An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
| Autor: | Elizabeth T. DeChene, Fang Fang, Javier Llorca, Gustavo Glusman, Xiting Yan, Catherine A. Brownstein, Kim L. McBride, Jason Sager, Kai Wang, Kelli K. Ryckman, Nic Meyer, Ofer Isakov, Michael M. Segal, Peining Li, Gholson J. Lyon, Edwin M. Stone, Katherine C. Flannery, Thomas B. Bair, Ingrid A. Holm, Marc S. Williams, Barry Moore, Soumya Raychaudhuri, Shuba Krishna, Timothy W. Yu, Kasper Lage, Saloni Agrawal, Eran Halperin, Mortiz Menzel, Michael F. Murray, Adam P. DeLuca, Martin G. Reese, Mark Yandell, Mengjie Chen, Donald J. Corsmeier, Mark E. Samuels, Luca Lovrečić, Matthew S. Lebo, Ignacio Varela, Oleg A. Shchelochkov, Jacek Majewski, David L. Newsom, Francisco M. De La Vega, Sven Perner, Anne E. Kwitek, Peter White, Katherine D. Mathews, Mikael Huss, Sabrina W. Yum, Janeen L. Andorf, Zayed Albertyn, Juan M. García-Lobo, Hatice Duzkale, Saskia Biskup, Jian Huang, Komal S. Sandhu, Daniel Nilsson, Anna Wedell, Bruce E. Bray, Kevin T. Booth, Bernward Klocke, Sarah L. Sawyer, Tune H. Pers, Lu Zhang, Asif Javed, David M. Margulies, Paz Polak, Juan Caballero, Kathryn Blair, Alexander T. Rakowsky, Yong Kong, Livija Medne, Huntington F. Willard, Rama Sompallae, Cong Li, Måns Magnusson, Max Schubach, Ying Huang, Paul I.W. de Bakker, Anja Palandačić, Tara Maga, Fulya Taylan, Pamela Trapane, Emily N. Price, Lovelace J. Luquette, Hongyu Zhao, Yu Bai, Barry Merriman, Alexander Hahn, Hannah C. Cox, Erik Edens, Devon Lamb-Thrush, Terry A. Braun, Dennis E. Bulman, Pauline C. Ng, Monkol Lek, Peter Szolovits, Can Yang, Renee Temme, María Cruz Rodríguez, Karin Panzer, Sara Vestecka, Gail E. Herman, Rachel Soemedi, Edward S. Kiruluta, Isaac S. Kohane, Peter Neupert, Jorge Barrera, E. Ann Black-Ziegelbein, Nathan O. Stitziel, Jillian S. Parboosingh, Ignaty Leshchiner, Sara Fitzgerald-Butt, Jared C. Roach, Monica A. Giovanni, Vamsi Veeramachaneni, Christian Gilissen, Steven A. Moore, Michele Cargill, Deniz Kural, David A. Stevenson, Aiden Eliot Shearer, Andrey Alexeyenko, Murat Gunel, Daniel R. Richards, Richard J.H. Smith, Alan H. Beggs, Nils Homer, Jonathan W. Heusel, Val C. Sheffield, Ivan Adzhubey, Bartha Maria Knoppers, Yan Zhang, Jon M. Sorenson, Greg Lennon, William G. Fairbrother, Domingo González-Lamuño, Todd E. Scheetz, Noam Shomron, Benjamin W. Darbro, Colleen A. Campbell, Christopher A. Cassa, Christopher R. Pierson, Christian R. Marshall, F. Anthony San Lucas, Elaine Lyon, Sarah K. Savage, Jessica M. Lindvall, Borut Peterlin, Peter Freisinger, Jeremy Schwartzentruber, Gerard Tromp, Eitan Friedman, Daniel G. MacArthur, Richard S. Finkel, Piotr Dworzynski, Robert E. Handsaker, A. Micheil Innes, Jochen Supper, David McCallie, Bregje W.M. van Bon, Aaron D. Bossler, Lee Rowen, Mario Deng, Laurent C. Francioli, Michael Cariaso, Shamil R. Sunyaev, Diana L. Kolbe, Nancy J. Mendelsohn, Denise E. Mauldin, Helger G. Yntema, Alexander G. Bassuk, Joseph A. Majzoub, Marcel R. Nelen, Paul M. K. Gordon, Zhengyuan Wang, Claudia Gugenmus, Aleš Maver, Heather M. McLaughlin, Meghan C. Towne, Ali Torkamani, Hela Azaiez, Karen Eilbeck, Thomas H. Wassink, Reece K. Hart, Henrik Stranneheim, Austin C. Alexander, Douglas J. Van Daele, Seth A. Ament, Manuel L. Gonzalez-Garay, Lin Hou, Birgit Funke, Kym M. Boycott, Heidi L. Rehm, Weidong Zhang, Alexander Hoischen, Martin Braun, Xiaowei Chen, C. Thomas Caskey |
|---|---|
| Přispěvatelé: | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Szolovits, Peter, Universidad de Cantabria, Thermo Fisher Scientific, Harvard Medical School, Boston Children’s Hospital, Beijing Genomics Institute |
| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Heart Defects
Congenital Male Best practice Genomics ComputingMilieux_LEGALASPECTSOFCOMPUTING Biology Bioinformatics Genome DNA sequencing law.invention law Databases Genetic medicine Humans Genetic Testing Child Exome Genetic testing Whole genome sequencing medicine.diagnostic_test Research Financing Organized Sequence Analysis DNA Data science CLARITY Female Myopathies Structural Congenital |
| Zdroj: | BioMed Central Ltd Genome Biology, 2014, 15, 53 Genome Biology Genome Biol. 2014 Mar 25;15(3):R53 UCrea Repositorio Abierto de la Universidad de Cantabria Universidad de Cantabria (UC) Digital.CSIC. Repositorio Institucional del CSIC instname Brownstein, C A, Beggs, A H, Homer, N, Merriman, B, Yu, T W, Flannery, K C, DeChene, E T, Towne, M C, Savage, S K, Price, E N & Dworzynski, P 2014, ' An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge ', Genome Biology (Online Edition), vol. 15, R53 . https://doi.org/10.1186/gb-2014-15-3-r53 |
| Popis: | This is an Open Access article distributed under the terms of the Creative Commons Attribution License.-- et al. [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. This work was supported by funds provided through the Gene Partnership and the Manton Center for Orphan Disease Research at Boston Children’s Hospital and the Center for Biomedical Informatics at Harvard Medical School and by generous donations in-kind of genomic sequencing services by Life Technologies (Carlsbad, CA, USA) and Complete Genomics (Mountain View, CA, USA). |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|