An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

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Title: An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
Authors: Brownstein, Catherine A
Beggs, Alan H
Homer, Nils
Merriman, Barry
Yu, Timothy W
Flannery, Katherine C
DeChene, Elizabeth T
Towne, Meghan C
Savage, Sarah K
Price, Emily N
Holm, Ingrid A
Luquette, Lovelace J
Lyon, Elaine
Majzoub, Joseph
Neupert, Peter
McCallie Jr, David
Szolovits, Peter
Willard, Huntington F
Mendelsohn, Nancy J
Temme, Renee
Finkel, Richard S
Yum, Sabrina W
Medne, Livija
Sunyaev, Shamil R
Adzhubey, Ivan
Cassa, Christopher A
de Bakker, Paul I
Duzkale, Hatice
Dworzyński, Piotr
Fairbrother, William
Francioli, Laurent
Funke, Birgit H
Giovanni, Monica A
Handsaker, Robert E
Lage, Kasper
Lebo, Matthew S
Lek, Monkol
Leshchiner, Ignaty
MacArthur, Daniel G
McLaughlin, Heather M
Murray, Michael F
Pers, Tune H
Polak, Paz P
Raychaudhuri, Soumya
Rehm, Heidi L
Soemedi, Rachel
Stitziel, Nathan O
Vestecka, Sara
Supper, Jochen
Gugenmus, Claudia
Klocke, Bernward
Hahn, Alexander
Schubach, Max
Menzel, Mortiz
Biskup, Saskia
Freisinger, Peter
Deng, Mario
Braun, Martin
Perner, Sven
Smith, Richard J
Andorf, Janeen L
Huang, Jian
Ryckman, Kelli
Sheffield, Val C
Stone, Edwin M
Bair, Thomas
Black-Ziegelbein, E A
Braun, Terry A
Darbro, Benjamin
DeLuca, Adam P
Kolbe, Diana L
Scheetz, Todd E
Shearer, Aiden E
Sompallae, Rama
Wang, Kai
Bassuk, Alexander G
Edens, Erik
Mathews, Katherine
Moore, Steven A
Shchelochkov, Oleg A
Trapane, Pamela
Bossler, Aaron
Campbell, Colleen A
Heusel, Jonathan W
Kwitek, Anne
Maga, Tara
Panzer, Karin
Wassink, Thomas
Van Daele, Douglas
Azaiez, Hela
Booth, Kevin
Meyer, Nic
Segal, Michael M
Williams, Marc S
Tromp, Gerard
White, Peter
Corsmeier, Donald
Fitzgerald-Butt, Sara
Herman, Gail
Lamb-Thrush, Devon
McBride, Kim L
Newsom, David
Pierson, Christopher R
Rakowsky, Alexander T
Maver, Aleš
Lovrečić, Luca
Palandačić, Anja
Peterlin, Borut
Torkamani, Ali
Wedell, Anna
Huss, Mikael
Alexeyenko, Andrey
Lindvall, Jessica M
Magnusson, Måns
Nilsson, Daniel
Stranneheim, Henrik
Taylan, Fulya
Gilissen, Christian
Hoischen, Alexander
van Bon, Bregje
Yntema, Helger
Nelen, Marcel
Zhang, Weidong
Sager, Jason
Zhang, Lu
Blair, Kathryn
Kural, Deniz
Cariaso, Michael
Lennon, Greg G
Javed, Asif
Agrawal, Saloni
Ng, Pauline C
Sandhu, Komal S
Krishna, Shuba
Veeramachaneni, Vamsi
Isakov, Ofer
Halperin, Eran
Friedman, Eitan
Shomron, Noam
Glusman, Gustavo
Roach, Jared C
Caballero, Juan
Cox, Hannah C
Mauldin, Denise
Ament, Seth A
Rowen, Lee
Richards, Daniel R
Lucas, F A S
Gonzalez-Garay, Manuel L
Caskey, C T
Bai, Yu
Huang, Ying
Fang, Fang
Zhang, Yan
Wang, Zhengyuan
Barrera, Jorge
Garcia-Lobo, Juan M
González-Lamuño, Domingo
Llorca, Javier
Rodriguez, Maria C
Varela, Ignacio
Reese, Martin G
De La Vega, Francisco M
Kiruluta, Edward
Cargill, Michele
Hart, Reece K
Sorenson, Jon M
Lyon, Gholson J
Stevenson, David A
Bray, Bruce E
Moore, Barry M
Eilbeck, Karen
Yandell, Mark
Zhao, Hongyu
Hou, Lin
Chen, Xiaowei
Yan, Xiting
Chen, Mengjie
Li, Cong
Yang, Can
Gunel, Murat
Li, Peining
Kong, Yong
Alexander, Austin C
Albertyn, Zayed I
Boycott, Kym M
Bulman, Dennis E
Gordon, Paul M
Innes, A M
Knoppers, Bartha M
Majewski, Jacek
Marshall, Christian R
Parboosingh, Jillian S
Sawyer, Sarah L
Samuels, Mark E
Schwartzentruber, Jeremy
Kohane, Isaac S
Margulies, David M
Date: 2014-03-25
Abstract: Abstract Background 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. Results 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. Conclusions 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.
URL: http://dx.doi.org/10.1186/gb-2014-15-3-r53
http://hdl.handle.net/10393/33940
CollectionLibre accès - Publications // Open Access - Publications
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