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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
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, Volume 15, No. 3, Article R53, Year 2014
Notification
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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. © 2014 Brownstein et al.
Authors & Co-Authors
Brownstein, Catherine A.
United States, Boston
Harvard Medical School
Beggs, Alan H.
United States, Boston
Harvard Medical School
Merriman, Barry
Unknown Affiliation
Yu, Timothy W.
United States, Boston
Harvard Medical School
DeChene, Elizabeth T.
United States, Boston
Harvard Medical School
Holm, Ingrid A.
United States, Boston
Harvard Medical School
Luquette, Lovelace J.
United States, Boston
Harvard Medical School
Majzoub, Joseph A.
United States, Boston
Harvard Medical School
Szolovits, Peter
United States, Cambridge
Massachusetts Institute of Technology
Mendelsohn, Nancy J.
United States, Minneapolis
Children's Hospitals and Clinics of Minnesota
Temme, Renee T.
United States, Minneapolis
Children's Hospitals and Clinics of Minnesota
Finkel, Richard S.
United States, Orlando
Nemours Children's Hospital
Yum, Sabrina W.
United States, Philadelphia
The Children's Hospital of Philadelphia
Medne, Līvija
United States, Philadelphia
The Children's Hospital of Philadelphia
Sunyaev, Shamil R.
United States, Boston
Harvard Medical School
de Bakker, Paul I.W.
United States, Boston
Harvard Medical School
Netherlands, Utrecht
University Medical Center Utrecht
Duzkale, Hatice
United States, Boston
Brigham and Women's Hospital
Dworzyński, Piotr
Denmark, Lyngby
Technical University of Denmark
Funke, Birgit H.
United States, Boston
Brigham and Women's Hospital
Lage, Kasper
United States, Boston
Harvard Medical School
Lek, Monkol
United States, Boston
Harvard Medical School
Leshchiner, Ignaty D.
United States, Boston
Harvard Medical School
United States, Boston
Brigham and Women's Hospital
MacArthur, Daniel G.
United States, Boston
Harvard Medical School
McLaughlin, Heather M.
United States, Boston
Brigham and Women's Hospital
Pers, Tune H.
United States, Boston
Boston Children's Hospital
Polak, Paz P.
United States, Boston
Harvard Medical School
Raychaudhuri, Soumya
United States, Boston
Harvard Medical School
Rehm, Heidi L.
United States, Boston
Brigham and Women's Hospital
Stitziel, Nathan Oliver
United States, Boston
Harvard Medical School
Hahn, Alexander
Germany, Munich
Genomatix ag
Biskup, Saskia
Germany, Tubingen
Cegat Gmbh
Freisinger, Peter
Germany, Tubingen
Cegat Gmbh
Perner, Sven R.
Germany, Bonn
Universitätsklinikum Bonn
Smith, Richard J.H.
United States, Iowa City
University of Iowa
Andorf, Jeaneen L.
United States, Iowa City
University of Iowa
Ryckman, Kelli K.
United States, Iowa City
University of Iowa
Sheffield, Val C.
United States, Iowa City
University of Iowa
United States, Chevy Chase
Howard Hughes Medical Institute
Stone, Edwin M.
United States, Iowa City
University of Iowa
United States, Chevy Chase
Howard Hughes Medical Institute
Bair, Thomas B.
United States, Iowa City
University of Iowa
Darbro, Benjamin W.
United States, Iowa City
University of Iowa
Kolbe, Diana L.
United States, Iowa City
University of Iowa
Wang, Kai
United States, Iowa City
University of Iowa
Bassuk, Alexander G.
United States, Iowa City
University of Iowa
Mathews, Katherine D.
United States, Iowa City
University of Iowa
Moore, Steven A.
United States, Iowa City
University of Iowa
Trapane, Pamela L.
United States, Iowa City
University of Iowa
Maga, Tara K.
United States, Iowa City
University of Iowa
Azaiez, Hela
United States, Iowa City
University of Iowa
Booth, Kevin T.A.
United States, Iowa City
University of Iowa
Segal, Michael M.
United States, Chestnut Hill
Simulconsult, Inc.
Williams, Marc S.
United States
Geisinger Health System
Tromp, Gerard C.
United States
Geisinger Health System
White, Peter
United States, Columbus
Nationwide Children’s Hospital
Fitzgerald-Butt, Sara M.
United States, Columbus
Nationwide Children’s Hospital
McBride, Kim L.
United States, Columbus
Nationwide Children’s Hospital
Newsom, David L.
Austria, Vienna
Naturhistorisches Museum, Vienna
Pierson, Christopher R.
United States, Columbus
Nationwide Children’s Hospital
Palandačić, Anja
Slovenia, Ljubljana
Univerzitetni Klinični Center Ljubljana
Austria, Vienna
Naturhistorisches Museum, Vienna
Torkamani, Ali A.
United States, La Jolla
Scripps Translational Science Institute
Wedell, Anna
Sweden, Solna
Science for Life Laboratory
Sweden, Stockholm
Karolinska Universitetssjukhuset
Sweden, Stockholm
Karolinska Institutet
Alexeyenko, Andrey V.
Sweden, Solna
Science for Life Laboratory
Magnusson, Måns
Sweden, Solna
Science for Life Laboratory
Sweden, Stockholm
Karolinska Universitetssjukhuset
Sweden, Stockholm
Karolinska Institutet
Nilsson, Daniel
Sweden, Solna
Science for Life Laboratory
Sweden, Stockholm
Karolinska Institutet
Sweden, Stockholm
Karolinska Universitetssjukhuset
Stranneheim, Henrik
Sweden, Solna
Science for Life Laboratory
Sweden, Stockholm
Karolinska Universitetssjukhuset
Sweden, Stockholm
Karolinska Institutet
Taylan, Fulya
Sweden, Solna
Science for Life Laboratory
Sweden, Stockholm
Karolinska Institutet
Gilissen, Christian
Netherlands, Nijmegen
Radboud University Medical Center
Hoischen, Alexander
Netherlands, Nijmegen
Radboud University Medical Center
van Bon, Bregje W.M.
Netherlands, Nijmegen
Radboud University Medical Center
Yntema, Helger G.
Netherlands, Nijmegen
Radboud University Medical Center
Javed, Asif
Singapore, Singapore City
Agency for Science, Technology and Research, Singapore
Ng, Pauline C.
Singapore, Singapore City
Agency for Science, Technology and Research, Singapore
Isakov, Ofer
Israel, Tel Aviv-yafo
Tel Aviv University
Friedman, Eitan A.
Israel, Tel Aviv-yafo
Tel Aviv University
Shomron, Noam
Israel, Tel Aviv-yafo
Tel Aviv University
Rowen, Lee
United States, Seattle
Institute for Systems Biology
San Lucas, Francis Anthony
United States, Houston
The University of Texas Md Anderson Cancer Center
García-Lobo, Juan María
Spain, Madrid
Consejo Superior de Investigaciones Científicas
Spain, Santander
Universidad de Cantabria
Gonzalez-Lamuño, D.
Spain, Santander
Universidad de Cantabria
Spain, Santander
Hospital Universitario Marqués de Valdecilla
Llorca-Díaz, Javier Francisco
Spain, Santander
Universidad de Cantabria
Spain, Madrid
Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública
Spain, Santander
Hospital Universitario Marqués de Valdecilla
de la Vega, Francisco M.
United States, San Bruno
Real Time Genomics, Inc.
Lyon, Gholson J.
United States, Cold Spring Harbor
Cold Spring Harbor Laboratory
Stevenson, David A.
United States, Salt Lake City
The University of Utah
Bray, Bruce E.
United States, Salt Lake City
University of Utah School of Medicine
Yandell, Mark D.
United States, Salt Lake City
University of Utah Health
Zhao, Hongyu
United States, New Haven
Yale University
Chen, Mengjie
United States, New Haven
Yale University
Günel, Murat
United States, New Haven
Yale University
Li, Peining
United States, New Haven
Yale University
Boycott, Kym M.
Canada, Ottawa
University of Ottawa
Bulman, Dennis E.
Canada, Ottawa
University of Ottawa
Gordon, Paul M.K.
Canada, Calgary
Alberta Children’s Hospital Research Institute
Innes, A. Micheil
Canada, Calgary
Alberta Children’s Hospital Research Institute
Knoppers, Bartha Maria
Canada, Montreal
Université Mcgill
Majewski, Jacek
Canada, Montreal
Université Mcgill
Marshall, Christian R.
Canada, Toronto
Hospital for Sick Children University of Toronto
Parboosingh, Jillian S.
Canada, Calgary
Alberta Children’s Hospital Research Institute
Sawyer, Sarah L.
Canada, Ottawa
University of Ottawa
Samuels, Mark E.
Canada, Montreal
University of Montreal
Schwartzentruber, Jeremy A.
Canada, Montreal
Université Mcgill
Kohane, Isaac S.
United States, Boston
Harvard Medical School
Margulies, David M.
United States, Boston
Harvard Medical School
Statistics
Citations: 307
Authors: 101
Affiliations: 54
Identifiers
Doi:
10.1186/gb-2014-15-3-r53
ISSN:
14747596
Research Areas
Genetics And Genomics
Health System And Policy