An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
复制标题
DOI：
10.1186/gb-2014-15-3-r53
复制
发表时间：
2014-03-25
期刊：
影响因子：
12.3
通讯作者：
Margulies DM
中科院分区：
文献类型：
--
作者：
Brownstein CA;Beggs AH;Homer N;Merriman B;Yu TW;Flannery KC;DeChene ET;Towne MC;Savage SK;Price EN;Holm IA;Luquette LJ;Lyon E;Majzoub J;Neupert P;McCallie D Jr;Szolovits P;Willard HF;Mendelsohn NJ;Temme R;Finkel RS;Yum SW;Medne L;Sunyaev SR;Adzhubey I;Cassa CA;de Bakker PI;Duzkale H;Dworzyński P;Fairbrother W;Francioli L;Funke BH;Giovanni MA;Handsaker RE;Lage K;Lebo MS;Lek M;Leshchiner I;MacArthur DG;McLaughlin HM;Murray MF;Pers TH;Polak PP;Raychaudhuri S;Rehm HL;Soemedi R;Stitziel NO;Vestecka S;Supper J;Gugenmus C;Klocke B;Hahn A;Schubach M;Menzel M;Biskup S;Freisinger P;Deng M;Braun M;Perner S;Smith RJ;Andorf JL;Huang J;Ryckman K;Sheffield VC;Stone EM;Bair T;Black-Ziegelbein EA;Braun TA;Darbro B;DeLuca AP;Kolbe DL;Scheetz TE;Shearer AE;Sompallae R;Wang K;Bassuk AG;Edens E;Mathews K;Moore SA;Shchelochkov OA;Trapane P;Bossler A;Campbell CA;Heusel JW;Kwitek A;Maga T;Panzer K;Wassink T;Van Daele D;Azaiez H;Booth K;Meyer N;Segal MM;Williams MS;Tromp G;White P;Corsmeier D;Fitzgerald-Butt S;Herman G;Lamb-Thrush D;McBride KL;Newsom D;Pierson CR;Rakowsky AT;Maver A;Lovrečić L;Palandačić A;Peterlin B;Torkamani A;Wedell A;Huss M;Alexeyenko A;Lindvall JM;Magnusson M;Nilsson D;Stranneheim H;Taylan F;Gilissen C;Hoischen A;van Bon B;Yntema H;Nelen M;Zhang W;Sager J;Zhang L;Blair K;Kural D;Cariaso M;Lennon GG;Javed A;Agrawal S;Ng PC;Sandhu KS;Krishna S;Veeramachaneni V;Isakov O;Halperin E;Friedman E;Shomron N;Glusman G;Roach JC;Caballero J;Cox HC;Mauldin D;Ament SA;Rowen L;Richards DR;San Lucas FA;Gonzalez-Garay ML;Caskey CT;Bai Y;Huang Y;Fang F;Zhang Y;Wang Z;Barrera J;Garcia-Lobo JM;González-Lamuño D;Llorca J;Rodriguez MC;Varela I;Reese MG;De La Vega FM;Kiruluta E;Cargill M;Hart RK;Sorenson JM;Lyon GJ;Stevenson DA;Bray BE;Moore BM;Eilbeck K;Yandell M;Zhao H;Hou L;Chen X;Yan X;Chen M;Li C;Yang C;Gunel M;Li P;Kong Y;Alexander AC;Albertyn ZI;Boycott KM;Bulman DE;Gordon PM;Innes AM;Knoppers BM;Majewski J;Marshall CR;Parboosingh JS;Sawyer SL;Samuels ME;Schwartzentruber J;Kohane IS;Margulies DM
一旦基因组测序成为常规，它将有巨大的潜力来改善临床诊断和护理，但这将需要在序列数据生成、分析、解释和报告领域将研究方法正式化为临床最佳实践。CLARITY挑战赛旨在促进从临床病例史和基因组测序数据开始的遗传病诊断方法的趋同。从三个具有遗传性遗传病的家庭获得DNA样本，基因组序列数据由测序平台供应商提供。挑战在于分析和解释这些数据，以确定致病变异并以临床有用的格式报告结果。参加比赛的选手团体被广泛征集，一个独立的评委小组对他们的表现进行了评估。总共有30个国际团体参与。这些条目揭示了在分析和解释过程的大多数要素上的实践的一般趋同。然而，即使考虑到这种方法的共性，只有两组在所有疾病病例中确定了共识的候选变异，这表明需要对普遍接受的方法进行一致的微调。在最终临床报告内容和患者同意过程中存在更大的多样性，表明这些领域需要进一步的探索和标准化。CLARITY挑战赛对目前使用基因组测序诊断和报告遗传疾病的做法进行了全面评估。生物信息学技术有显著的融合，但医学解释和报告是许多团体需要进一步发展的领域。
There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
登录
查看更多内容
影响因子：
64.8
作者：
Ellis, Matthew J.;Ding, Li;Shen, Dong;Luo, Jingqin;Suman, Vera J.;Wallis, John W.;Van Tine, Brian A.;Hoog, Jeremy;Goiffon, Reece J.;Goldstein, Theodore C.;Ng, Sam;Lin, Li;Crowder, Robert;Snider, Jacqueline;Ballman, Karla;Weber, Jason;Chen, Ken;Koboldt, Daniel C.;Kandoth, Cyriac;Schierding, William S.;McMichael, Joshua F.;Miller, Christopher A.;Lu, Charles;Harris, Christopher C.;McLellan, Michael D.;Wendl, Michael C.;DeSchryver, Katherine;Allred, D. Craig;Esserman, Laura;Unzeitig, Gary;Margenthaler, Julie;Babiera, G. V.;Marcom, P. Kelly;Guenther, J. M.;Leitch, Marilyn;Hunt, Kelly;Olson, John;Tao, Yu;Maher, Christopher A.;Fulton, Lucinda L.;Fulton, Robert S.;Harrison, Michelle;Oberkfell, Ben;Du, Feiyu;Demeter, Ryan;Vickery, Tammi L.;Elhammali, Adnan;Piwnica-Worms, Helen;McDonald, Sandra;Watson, Mark;Dooling, David J.;Ota, David;Chang, Li-Wei;Bose, Ron;Ley, Timothy J.;Piwnica-Worms, David;Stuart, Joshua M.;Wilson, Richard K.;Mardis, Elaine R.
通讯作者：
Mardis, Elaine R.
来自1,092个人基因组的遗传变异的综合图。
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew
影响因子：
64.8
作者：
Kong A;Frigge ML;Masson G;Besenbacher S;Sulem P;Magnusson G;Gudjonsson SA;Sigurdsson A;Jonasdottir A;Jonasdottir A;Wong WS;Sigurdsson G;Walters GB;Steinberg S;Helgason H;Thorleifsson G;Gudbjartsson DF;Helgason A;Magnusson OT;Thorsteinsdottir U;Stefansson K
通讯作者：
Stefansson K
DOI：
10.1038/gim.2013.73
发表时间：
2013-07
期刊：
Genetics in medicine : official journal of the American College of Medical Genetics
影响因子：
--
作者：
通讯作者：
--