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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dc.contributor.authorBrownstein, Catherine A
dc.contributor.authorBeggs, Alan H
dc.contributor.authorHomer, Nils
dc.contributor.authorMerriman, Barry
dc.contributor.authorYu, Timothy W
dc.contributor.authorFlannery, Katherine C
dc.contributor.authorDeChene, Elizabeth T
dc.contributor.authorTowne, Meghan C
dc.contributor.authorSavage, Sarah K
dc.contributor.authorPrice, Emily N
dc.contributor.authorHolm, Ingrid A
dc.contributor.authorLuquette, Lovelace J
dc.contributor.authorLyon, Elaine
dc.contributor.authorMajzoub, Joseph
dc.contributor.authorNeupert, Peter
dc.contributor.authorMcCallie Jr, David
dc.contributor.authorSzolovits, Peter
dc.contributor.authorWillard, Huntington F
dc.contributor.authorMendelsohn, Nancy J
dc.contributor.authorTemme, Renee
dc.contributor.authorFinkel, Richard S
dc.contributor.authorYum, Sabrina W
dc.contributor.authorMedne, Livija
dc.contributor.authorSunyaev, Shamil R
dc.contributor.authorAdzhubey, Ivan
dc.contributor.authorCassa, Christopher A
dc.contributor.authorde Bakker, Paul I
dc.contributor.authorDuzkale, Hatice
dc.contributor.authorDworzyński, Piotr
dc.contributor.authorFairbrother, William
dc.contributor.authorFrancioli, Laurent
dc.contributor.authorFunke, Birgit H
dc.contributor.authorGiovanni, Monica A
dc.contributor.authorHandsaker, Robert E
dc.contributor.authorLage, Kasper
dc.contributor.authorLebo, Matthew S
dc.contributor.authorLek, Monkol
dc.contributor.authorLeshchiner, Ignaty
dc.contributor.authorMacArthur, Daniel G
dc.contributor.authorMcLaughlin, Heather M
dc.contributor.authorMurray, Michael F
dc.contributor.authorPers, Tune H
dc.contributor.authorPolak, Paz P
dc.contributor.authorRaychaudhuri, Soumya
dc.contributor.authorRehm, Heidi L
dc.contributor.authorSoemedi, Rachel
dc.contributor.authorStitziel, Nathan O
dc.contributor.authorVestecka, Sara
dc.contributor.authorSupper, Jochen
dc.contributor.authorGugenmus, Claudia
dc.contributor.authorKlocke, Bernward
dc.contributor.authorHahn, Alexander
dc.contributor.authorSchubach, Max
dc.contributor.authorMenzel, Mortiz
dc.contributor.authorBiskup, Saskia
dc.contributor.authorFreisinger, Peter
dc.contributor.authorDeng, Mario
dc.contributor.authorBraun, Martin
dc.contributor.authorPerner, Sven
dc.contributor.authorSmith, Richard J
dc.contributor.authorAndorf, Janeen L
dc.contributor.authorHuang, Jian
dc.contributor.authorRyckman, Kelli
dc.contributor.authorSheffield, Val C
dc.contributor.authorStone, Edwin M
dc.contributor.authorBair, Thomas
dc.contributor.authorBlack-Ziegelbein, E A
dc.contributor.authorBraun, Terry A
dc.contributor.authorDarbro, Benjamin
dc.contributor.authorDeLuca, Adam P
dc.contributor.authorKolbe, Diana L
dc.contributor.authorScheetz, Todd E
dc.contributor.authorShearer, Aiden E
dc.contributor.authorSompallae, Rama
dc.contributor.authorWang, Kai
dc.contributor.authorBassuk, Alexander G
dc.contributor.authorEdens, Erik
dc.contributor.authorMathews, Katherine
dc.contributor.authorMoore, Steven A
dc.contributor.authorShchelochkov, Oleg A
dc.contributor.authorTrapane, Pamela
dc.contributor.authorBossler, Aaron
dc.contributor.authorCampbell, Colleen A
dc.contributor.authorHeusel, Jonathan W
dc.contributor.authorKwitek, Anne
dc.contributor.authorMaga, Tara
dc.contributor.authorPanzer, Karin
dc.contributor.authorWassink, Thomas
dc.contributor.authorVan Daele, Douglas
dc.contributor.authorAzaiez, Hela
dc.contributor.authorBooth, Kevin
dc.contributor.authorMeyer, Nic
dc.contributor.authorSegal, Michael M
dc.contributor.authorWilliams, Marc S
dc.contributor.authorTromp, Gerard
dc.contributor.authorWhite, Peter
dc.contributor.authorCorsmeier, Donald
dc.contributor.authorFitzgerald-Butt, Sara
dc.contributor.authorHerman, Gail
dc.contributor.authorLamb-Thrush, Devon
dc.contributor.authorMcBride, Kim L
dc.contributor.authorNewsom, David
dc.contributor.authorPierson, Christopher R
dc.contributor.authorRakowsky, Alexander T
dc.contributor.authorMaver, Aleš
dc.contributor.authorLovrečić, Luca
dc.contributor.authorPalandačić, Anja
dc.contributor.authorPeterlin, Borut
dc.contributor.authorTorkamani, Ali
dc.contributor.authorWedell, Anna
dc.contributor.authorHuss, Mikael
dc.contributor.authorAlexeyenko, Andrey
dc.contributor.authorLindvall, Jessica M
dc.contributor.authorMagnusson, Måns
dc.contributor.authorNilsson, Daniel
dc.contributor.authorStranneheim, Henrik
dc.contributor.authorTaylan, Fulya
dc.contributor.authorGilissen, Christian
dc.contributor.authorHoischen, Alexander
dc.contributor.authorvan Bon, Bregje
dc.contributor.authorYntema, Helger
dc.contributor.authorNelen, Marcel
dc.contributor.authorZhang, Weidong
dc.contributor.authorSager, Jason
dc.contributor.authorZhang, Lu
dc.contributor.authorBlair, Kathryn
dc.contributor.authorKural, Deniz
dc.contributor.authorCariaso, Michael
dc.contributor.authorLennon, Greg G
dc.contributor.authorJaved, Asif
dc.contributor.authorAgrawal, Saloni
dc.contributor.authorNg, Pauline C
dc.contributor.authorSandhu, Komal S
dc.contributor.authorKrishna, Shuba
dc.contributor.authorVeeramachaneni, Vamsi
dc.contributor.authorIsakov, Ofer
dc.contributor.authorHalperin, Eran
dc.contributor.authorFriedman, Eitan
dc.contributor.authorShomron, Noam
dc.contributor.authorGlusman, Gustavo
dc.contributor.authorRoach, Jared C
dc.contributor.authorCaballero, Juan
dc.contributor.authorCox, Hannah C
dc.contributor.authorMauldin, Denise
dc.contributor.authorAment, Seth A
dc.contributor.authorRowen, Lee
dc.contributor.authorRichards, Daniel R
dc.contributor.authorLucas, F A S
dc.contributor.authorGonzalez-Garay, Manuel L
dc.contributor.authorCaskey, C T
dc.contributor.authorBai, Yu
dc.contributor.authorHuang, Ying
dc.contributor.authorFang, Fang
dc.contributor.authorZhang, Yan
dc.contributor.authorWang, Zhengyuan
dc.contributor.authorBarrera, Jorge
dc.contributor.authorGarcia-Lobo, Juan M
dc.contributor.authorGonzález-Lamuño, Domingo
dc.contributor.authorLlorca, Javier
dc.contributor.authorRodriguez, Maria C
dc.contributor.authorVarela, Ignacio
dc.contributor.authorReese, Martin G
dc.contributor.authorDe La Vega, Francisco M
dc.contributor.authorKiruluta, Edward
dc.contributor.authorCargill, Michele
dc.contributor.authorHart, Reece K
dc.contributor.authorSorenson, Jon M
dc.contributor.authorLyon, Gholson J
dc.contributor.authorStevenson, David A
dc.contributor.authorBray, Bruce E
dc.contributor.authorMoore, Barry M
dc.contributor.authorEilbeck, Karen
dc.contributor.authorYandell, Mark
dc.contributor.authorZhao, Hongyu
dc.contributor.authorHou, Lin
dc.contributor.authorChen, Xiaowei
dc.contributor.authorYan, Xiting
dc.contributor.authorChen, Mengjie
dc.contributor.authorLi, Cong
dc.contributor.authorYang, Can
dc.contributor.authorGunel, Murat
dc.contributor.authorLi, Peining
dc.contributor.authorKong, Yong
dc.contributor.authorAlexander, Austin C
dc.contributor.authorAlbertyn, Zayed I
dc.contributor.authorBoycott, Kym M
dc.contributor.authorBulman, Dennis E
dc.contributor.authorGordon, Paul M
dc.contributor.authorInnes, A M
dc.contributor.authorKnoppers, Bartha M
dc.contributor.authorMajewski, Jacek
dc.contributor.authorMarshall, Christian R
dc.contributor.authorParboosingh, Jillian S
dc.contributor.authorSawyer, Sarah L
dc.contributor.authorSamuels, Mark E
dc.contributor.authorSchwartzentruber, Jeremy
dc.contributor.authorKohane, Isaac S
dc.contributor.authorMargulies, David M
dc.date.accessioned2015-12-18T10:58:05Z
dc.date.available2015-12-18T10:58:05Z
dc.date.issued2014-03-25
dc.identifier.citationGenome Biology. 2014 Mar 25;15(3):R53
dc.identifier.urihttp://dx.doi.org/10.1186/gb-2014-15-3-r53
dc.identifier.urihttp://hdl.handle.net/10393/33940
dc.description.abstractAbstract 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.
dc.titleAn international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
dc.typeJournal Article
dc.date.updated2015-12-18T10:58:05Z
dc.language.rfc3066en
dc.rights.holderBrownstein et al.; licensee BioMed Central Ltd.
CollectionLibre accès - Publications // Open Access - Publications

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