WEScover: whole exome sequencing vs. gene panel testing
作者： Kenneth D. Mandl , Carles Hernandez-Ferrer , Sek Won Kong , Sek Won Kong , In-Hee Lee
DOI: 10.1101/367607
关键词:
摘要: Abstract Motivation Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, the potential for false negatives due to incomplete breadth depth of coverage some exons has been reported. In cases, targeted gene panel testing could be a reliable option ascertain true phenotype-associated genomic variants. We developed tool quickly gauging whether all genes interest are comprehensively covered by WES or should instead considered minimize candidate genes. Results WEScover novel web application providing an interface discovering across population scale datasets, searching either phenotype, panels Moreover, shows metrics from Genome Aggregation Database provide gene-centric view on coverage. Availability available at http://gNOME.tchlab.org/WEScover/. The source code https://github.com/bch-gnome/WEScover. Contact sekwon.kong@childrens.harvard.edu
sci-hub.st 参考文章(11)
Jason Wang, Garrett Gotway, Juan M. Pascual, Jason Y. Park, Diagnostic yield of clinical next-generation sequencing panels for epilepsy. JAMA Neurology. ,vol. 71, pp. 650- 651 ,(2014) , 10.1001/JAMANEUROL.2014.405
Wendy S. Rubinstein, Donna R. Maglott, Jennifer M. Lee, Brandi L. Kattman, Adriana J. Malheiro, Michael Ovetsky, Vichet Hem, Viatcheslav Gorelenkov, Guangfeng Song, Craig Wallin, Nora Husain, Shanmuga Chitipiralla, Kenneth S. Katz, Douglas Hoffman, Wonhee Jang, Mark Johnson, Fedor Karmanov, Alexander Ukrainchik, Mikhail Denisenko, Cathy Fomous, Kathy Hudson, James M. Ostell, The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency Nucleic Acids Research. ,vol. 41, pp. 925- 935 ,(2012) , 10.1093/NAR/GKS1173
K. Zerjavic, I. Keller, M. Okoniewski, A. Patrignani, K. Ludin, Z. Xu, B. Steinmann, T. Carrel, B. Rothlisberger, R. Schlapbach, R. Bruggmann, G. Matyas, J. Meienberg, New insights into the performance of human whole-exome capture platforms Nucleic Acids Research. ,vol. 43, ,(2015) , 10.1093/NAR/GKV216
Kim D Pruitt, Jennifer Harrow, Rachel A Harte, Craig Wallin, Mark Diekhans, Donna R Maglott, Steve Searle, Catherine M Farrell, Jane E Loveland, Barbara J Ruef, Elizabeth Hart, Marie-Marthe Suner, Melissa J Landrum, Bronwen Aken, Sarah Ayling, Robert Baertsch, Julio Fernandez-Banet, Joshua L Cherry, Val Curwen, Michael DiCuccio, Manolis Kellis, Jennifer Lee, Michael F Lin, Michael Schuster, Andrew Shkeda, Clara Amid, Garth Brown, Oksana Dukhanina, Adam Frankish, Jennifer Hart, Bonnie L Maidak, Jonathan Mudge, Michael R Murphy, Terence Murphy, Jeena Rajan, Bhanu Rajput, Lillian D Riddick, Catherine Snow, Charles Steward, David Webb, Janet A Weber, Laurens Wilming, Wenyu Wu, Ewan Birney, David Haussler, Tim Hubbard, James Ostell, Richard Durbin, David Lipman, The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes Genome Research. ,vol. 19, pp. 1316- 1323 ,(2009) , 10.1101/GR.080531.108
, A global reference for human genetic variation. Nature. ,vol. 526, pp. 68- 74 ,(2015) , 10.1038/NATURE15393
Alison M Meynert, Morad Ansari, David R FitzPatrick, Martin S Taylor, Variant detection sensitivity and biases in whole genome and exome sequencing BMC Bioinformatics. ,vol. 15, pp. 247- 247 ,(2014) , 10.1186/1471-2105-15-247
Sebastian Köhler, Sandra C Doelken, Christopher J Mungall, Sebastian Bauer, Helen V Firth, Isabelle Bailleul-Forestier, Graeme CM Black, Danielle L Brown, Michael Brudno, Jennifer Campbell, David R FitzPatrick, Janan T Eppig, Andrew P Jackson, Kathleen Freson, Marta Girdea, Ingo Helbig, Jane A Hurst, Johanna Jähn, Laird G Jackson, Anne M Kelly, David H Ledbetter, Sahar Mansour, Christa L Martin, Celia Moss, Andrew Mumford, Willem H Ouwehand, Soo-Mi Park, Erin Rooney Riggs, Richard H Scott, Sanjay Sisodiya, Steven Van Vooren, Ronald J Wapner, Andrew OM Wilkie, Caroline F Wright, Anneke T Vulto-van Silfhout, Nicole de Leeuw, Bert BA De Vries, Nicole L Washingthon, Cynthia L Smith, Monte Westerfield, Paul Schofield, Barbara J Ruef, Georgios V Gkoutos, Melissa Haendel, Damian Smedley, Suzanna E Lewis, Peter N Robinson, None, The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data Nucleic Acids Research. ,vol. 42, pp. 966- 974 ,(2014) , 10.1093/NAR/GKT1026
Dimitri J Stavropoulos, Daniele Merico, Rebekah Jobling, Sarah Bowdin, Nasim Monfared, Bhooma Thiruvahindrapuram, Thomas Nalpathamkalam, Giovanna Pellecchia, Ryan K C Yuen, Michael J Szego, Robin Z Hayeems, Randi Zlotnik Shaul, Michael Brudno, Marta Girdea, Brendan Frey, Babak Alipanahi, Sohnee Ahmed, Riyana Babul-Hirji, Ramses Badilla Porras, Melissa T Carter, Lauren Chad, Ayeshah Chaudhry, David Chitayat, Soghra Jougheh Doust, Cheryl Cytrynbaum, Lucie Dupuis, Resham Ejaz, Leona Fishman, Andrea Guerin, Bita Hashemi, Mayada Helal, Stacy Hewson, Michal Inbar-Feigenberg, Peter Kannu, Natalya Karp, Raymond H Kim, Jonathan Kronick, Eriskay Liston, Heather MacDonald, Saadet Mercimek-Mahmutoglu, Roberto Mendoza-Londono, Enas Nasr, Graeme Nimmo, Nicole Parkinson, Nada Quercia, Julian Raiman, Maian Roifman, Andreas Schulze, Andrea Shugar, Cheryl Shuman, Pierre Sinajon, Komudi Siriwardena, Rosanna Weksberg, Grace Yoon, Chris Carew, Raith Erickson, Richard A Leach, Robert Klein, Peter N Ray, M Stephen Meyn, Stephen W Scherer, Ronald D Cohn, Christian R Marshall, Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine npj Genomic Medicine. ,vol. 1, pp. 15012- ,(2016) , 10.1038/NPJGENMED.2015.12
Monkol Lek, Konrad J Karczewski, Eric V Minikel, Kaitlin E Samocha, Eric Banks, Timothy Fennell, Anne H O’Donnell-Luria, James S Ware, Andrew J Hill, Beryl B Cummings, Taru Tukiainen, Daniel P Birnbaum, Jack A Kosmicki, Laramie E Duncan, Karol Estrada, Fengmei Zhao, James Zou, Emma Pierce-Hoffman, Joanne Berghout, David N Cooper, Nicole Deflaux, Mark DePristo, Ron Do, Jason Flannick, Menachem Fromer, Laura Gauthier, Jackie Goldstein, Namrata Gupta, Daniel Howrigan, Adam Kiezun, Mitja I Kurki, Ami Levy Moonshine, Pradeep Natarajan, Lorena Orozco, Gina M Peloso, Ryan Poplin, Manuel A Rivas, Valentin Ruano-Rubio, Samuel A Rose, Douglas M Ruderfer, Khalid Shakir, Peter D Stenson, Christine Stevens, Brett P Thomas, Grace Tiao, Maria T Tusie-Luna, Ben Weisburd, Hong-Hee Won, Dongmei Yu, David M Altshuler, Diego Ardissino, Michael Boehnke, John Danesh, Stacey Donnelly, Roberto Elosua, Jose C Florez, Stacey B Gabriel, Gad Getz, Stephen J Glatt, Christina M Hultman, Sekar Kathiresan, Markku Laakso, Steven McCarroll, Mark I McCarthy, Dermot McGovern, Ruth McPherson, Benjamin M Neale, Aarno Palotie, Shaun M Purcell, Danish Saleheen, Jeremiah M Scharf, Pamela Sklar, Patrick F Sullivan, Jaakko Tuomilehto, Ming T Tsuang, Hugh C Watkins, James G Wilson, Mark J Daly, Daniel G MacArthur, Exome Aggregation Consortium, Analysis of protein-coding genetic variation in 60,706 humans Nature. ,vol. 536, pp. 285- 291 ,(2016) , 10.1038/NATURE19057
Sek Won Kong, In-Hee Lee, Xuanshi Liu, Joel N Hirschhorn, Kenneth D Mandl, Measuring coverage and accuracy of whole-exome sequencing in clinical context. Genetics in Medicine. ,vol. 20, pp. 1617- 1626 ,(2018) , 10.1038/GIM.2018.51