An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in ... View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-03

AUTHORS

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

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. More... »

PAGES

r53

Journal

TITLE

Genome Biology

ISSUE

3

VOLUME

15

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/gb-2014-15-3-r53

DOI

http://dx.doi.org/10.1186/gb-2014-15-3-r53

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1000435282

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24667040


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85 schema:description 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.
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