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

Brownstein, Catherine A. (author): Karolinska Institutet

Beggs, Alan H. (author)

Homer, Nils (author)

Merriman, Barry (author)

Yu, Timothy W. (author)

Flannery, Katherine C. (author)

DeChene, Elizabeth T. (author)

Towne, Meghan C. (author)

Savage, Sarah K. (author)

Price, Emily N. (author)

Holm, Ingrid A. (author)

Luquette, Lovelace J. (author)

Lyon, Elaine (author)

Majzoub, Joseph (author)

Neupert, Peter (author)

McCallie, David, Jr. (author)

Szolovits, Peter (author)

Willard, Huntington F. (author)

Mendelsohn, Nancy J. (author)

Temme, Renee (author)

Finkel, Richard S. (author)

Yum, Sabrina W. (author)

Medne, Livija (author)

Sunyaev, Shamil R. (author)

Adzhubey, Ivan (author)

Cassa, Christopher A. (author)

de Bakker, Paul I. W. (author)

Duzkale, Hatice (author)

Dworzynski, Piotr (author)

Fairbrother, William (author)

Francioli, Laurent (author)

Funke, Birgit H. (author)

Giovanni, Monica A. (author)

Handsaker, Robert E. (author)

Lage, Kasper (author)

Lebo, Matthew S. (author)

Lek, Monkol (author)

Leshchiner, Ignaty (author)

MacArthur, Daniel G. (author)

McLaughlin, Heather M. (author): Karolinska Institutet

Murray, Michael F. (author)

Pers, Tune H. (author)

Polak, Paz P. (author)

Raychaudhuri, Soumya (author)

Rehm, Heidi L. (author)

Soemedi, Rachel (author)

Stitziel, Nathan O. (author)

Vestecka, Sara (author)

Supper, Jochen (author)

Gugenmus, Claudia (author)

Klocke, Bernward (author)

Hahn, Alexander (author)

Schubach, Max (author)

Menzel, Mortiz (author)

Biskup, Saskia (author)

Freisinger, Peter (author)

Deng, Mario (author)

Braun, Martin (author)

Perner, Sven (author)

Smith, Richard J. H. (author)

Andorf, Janeen L. (author)

Huang, Jian (author)

Ryckman, Kelli (author)

Sheffield, Val C. (author)

Stone, Edwin M. (author)

Bair, Thomas (author)

Black-Ziegelbein, E. Ann (author)

Braun, Terry A. (author)

Darbro, Benjamin (author)

DeLuca, Adam P. (author)

Kolbe, Diana L. (author)

Scheetz, Todd E. (author)

Shearer, Aiden E. (author)

Sompallae, Rama (author)

Wang, Kai (author)

Bassuk, Alexander G. (author)

Edens, Erik (author)

Mathews, Katherine (author)

Moore, Steven A. (author)

Shchelochkov, Oleg A. (author)

Trapane, Pamela (author)

Bossler, Aaron (author)

Campbell, Colleen A. (author)

Heusel, Jonathan W. (author)

Kwitek, Anne (author)

Maga, Tara (author)

Panzer, Karin (author)

Wassink, Thomas (author)

Van Daele, Douglas (author)

Azaiez, Hela (author)

Booth, Kevin (author)

Meyer, Nic (author)

Segal, Michael M. (author)

Williams, Marc S. (author)

Tromp, Gerard (author)

White, Peter (author)

Corsmeier, Donald (author)

Fitzgerald-Butt, Sara (author)

Herman, Gail (author)

Lamb-Thrush, Devon (author)

McBride, Kim L. (author)

Newsom, David (author)

Pierson, Christopher R. (author)

Rakowsky, Alexander T. (author)

Maver, Ales (author)

Lovrecic, Luca (author)

Palandacic, Anja (author)

Peterlin, Borut (author)

Torkamani, Ali (author)

Wedell, Anna (author): Karolinska Institutet

Huss, Mikael (author): Stockholms universitet,Institutionen för biokemi och biofysik

Alexeyenko, Andrey (author): KTH,Genteknologi,Science for Life Laboratory, SciLifeLab,Stockholm Bioinformatics Centre, Science for Life Laboratory, Solna, Sweden

Lindvall, Jessica M. (author)

Magnusson, Mans (author)

Nilsson, Daniel (author): Karolinska Institutet

Stranneheim, Henrik (author): Karolinska Institutet

Taylan, Fulya (author): Karolinska Institutet

Gilissen, Christian (author)

Hoischen, Alexander (author)

van Bon, Bregje (author)

Yntema, Helger (author)

Nelen, Marcel (author)

Zhang, Weidong (author)

Sager, Jason (author)

Zhang, Lu (author)

Blair, Kathryn (author)

Kural, Deniz (author)

Cariaso, Michael (author)

Lennon, Greg G. (author)

Javed, Asif (author)

Agrawal, Saloni (author)

Ng, Pauline C. (author)

Sandhu, Komal S. (author)

Krishna, Shuba (author)

Veeramachaneni, Vamsi (author)

Isakov, Ofer (author)

Halperin, Eran (author)

Friedman, Eitan (author)

Shomron, Noam (author)

Glusman, Gustavo (author)

Roach, Jared C. (author)

Caballero, Juan (author)

Cox, Hannah C. (author)

Mauldin, Denise (author)

Ament, Seth A. (author)

Rowen, Lee (author)

Richards, Daniel R. (author)

San Lucas, F. Anthony (author)

Gonzalez-Garay, Manuel L. (author)

Caskey, C. Thomas (author)

Bai, Yu (author)

Huang, Ying (author)

Fang, Fang (author)

Zhang, Yan (author)

Wang, Zhengyuan (author)

Barrera, Jorge (author)

Garcia-Lobo, Juan M. (author)

Gonzalez-Lamuno, Domingo (author)

Llorca, Javier (author)

Rodriguez, Maria C. (author)

Varela, Ignacio (author)

Reese, Martin G. (author)

De la Vega, Francisco M. (author)

Kiruluta, Edward (author)

Cargill, Michele (author)

Hart, Reece K. (author)

Sorenson, Jon M. (author)

Lyon, Gholson J. (author)

Stevenson, David A. (author)

Bray, Bruce E. (author)

Moore, Barry M. (author)

Eilbeck, Karen (author)

Yandell, Mark (author)

Zhao, Hongyu (author)

Hou, Lin (author)

Chen, Xiaowei (author)

Yan, Xiting (author)

Chen, Mengjie (author)

Li, Cong (author)

Yang, Can (author)

Gunel, Murat (author)

Li, Peining (author)

Kong, Yong (author)

Alexander, Austin C. (author)

Albertyn, Zayed I. (author)

Boycott, Kym M. (author)

Bulman, Dennis E. (author)

Gordon, Paul M. K. (author)

Innes, A. Micheil (author)

Knoppers, Bartha M. (author)

Majewski, Jacek (author)

Marshall, Christian R. (author)

Parboosingh, Jillian S. (author)

Sawyer, Sarah L. (author)

Samuels, Mark E. (author)

Schwartzentruber, Jeremy (author)

Kohane, Isaac S. (author)

Margulies, David M. (author)

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(creator_code:org_t)

Springer Science and Business Media LLC, 2014
2014
English.
In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-

Related links:: https://genomebiolog...; show more...; https://doi.org/10.1...; https://urn.kb.se/re...; https://doi.org/10.1...; http://kipublication...; https://urn.kb.se/re...; show less...

Journal article (peer-reviewed)

Abstract Subject headings

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.

Subject headings

NATURVETENSKAP -- Biologi (hsv//swe)
NATURAL SCIENCES -- Biological Sciences (hsv//eng)
MEDICIN OCH HÄLSOVETENSKAP -- Medicinsk bioteknologi (hsv//swe)
MEDICAL AND HEALTH SCIENCES -- Medical Biotechnology (hsv//eng)

Keyword

Burrows-Wheeler Transform
De-Novo Mutations
Whole-Genome
Genetic-Variation
Centronuclear Myopathy
Read Alignment
Titin Gene
Exome
Disease
Variants

Publication and Content Type

ref (subject category)
art (subject category)

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By the author/editor: Brownstein, Cath ...; Beggs, Alan H.; Homer, Nils; Merriman, Barry; Yu, Timothy W.; Flannery, Kather ...; show more...; DeChene, Elizabe ...; Towne, Meghan C.; Savage, Sarah K.; Price, Emily N.; Holm, Ingrid A.; Luquette, Lovela ...; Lyon, Elaine; Majzoub, Joseph; Neupert, Peter; McCallie, David, ...; Szolovits, Peter; Willard, Hunting ...; Mendelsohn, Nanc ...; Temme, Renee; Finkel, Richard ...; Yum, Sabrina W.; Medne, Livija; Sunyaev, Shamil ...; Adzhubey, Ivan; Cassa, Christoph ...; de Bakker, Paul ...; Duzkale, Hatice; Dworzynski, Piot ...; Fairbrother, Wil ...; Francioli, Laure ...; Funke, Birgit H.; Giovanni, Monica ...; Handsaker, Rober ...; Lage, Kasper; Lebo, Matthew S.; Lek, Monkol; Leshchiner, Igna ...; MacArthur, Danie ...; McLaughlin, Heat ...; Murray, Michael ...; Pers, Tune H.; Polak, Paz P.; Raychaudhuri, So ...; Rehm, Heidi L.; Soemedi, Rachel; Stitziel, Nathan ...; Vestecka, Sara; Supper, Jochen; Gugenmus, Claudi ...; Klocke, Bernward; Hahn, Alexander; Schubach, Max; Menzel, Mortiz; Biskup, Saskia; Freisinger, Pete ...; 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 ...; Braun, Terry A.; Darbro, Benjamin; DeLuca, Adam P.; Kolbe, Diana L.; Scheetz, Todd E.; Shearer, Aiden E ...; Sompallae, Rama; Wang, Kai; Bassuk, Alexande ...; Edens, Erik; Mathews, Katheri ...; Moore, Steven A.; Shchelochkov, Ol ...; Trapane, Pamela; Bossler, Aaron; Campbell, Collee ...; Heusel, Jonathan ...; Kwitek, Anne; Maga, Tara; Panzer, Karin; Wassink, Thomas; Van Daele, Dougl ...; Azaiez, Hela; Booth, Kevin; Meyer, Nic; Segal, Michael M ...; Williams, Marc S ...; Tromp, Gerard; White, Peter; Corsmeier, Donal ...; Fitzgerald-Butt, ...; Herman, Gail; Lamb-Thrush, Dev ...; McBride, Kim L.; Newsom, David; Pierson, Christo ...; Rakowsky, Alexan ...; Maver, Ales; Lovrecic, Luca; Palandacic, Anja; Peterlin, Borut; Torkamani, Ali; Wedell, Anna; Huss, Mikael; Alexeyenko, Andr ...; Lindvall, Jessic ...; Magnusson, Mans; Nilsson, Daniel; Stranneheim, Hen ...; Taylan, Fulya; Gilissen, Christ ...; Hoischen, Alexan ...; 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, ...; 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 ...; San Lucas, F. An ...; Gonzalez-Garay, ...; Caskey, C. Thoma ...; Bai, Yu; Huang, Ying; Fang, Fang; Zhang, Yan; Wang, Zhengyuan; Barrera, Jorge; Garcia-Lobo, Jua ...; Gonzalez-Lamuno, ...; Llorca, Javier; Rodriguez, Maria ...; Varela, Ignacio; Reese, Martin G.; De la Vega, Fran ...; Kiruluta, Edward; Cargill, Michele; Hart, Reece K.; Sorenson, Jon M.; Lyon, Gholson J.; Stevenson, David ...; 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, Austi ...; Albertyn, Zayed ...; Boycott, Kym M.; Bulman, Dennis E ...; Gordon, Paul M. ...; Innes, A. Michei ...; Knoppers, Bartha ...; Majewski, Jacek; Marshall, Christ ...; Parboosingh, Jil ...; Sawyer, Sarah L.; Samuels, Mark E.; Schwartzentruber ...; Kohane, Isaac S.; Margulies, David ...; show less...

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...

MEDICAL AND HEALTH SCIENCES: MEDICAL AND HEAL ...; and Medical Biotechn ...

Articles in the publication: Genome Biology

By the university: Royal Institute of Technology; Karolinska Institutet; Stockholm University

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