9. [PMID: 25356532 DOI: 10.1001/jamaophthalmol.2014.4266] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Abstract IMPORTANCE The families evaluated in this study represent the second report of cone-rod dystrophy (CRD) cases caused by mutations in RAB28, a recently discovered gene associated with CRD. OBJECTIVE To determine the disease-causing gene in 2 families of Spanish descent presenting with CRD who do not have ABCA4 mutations. DESIGN, SETTING, AND PARTICIPANTS Molecular genetics and observational case studies of 2 families, each with 1 affected proband with CRD and 3 or 5 unaffected family members. The affected individual from each family received a complete ophthalmic examination including assessment of refractive errors and best-corrected visual acuity, biomicroscopy, color fundus photography, electroretinography analysis, and visual-evoked potential analysis. After complete sequencing of the ABCA4 gene with negative results, the screening for disease-causing mutations was performed by whole-exome sequencing. Possible disease-associated variants were determined by filtering based on minor allele frequency, predicted pathogenicity, and segregation analysis in all family members. MAIN OUTCOMES AND MEASURES The appearance of the macula was evaluated by clinical examination, fundus photography, and fundus autofluorescence imaging, and visual function was assessed by electroretinography. Disease-causing mutations were assessed by sequence analyses. RESULTS Ophthalmologic findings included markedly reduced visual acuity, bull's eye maculopathy, foveal hyperpigmentation, peripapillary atrophy, dyschromatopsia, extinguished photopic responses, and reduced scotopic responses observed on electroretinography consistent with the CRD phenotype often associated with ABCA4 mutations. Although no ABCA4 mutations were detected in either patient, whole-exome sequencing analysis identified 2 new homozygous mutations in the recently described RAB28 gene, the c.172 + 1G>C splice site variant in IVS2 and the missense c.T651G:p.C217W substitution. Both variants were determined as deleterious by predictive programs and were segregated with the disease in both families. Sequencing of 107 additional patients of Spanish descent with CRD did not reveal other cases with RAB28 mutations. CONCLUSIONS AND RELEVANCE Deleterious mutations in RAB28 result in a classic CRD phenotype and are an infrequent cause of CRD in the Spanish population. Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
62	Yu B, Li AH, Muzny D, Veeraraghavan N, de Vries PS, Bis JC, Musani SK, Alexander D, Morrison AC, Franco OH, Uitterlinden A, Hofman A, Dehghan A, Wilson JG, Psaty BM, Gibbs R, Wei P, Boerwinkle E. Association of Rare Loss-Of-Function Alleles in HAL, Serum Histidine: Levels and Incident Coronary Heart Disease. ACTA ACUST UNITED AC 2015;8:351-5. [PMID: 25575548 DOI: 10.1161/circgenetics.114.000697] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 12/02/2014] [Indexed: 12/12/2022] Abstract BACKGROUND Histidine is a semiessential amino acid with antioxidant and anti-inflammatory properties. Few data are available on the associations between genetic variants, histidine levels, and incident coronary heart disease (CHD) in a population-based sample. METHODS AND RESULTS By conducting whole exome sequencing on 1152 African Americans in the Atherosclerosis Risk in Communities (ARIC) study and focusing on loss-of-function (LoF) variants, we identified 3 novel rare LoF variants in HAL, a gene that encodes histidine ammonia-lyase in the first step of histidine catabolism. These LoF variants had large effects on blood histidine levels (β=0.26; P=1.2×10(-13)). The positive association with histidine levels was replicated by genotyping an independent sample of 718 ARIC African Americans (minor allele frequency=1%; P=1.2×10(-4)). In addition, high blood histidine levels were associated with reduced risk of developing incident CHD with an average of 21.5 years of follow-up among African Americans (hazard ratio=0.18; P=1.9×10(-4)). This finding was validated in an independent sample of European Americans from the Framingham Heart Study (FHS) Offspring Cohort. However, LoF variants in HAL were not directly significantly associated with incident CHD after meta-analyzing results from the CHARGE Consortium. CONCLUSIONS Three LoF mutations in HAL were associated with increased histidine levels, which in turn were shown to be inversely related to the risk of CHD among both African Americans and European Americans. Future investigations on the association between HAL gene variation and CHD are warranted. Collapse Key Words coronary disease histidine histidine ammonia-lyase Collapse MESH Headings Adult Black or African American/genetics Alleles Coronary Disease/blood Coronary Disease/genetics Female Histidine/blood Histidine Ammonia-Lyase/genetics Humans Male Mutation White People/genetics Collapse Grants HHSN268201100012C NHLBI NIH HHS N01-HC-25195 NHLBI NIH HHS RC2 HL102419 NHLBI NIH HHS R01 HL103612 NHLBI NIH HHS HHSN268201100009I NHLBI NIH HHS UL1TR000124 NCATS NIH HHS R01DK081572 NIDDK NIH HHS R01 HL120393 NHLBI NIH HHS R01HL59367 NHLBI NIH HHS HHSN268201100010C NHLBI NIH HHS HL102419 NHLBI NIH HHS HHSN268201100008C NHLBI NIH HHS U01 HL080295 NHLBI NIH HHS U54 HG006542 NHGRI NIH HHS HHSN268201100005G NHLBI NIH HHS HHSN268201100008I NHLBI NIH HHS R01 HL068986 NHLBI NIH HHS R01 HL059367 NHLBI NIH HHS HHSN268201100007C NHLBI NIH HHS HL105756 NHLBI NIH HHS HHSN268200800007C NHLBI NIH HHS U01 HL120393 NHLBI NIH HHS R01 DK081572 NIDDK NIH HHS HHSN268201100011I NHLBI NIH HHS HHSN268201100011C NHLBI NIH HHS R01 HL086694 NHLBI NIH HHS HHSN268201300048C NHLBI NIH HHS R01 HL087652 NHLBI NIH HHS U01 HG004402 NHGRI NIH HHS UM1 HG006542 NHGRI NIH HHS HL087652 NHLBI NIH HHS UL1 TR000124 NCATS NIH HHS N01HC55222 NHLBI NIH HHS U54 HG003273 NHGRI NIH HHS HL120393 NHLBI NIH HHS HL068986 NHLBI NIH HHS N01HC85086 NHLBI NIH HHS R01 HL105756 NHLBI NIH HHS U01HG004402 NHGRI NIH HHS R01 HL116720 NHLBI NIH HHS HG006542 NHGRI NIH HHS T32 HL007208 NHLBI NIH HHS P30 DK063491 NIDDK NIH HHS HHSN268201100006C NHLBI NIH HHS HHSN268201300049C NHLBI NIH HHS HHSN268201200036C NHLBI NIH HHS R01HL087641 NHLBI NIH HHS HHSN268201100005I NHLBI NIH HHS HHSN268201300047C NHLBI NIH HHS HHSN268201300050C NHLBI NIH HHS R01 HL080295 NHLBI NIH HHS N01HC85082 NHLBI NIH HHS HHSN268201100009C NHLBI NIH HHS N01HC85083 NHLBI NIH HHS HHSN268201100005C NHLBI NIH HHS N01HC25195 NHLBI NIH HHS DK063491 NIDDK NIH HHS HHSN268201100007I NHLBI NIH HHS HHSN268201300046C NHLBI NIH HHS HG003273 NHGRI NIH HHS HL080295 NHLBI NIH HHS N01HC85079 NHLBI NIH HHS R01 AG023629 NIA NIH HHS R01 HL087641 NHLBI NIH HHS HL103612 NHLBI NIH HHS N01HC85080 NHLBI NIH HHS AG023629 NIA NIH HHS HG004402 NHGRI NIH HHS R56 AG023629 NIA NIH HHS N01HC85081 NHLBI NIH HHS R01HL086694 NHLBI NIH HHS UL1 TR000371 NCATS NIH HHS Collapse
63	Ritter DI, Haines K, Cheung H, Davis CF, Lau CC, Berg JS, Brown CW, Thompson PA, Gibbs R, Wheeler DA, Plon SE. Identifying gene disruptions in novel balanced de novo constitutional translocations in childhood cancer patients by whole-genome sequencing. Genet Med 2015;17:831-5. [PMID: 25569436 PMCID: PMC4496310 DOI: 10.1038/gim.2014.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 11/16/2014] [Indexed: 12/18/2022] Open Abstract Purpose We applied whole genome sequencing to children diagnosed with neoplasms and found to carry apparently balanced constitutional translocations, to discover novel genic disruptions. Methods We applied SV calling programs CREST, Break Dancer, SV-STAT and CGAP-CNV, and developed an annotative filtering strategy to achieve nucleotide resolution at the translocations. Results We identified the breakpoints for t(6;12) (p21.1;q24.31) disrupting HNF1A in a patient diagnosed with hepatic adenomas and Maturity Onset Diabetes of the Young (MODY). Translocation as the disruptive event of HNF1A, a gene known to be involved in MODY3, has not been previously reported. In a subject with Hodgkin’s lymphoma and subsequent low-grade glioma, we identified t(5;18) (q35.1;q21.2), disrupting both SLIT3 and DCC, genes previously implicated in both glioma and lymphoma. Conclusions These examples suggest that implementing clinical whole genome sequencing in the diagnostic work-up of patients with novel but apparently balanced translocations may reveal unanticipated disruption of disease-associated genes and aid in prediction of the clinical phenotype. Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
64	Dong C, Wei P, Jian X, Gibbs R, Boerwinkle E, Wang K, Liu X. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet 2014;24:2125-37. [PMID: 25552646 DOI: 10.1093/hmg/ddu733] [Citation(s) in RCA: 737] [Impact Index Per Article: 73.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open Abstract Accurate deleteriousness prediction for nonsynonymous variants is crucial for distinguishing pathogenic mutations from background polymorphisms in whole exome sequencing (WES) studies. Although many deleteriousness prediction methods have been developed, their prediction results are sometimes inconsistent with each other and their relative merits are still unclear in practical applications. To address these issues, we comprehensively evaluated the predictive performance of 18 current deleteriousness-scoring methods, including 11 function prediction scores (PolyPhen-2, SIFT, MutationTaster, Mutation Assessor, FATHMM, LRT, PANTHER, PhD-SNP, SNAP, SNPs&GO and MutPred), 3 conservation scores (GERP++, SiPhy and PhyloP) and 4 ensemble scores (CADD, PON-P, KGGSeq and CONDEL). We found that FATHMM and KGGSeq had the highest discriminative power among independent scores and ensemble scores, respectively. Moreover, to ensure unbiased performance evaluation of these prediction scores, we manually collected three distinct testing datasets, on which no current prediction scores were tuned. In addition, we developed two new ensemble scores that integrate nine independent scores and allele frequency. Our scores achieved the highest discriminative power compared with all the deleteriousness prediction scores tested and showed low false-positive prediction rate for benign yet rare nonsynonymous variants, which demonstrated the value of combining information from multiple orthologous approaches. Finally, to facilitate variant prioritization in WES studies, we have pre-computed our ensemble scores for 87 347 044 possible variants in the whole-exome and made them publicly available through the ANNOVAR software and the dbNSFP database. Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
65	Ericsen AJ, Starrett GJ, Greene JM, Lauck M, Raveendran M, Deiros DR, Mohns MS, Vince N, Cain BT, Pham NH, Weinfurter JT, Bailey AL, Budde ML, Wiseman RW, Gibbs R, Muzny D, Friedrich TC, Rogers J, O'Connor DH. Whole genome sequencing of SIV-infected macaques identifies candidate loci that may contribute to host control of virus replication. Genome Biol 2014;15:478. [PMID: 25418588 PMCID: PMC4223156 DOI: 10.1186/s13059-014-0478-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 09/17/2014] [Indexed: 12/22/2022] Open Abstract Background A small percentage of human immunodeficiency virus (HIV)-infected people and simian immunodeficiency virus (SIV)-infected macaques control virus replication without antiretroviral treatment. The major determinant of this control is host expression of certain major histocompatibility complex alleles. However, this association is incompletely penetrant, suggesting that additional loci modify the major histocompatibility complex’s protective effect. Here, to identify candidate control-modifying loci, we sequence the genomes of 12 SIV-infected Mauritian cynomolgus macaques that experienced divergent viral load set points despite sharing the protective M1 major histocompatibility complex haplotype. Results Our genome-wide analysis of haplotype-level variation identifies seven candidate control-modifying loci on chromosomes 2, 3, 7, 8, 9, 10, and 14. The highest variant density marks the candidate on chromosome 7, which is the only control-modifying locus to comprise genes with known immunological function. Upon closer inspection, we found an allele for one of these genes, granzyme B, to be enriched in M1(+) controllers. Given its established role as a cytotoxic effector molecule that participates in CD8-mediated killing of virus-infected cells, we test the role of variation within gzmb in modifying SIV control by prospectively challenging M1(+) granzyme B-defined macaques. Conclusions Our study establishes a framework for using whole genome sequencing to identify haplotypes that may contribute to complex clinical phenotypes. Further investigation into the immunogenetics underlying spontaneous HIV control may contribute to the rational design of a vaccine that prevents acquired immune deficiency syndrome. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0478-z) contains supplementary material, which is available to authorized users. Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
66	Jerome E, Gibbs R. Evaluating the management of surgical patients requiring emergency laparotomies at a medium-sized general hospital. Int J Surg 2014. [DOI: 10.1016/j.ijsu.2014.08.209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Abstract Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
67	Wang L, Yamaguchi S, Terashima K, Burstein MD, Nakamura H, Susuki T, Nishikawa R, Natsume A, Terasaka S, Ng HK, Adesina A, Gibbs R, Wheeler D, Lau C. Abstract PR04: Novel somatic and germline mutations in intracranial germ cell tumors. Cancer Res 2014. [DOI: 10.1158/1538-7445.pedcan-pr04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Abstract Abstract Intracranial germ cell tumors (IGCTs) are rare and biologically diversified tumors affecting mainly male adolescents with the highest incidence in Japan and other Asian countries2. They are divided into two main groups, pure germinoma and nongerminomatous GCTs (NGGCTs). About 10% of germinomas and most NGGCTs remain refractory to multimodality therapy. Little is currently known about IGCTs except for KIT mutation/overexpression, which is observed in ∼25% of pure germinomas and is rarely seen in NGGCTs. As yet, there are no clues for the puzzle of onset during puberty, geographic and gender discrepancy in incidence of IGCTs. Here we report the analysis of 62 cases by whole-exome sequencing, deep-targeted sequencing and SNP array. The KIT/RAS pathway was frequently mutated in pure germinomas and mixed GCTs with germinoma components. In contrast, NGGCTs appear to have a paucity of clinically actionable mutations. We identified novel recurrent somatic mutations in KIT and 8 additional genes in KIT/RAS pathway that have not been previously associated with IGCTs: downstream mediators of KIT including KRAS, NRAS, MTOR, AKT1 and its negative regulator CBL (11%). We showed frequent focal amplification at AKT1 locus (19%), leading to AKT1 overexpression. Moreover, we identified loss-of-function mutations in BCORL1 (10%), a transcriptional corepressor and tumor suppressor. Furthermore, we report for the first time, significant enrichment of novel and rare germline variants in JMJD1C, a histone demethylase and coactivator of the androgen receptor, among Japanese IGCT patients. Our data suggested a strong association of JMJD1C variants and the risk of developing of IGCTs (odds ratio=3.57). This study establishes a molecular foundation for understanding the biology of IGCTs and suggests potential promising targets for development of novel therapeutics. This abstract is also presented as Poster A14. Citation Format: Linghua Wang, Shigeru Yamaguchi, Keita Terashima, Mathew D. Burstein, Hideo Nakamura, Tomonari Susuki, Ryo Nishikawa, Atsushi Natsume, Shunsuke Terasaka, Ho Keung Ng, Adekunle Adesina, Richard Gibbs, David Wheeler, Ching Lau. Novel somatic and germline mutations in intracranial germ cell tumors. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr PR04. Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
68	Ericsen A, Starrett G, Greene J, Lauck M, Mohns M, Cain B, Pham N, Raveendran M, Deiros DR, Weinfurter J, Bailey A, Karl J, Wiseman R, Muzny D, Friedrich T, Gibbs R, Rogers J, O'Connor DH. Candidate Loci Associated with AIDS Virus Replication Identified by Whole Genome Sequencing of SIV-Infected Macaques. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5067.abstract] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open Abstract Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
69	Schick UM, Auer PL, Bis JC, Lin H, Wei P, Pankratz N, Lange LA, Brody J, Stitziel NO, Kim DS, Carlson CS, Fornage M, Haessler J, Hsu L, Jackson RD, Kooperberg C, Leal SM, Psaty BM, Boerwinkle E, Tracy R, Ardissino D, Shah S, Willer C, Loos R, Melander O, Mcpherson R, Hovingh K, Reilly M, Watkins H, Girelli D, Fontanillas P, Chasman DI, Gabriel SB, Gibbs R, Nickerson DA, Kathiresan S, Peters U, Dupuis J, Wilson JG, Rich SS, Morrison AC, Benjamin EJ, Gross MD, Reiner AP. Association of exome sequences with plasma C-reactive protein levels in >9000 participants. Hum Mol Genet 2014;24:559-71. [PMID: 25187575 DOI: 10.1093/hmg/ddu450] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open Abstract C-reactive protein (CRP) concentration is a heritable systemic marker of inflammation that is associated with cardiovascular disease risk. Genome-wide association studies have identified CRP-associated common variants associated in ∼25 genes. Our aims were to apply exome sequencing to (1) assess whether the candidate loci contain rare coding variants associated with CRP levels and (2) perform an exome-wide search for rare variants in novel genes associated with CRP levels. We exome-sequenced 6050 European-Americans (EAs) and 3109 African-Americans (AAs) from the NHLBI-ESP and the CHARGE consortia, and performed association tests of sequence data with measured CRP levels. In single-variant tests across candidate loci, a novel rare (minor allele frequency = 0.16%) CRP-coding variant (rs77832441-A; p.Thr59Met) was associated with 53% lower mean CRP levels (P = 2.9 × 10(-6)). We replicated the association of rs77832441 in an exome array analysis of 11 414 EAs (P = 3.0 × 10(-15)). Despite a strong effect on CRP levels, rs77832441 was not associated with inflammation-related phenotypes including coronary heart disease. We also found evidence for an AA-specific association of APOE-ε2 rs7214 with higher CRP levels. At the exome-wide significance level (P < 5.0 × 10(-8)), we confirmed associations for reported common variants of HNF1A, CRP, IL6R and TOMM40-APOE. In gene-based tests, a burden of rare/lower frequency variation in CRP in EAs (P ≤ 6.8 × 10(-4)) and in retinoic acid receptor-related orphan receptor α (RORA) in AAs (P = 1.7 × 10(-3)) were associated with CRP levels at the candidate gene level (P < 2.0 × 10(-3)). This inquiry did not elucidate novel genes, but instead demonstrated that variants distributed across the allele frequency spectrum within candidate genes contribute to CRP levels. Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
70	Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PSG, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, MA J, Markowitz V, Moore ERB, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki KI, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol 2014;12:e1001920. [PMID: 25093819 PMCID: PMC4122341 DOI: 10.1371/journal.pbio.1001920] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open Abstract This manuscript calls for an international effort to generate a comprehensive catalog from genome sequences of all the archaeal and bacterial type strains. Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment. Collapse Key Words Collapse MESH Headings Archaea/classification Archaea/genetics Bacteria/classification Bacteria/genetics Databases, Genetic Genome, Archaeal/genetics Genome, Bacterial/genetics Genomics Phylogeny Sequence Analysis, DNA Collapse Grants Collapse
71	Pickering CR, Zhang J, Neskey DM, Zhao M, Jasser SA, Wang J, Ward A, Tsai CJ, Ortega Alves MV, Zhou JH, Drummond J, El-Naggar AK, Gibbs R, Weinstein JN, Wheeler DA, Wang J, Frederick MJ, Myers JN. Squamous cell carcinoma of the oral tongue in young non-smokers is genomically similar to tumors in older smokers. Clin Cancer Res 2014;20:3842-8. [PMID: 24874835 PMCID: PMC4102633 DOI: 10.1158/1078-0432.ccr-14-0565] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Abstract PURPOSE Epidemiologic studies have identified an increasing incidence of squamous cell carcinoma of the oral tongue (SCCOT) in younger patients. EXPERIMENTAL DESIGN DNA isolated from tongue tumors of young (<45 years, non-smokers) and old (>45 years) patients at was subjected to whole-exome sequencing and copy-number analysis. These data were compared with data from similar patients in the TCGA (The Cancer Genome Atlas) project. RESULTS In this study, we found that gene-specific mutation and copy-number alteration frequencies were similar between young and old patients with SCCOT in two independent cohorts. Likewise, the types of base changes observed in the young cohort were similar to those in the old cohort even though they differed in smoking history. TCGA data also demonstrate that the genomic effects of smoking are tumor site-specific, and we find that smoking has only a minor impact on the types of mutations observed in SCCOT. CONCLUSIONS Overall, tumors from young patients with SCCOT appear genomically similar to those of older patients with SCCOT, and the cause for the increasing incidence of young SCCOT remains unknown. These data indicate that the functional impact of smoking on carcinogenesis in SCCOT is still poorly understood. Collapse Key Words young tongue cancer sccot head and neck/oral cancers tobacco Collapse MESH Headings Adult Age Factors Carcinoma, Squamous Cell/genetics DNA Copy Number Variations DNA Mutational Analysis Female Humans Male Middle Aged Mutation Prognosis Smoking/adverse effects Tongue Neoplasms/genetics Collapse Grants P30 CA016672 NCI NIH HHS P50 CA097007 NCI NIH HHS RC2DE020958 NIDCR NIH HHS RC2 DE020958 NIDCR NIH HHS P50CA097007 NCI NIH HHS P30CA16672 NCI NIH HHS T32 CA163185 NCI NIH HHS Collapse
72	Xie YA, Lee W, Cai C, Gambin T, Nõupuu K, Sujirakul T, Ayuso C, Jhangiani S, Muzny D, Boerwinkle E, Gibbs R, Greenstein VC, Lupski JR, Tsang SH, Allikmets R. New syndrome with retinitis pigmentosa is caused by nonsense mutations in retinol dehydrogenase RDH11. Hum Mol Genet 2014;23:5774-80. [PMID: 24916380 DOI: 10.1093/hmg/ddu291] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open Abstract Retinitis pigmentosa (RP), a genetically heterogeneous group of retinopathies that occur in both non-syndromic and syndromic forms, is caused by mutations in ∼100 genes. Although recent advances in next-generation sequencing have aided in the discovery of novel RP genes, a number of the underlying contributing genes and loci remain to be identified. We investigated three siblings, born to asymptomatic parents of Italian-American descent, who each presented with atypical RP with systemic features, including facial dysmorphologies, psychomotor developmental delays recognized since early childhood, learning disabilities and short stature. RP-associated ophthalmological findings included salt-and-pepper retinopathy, attenuation of the arterioles and generalized rod-cone dysfunction as determined by almost extinguished electroretinogram in 2 of 3 siblings. Atypical for RP features included mottled macula at an early age and peripapillary sparing of the retinal pigment epithelium. Whole-exome sequencing data, queried under a recessive model of inheritance, identified compound heterozygous stop mutations, c.C199T:p.R67* and c.C322T:p.R108, in the retinol dehydrogenase 11 (RDH11) gene, resulting in a non-functional protein, in all affected children. In summary, deleterious mutations in RDH11, an important enzyme for vision-related and systemic retinoic acid metabolism, cause a new syndrome with RP. Collapse Key Words* Collapse MESH Headings Collapse Grants Collapse
73	Kannan V, Misra BK, Kapadia A, Bajpai R, Deshpande S, Almel S, Sankhe M, Desai K, Shaikh M, Anand V, Kannan A, Teo WY, Ross J, Bollo R, Seow WT, Tan AM, Kang SG, Kim DS, Li XN, Lau CC, Mohila CA, Adesina A, Su J, Ichimura K, Fukushima S, Matsushita Y, Tomiyama A, Niwa T, Suzuki T, Nakazato Y, Mukasa A, Kumabe T, Nagane M, Iuchi T, Mizoguchi M, Tamura K, Sugiyama K, Nakada M, Kanemura Y, Yokogami K, Matsutani M, Shibata T, Nishikawa R, Takami H, Fukushima S, Fukuoka K, Yanagisawa T, Nakamura T, Arita H, Narita Y, Shibui S, Nishikawa R, Ichimura K, Matsutani M, Sands S, Guerry W, Kretschmar C, Donahue B, Allen J, Matsutani M, Nishikawa R, Kumabe T, Sugiyama K, Nakamura H, Sawamura Y, Fujimaki T, Hattori E, Arakawa Y, Kawabata Y, Aoki T, Miyamoto S, Kagawa N, Hirayama R, Fujimoto Y, Chiba Y, Kinoshita M, Takano K, Eino D, Fukuya S, Nakanishi K, Yamamoto F, Hashii Y, Hashimoto N, Hara J, Yoshimine T, Murray M, Bartels U, Nishikawa R, Fangusaro J, Matsutani M, Nicholson J, Sumerauer D, Zapotocky M, Churackova M, Cyprova S, Zamecnik J, Malinova B, Kyncl M, Tichy M, Stary J, Lassen-Ramshad Y, von Oettingen G, Agerbaek M, Ohnishi T, Kohno S, Inoue A, Ohue S, Kohno S, Iwata S, Inoue A, Ohue S, Kumon Y, Ohnishi T, Acharya S, DeWees T, Shinohara E, Perkins S, Kato H, Fuji H, Nakasu Y, Ishida Y, Okawada S, Yang Q, Guo C, Chen Z, Alapetite C, Faure-Conter C, Verite C, Pagnier A, Laithier V, Entz-Werle N, Gorde-Grosjean S, Palenzuela G, Lemoine P, Frappaz D, Nguyen HA, Bui L, Ngoc, Cerbone M, Ederies A, Losa L, Moreno C, Sun K, Spoudeas HA, Nakano Y, Okada K, Kosaka Y, Nagashima T, Hashii Y, Kagawa N, Soejima T, Osugi Y, Sakamoto H, Hara J, Nicholson J, Alapetite C, Kortmann RD, Garre ML, Ricardi U, Saran F, Frappaz D, Calaminus G, Muda Z, Menon B, Ibrahim H, Rahman EJA, Muhamad M, Othman IS, Thevarajah A, Cheng S, Kilday JP, Laperriere N, Drake J, Bouffet E, Bartels U, Sakamoto H, Matsusaka Y, Watanabe Y, Umaba R, Hara J, Osugi Y, Alapetite C, Ruffier-Loubiere A, De Marzi L, Bolle S, Claude L, Habrand JL, Brisse H, Frappaz D, Doz F, Bourdeaut F, Dendale R, Mazal A, Fournier-Bidoz N, Fujimaki T, Fukuoka K, Shirahata M, Suzuki T, Adachi JI, Mishima K, Wakiya K, Matsutani M, Nishikawa R, Fukushima S, Yamashita S, Kato M, Nakamura H, Takami H, Suzuki T, Yanagisawa T, Mukasa A, Kumabe T, Nagane M, Sugiyama K, Tamura K, Narita Y, Shibui S, Shibata T, Ushijima T, Matsutani M, Nishikawa R, Ichimura K, Consortium IGA, Calaminus G, Kortmann RD, Frappaz D, Alapetite C, Garre ML, Ricardi U, Saran FH, Nicholson J, Calaminus G, Kortmann RD, Frappaz D, Alapetite C, Garre ML, Ricardi U, Saran FH, Nicholson J, Czech T, Nicholson J, Frappaz D, Kortmann RD, Alapetite C, Garre ML, Ricardi U, Saran F, Calaminus G, Hayden J, Bartels U, Calaminus G, Joseph R, Nicholson J, Hale J, Lindsay H, Kogiso M, Qi L, Yee TW, Huang Y, Mao H, Lin F, Baxter P, Su J, Terashima K, Perlaky L, Lau C, Parsons D, Chintagumpala M, Li XAN, Osorio D, Vaughn D, Gardner S, Mrugala M, Ferreira M, Keene C, Gonzalez-Cuyar L, Hebb A, Rockhill J, Wang L, Yamaguchi S, Burstein M, Terashima K, Ng HK, Nakamura H, He Z, Suzuki T, Nishikawa R, Natsume A, Terasaka S, Dauser R, Whitehead W, Adesina A, Sun J, Munzy D, Gibbs R, Leal S, Wheeler D, Lau C, Dhall G, Robison N, Judkins A, Krieger M, Gilles F, Park J, Lee SU, Kim T, Choi Y, Park HJ, Shin SH, Kim JY, Robison N, Dhir N, Khamani J, Margol A, Wong K, Britt B, Evans A, Nelson M, Grimm J, Finlay J, Dhall G. GERM CELL TUMOURS. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open Abstract Collapse Key Words Collapse MESH Headings Collapse Grants Collapse
74	Bis JC, White CC, Franceschini N, Brody J, Zhang X, Muzny D, Santibanez J, Gibbs R, Liu X, Lin H, Boerwinkle E, Psaty BM, North KE, Cupples LA, O’Donnell CJ. Sequencing of 2 subclinical atherosclerosis candidate regions in 3669 individuals: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study. CIRCULATION. CARDIOVASCULAR GENETICS 2014;7:359-64. [PMID: 24951662 PMCID: PMC4112104 DOI: 10.1161/circgenetics.113.000116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Abstract BACKGROUND Atherosclerosis, the precursor to coronary heart disease and stroke, is characterized by an accumulation of fatty cells in the arterial intimal-medial layers. Common carotid intima media thickness (cIMT) and plaque are subclinical atherosclerosis measures that predict cardiovascular disease events. Previously, genome-wide association studies demonstrated evidence for association with cIMT (SLC17A4) and plaque (PIK3CG). METHODS AND RESULTS We sequenced 120 kb around SLC17A4 (6p22.2) and 251 kb around PIK3CG (7q22.3) among 3669 European ancestry participants from the Atherosclerosis Risk in Communities (ARIC) study, Cardiovascular Health Study (CHS), and Framingham Heart Study (FHS) in Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. Primary analyses focused on 438 common variants (minor allele frequency ≥1%), which were independently meta-analyzed. A 3' untranslated region CCDC71L variant (rs2286149), upstream from PIK3CG, was the most significant finding in cIMT (P=0.00033) and plaque (P=0.0004) analyses. A SLC17A4 intronic variant was also associated with cIMT (P=0.008). Both were in low linkage disequilibrium with the genome-wide association study single nucleotide polymorphisms. Gene-based tests including T1 count and sequence kernel association test for rare variants (minor allele frequency <1%) did not yield statistically significant associations. However, we observed nominal associations for rare variants in CCDC71L and SLC17A3 with cIMT and of the entire 7q22 region with plaque (P=0.05). CONCLUSIONS Common and rare variants in PIK3CG and SLC17A4 regions demonstrated modest association with subclinical atherosclerosis traits. Although not conclusive, these findings may help to understand the genetic architecture of regions previously implicated by genome-wide association studies and identify variants within these regions for further investigation in larger samples. Collapse Key Words atherosclerosis carotid artery, common epidemiology genetics plaque, atherosclerotic sequence analysis, DNA Collapse MESH Headings Aged Aged, 80 and over Aging/genetics Atherosclerosis/epidemiology Atherosclerosis/genetics Class Ib Phosphatidylinositol 3-Kinase/genetics Cohort Studies Female Genetic Variation Genome-Wide Association Study Genomics Humans Male Middle Aged Polymorphism, Single Nucleotide Sequence Analysis, DNA Sodium-Phosphate Cotransporter Proteins, Type I/genetics White People/genetics Collapse Grants UL1TR000124 NCATS NIH HHS R01 HL059367 NHLBI NIH HHS R01 HL087652 NHLBI NIH HHS R01 HL105756 NHLBI NIH HHS HHSN268201100006C NHLBI NIH HHS HHSN268201100005I NHLBI NIH HHS HHSN268201100002C WHI NIH HHS HHSN268201100007I NHLBI NIH HHS HHSN268201100012C NHLBI NIH HHS HHSN268201000010C NHLBI NIH HHS N02-HL-6-4278 NHLBI NIH HHS N01-HC-25195 NHLBI NIH HHS RC2 HL102419 NHLBI NIH HHS R01 HL103612 NHLBI NIH HHS HHSN268201100001I NHLBI NIH HHS HHSN268201100009I NHLBI NIH HHS 5RC2HL102419 NHLBI NIH HHS R01 HL120393 NHLBI NIH HHS R01HL59367 NHLBI NIH HHS HHSN268201100010C NHLBI NIH HHS R01 AG015928 NIA NIH HHS HHSN268201100008C NHLBI NIH HHS U01 HL080295 NHLBI NIH HHS HHSN268201100005G NHLBI NIH HHS HHSN268201100008I NHLBI NIH HHS HHSN268201100007C NHLBI NIH HHS HL105756 NHLBI NIH HHS R56 AG020098 NIA NIH HHS N01HC85085 NHLBI NIH HHS HHSN268201100011I NHLBI NIH HHS HHSN268201100011C NHLBI NIH HHS R01 HL086694 NHLBI NIH HHS N01 HC085085 NHLBI NIH HHS HHSN268201000011C NHLBI NIH HHS HL087652 NHLBI NIH HHS UL1 TR000124 NCATS NIH HHS N01HC55222 NHLBI NIH HHS U54 HG003273 NHGRI NIH HHS HL120393 NHLBI NIH HHS N01HC85086 NHLBI NIH HHS N01HC45133 NHLBI NIH HHS HHSN268201200036C NHLBI NIH HHS R01HL087641 NHLBI NIH HHS R01 HL080295 NHLBI NIH HHS ZIA HL006002-06 Intramural NIH HHS N01 HC085084 NHLBI NIH HHS R01 AG020098 NIA NIH HHS N01HC85082 NHLBI NIH HHS N01HC75150 NHLBI NIH HHS HHSN268201100009C NHLBI NIH HHS N01HC85083 NHLBI NIH HHS HHSN268201100005C NHLBI NIH HHS N01HC25195 NHLBI NIH HHS Z99 HL999999 Intramural NIH HHS DK063491 NIDDK NIH HHS HHSN268201100002I NHLBI NIH HHS HL080295 NHLBI NIH HHS HHSN268200800007C NHLBI NIH HHS HHSN268201000012C NHLBI NIH HHS N01HC85079 NHLBI NIH HHS R01 AG023629 NIA NIH HHS R01 HL087641 NHLBI NIH HHS HL103612 NHLBI NIH HHS R01 AG027058 NIA NIH HHS N01HC85080 NHLBI NIH HHS AG023629 NIA NIH HHS R56 AG023629 NIA NIH HHS HHSN268201100001C WHI NIH HHS N01HC85081 NHLBI NIH HHS R01HL086694 NHLBI NIH HHS Collapse
75	Bronner S, Ojofeitimi S, Lora JB, Southwick H, Kulak MC, Gamboa J, Rooney M, Gilman G, Gibbs R. A preseason cardiorespiratory profile of dancers in nine professional ballet and modern companies. J Dance Med Sci 2014;18:74-85. [PMID: 24844424 DOI: 10.12678/1089-313x.18.2.74] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Abstract While studies have investigated the physical demands of dance in terms of cardiorespiratory fitness, there are no recent comparisons of cardiorespiratory response to exercise among professional dancers of different genres. Our purpose was to: 1. develop a cardiorespiratory profile of professional dancers; 2. investigate differences in peak and recovery heart rate (HR) between professional modern and ballet dancers using an accelerated 3-minute step test; 3. demonstrate the relationship between cardiorespiratory variables; and 4. investigate the effects of company and work variables on the dancers' cardiorespiratory profiles. We hypothesized greater cardiorespiratory fitness in modern dancers than in ballet dancers, due to the nature of their repertory. Furthermore, we hypothesized that company profiles would reflect differences in work variables. Two hundred and eleven dancers (mean age 24.6 ± 4.7) from nine companies (two modern and seven ballet) performed a 3-minute step test. Demographics, height, mass, blood pressure (BP), smoking history, and resting peak and recovery HR were recorded. Body mass index (BMI) and fitness category were calculated. Independent t-tests were used to compare differences in demographics and cardiorespiratory variables due to genre, MANOVA were conducted to compare differences due to company, and correlations were calculated to determine the relationships between cardiorespiratory variables (p < 0.05). Modern dancers demonstrated higher mass and BMI, lower BP, lower resting HR and HR recovery, and a higher percentage were categorized as "fit" compared to ballet dancers (p < 0.03). There were differences between companies in age, experience, BMI, BP, resting, peak, and recovery HR, and fitness category (p < 0.001). The differences in cardiorespiratory fitness levels that may be related to rigor of repertory, rehearsal and performance seasons, or off-season exercise training are discussed. Results support the need for comprehensive physical fitness screening to identify dancers who could benefit from aerobic conditioning to enhance overall performance preparedness and to minimize fatigue effects. Collapse Key Words Collapse MESH Headings Collapse Grants Collapse