MOTIVATION: The sequencing of tumors and their matched normals is frequently used to study the genetic composition of cancer. Despite this fact, there remains a dearth of available software tools designed to compare sequences in pairs of samples and identify sites that are likely to be unique to one sample. RESULTS: In this article, we describe the mathematical basis of our SomaticSniper software for comparing tumor and normal pairs. We estimate its sensitivity and precision, and present several common sources of error resulting in miscalls. AVAILABILITY AND IMPLEMENTATION: Binaries are freely available for download at http://gmt.genome.wustl.edu/somatic-sniper/current/, implemented in C and supported on Linux and Mac OS X. CONTACT: delarson@wustl.edu; lding@wustl.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: The sequencing of tumors and their matched normals is frequently used to study the genetic composition of cancer. Despite this fact, there remains a dearth of available software tools designed to compare sequences in pairs of samples and identify sites that are likely to be unique to one sample. RESULTS: In this article, we describe the mathematical basis of our SomaticSniper software for comparing tumor and normal pairs. We estimate its sensitivity and precision, and present several common sources of error resulting in miscalls. AVAILABILITY AND IMPLEMENTATION: Binaries are freely available for download at http://gmt.genome.wustl.edu/somatic-sniper/current/, implemented in C and supported on Linux and Mac OS X. CONTACT: delarson@wustl.edu; lding@wustl.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Sohrab P Shah; Martin Köbel; Janine Senz; Ryan D Morin; Blaise A Clarke; Kimberly C Wiegand; Gillian Leung; Abdalnasser Zayed; Erika Mehl; Steve E Kalloger; Mark Sun; Ryan Giuliany; Erika Yorida; Steven Jones; Richard Varhol; Kenneth D Swenerton; Dianne Miller; Philip B Clement; Colleen Crane; Jason Madore; Diane Provencher; Peter Leung; Anna DeFazio; Jaswinder Khattra; Gulisa Turashvili; Yongjun Zhao; Thomas Zeng; J N Mark Glover; Barbara Vanderhyden; Chengquan Zhao; Christine A Parkinson; Mercedes Jimenez-Linan; David D L Bowtell; Anne-Marie Mes-Masson; James D Brenton; Samuel A Aparicio; Niki Boyd; Martin Hirst; C Blake Gilks; Marco Marra; David G Huntsman Journal: N Engl J Med Date: 2009-06-10 Impact factor: 91.245
Authors: Erin D Pleasance; R Keira Cheetham; Philip J Stephens; David J McBride; Sean J Humphray; Chris D Greenman; Ignacio Varela; Meng-Lay Lin; Gonzalo R Ordóñez; Graham R Bignell; Kai Ye; Julie Alipaz; Markus J Bauer; David Beare; Adam Butler; Richard J Carter; Lina Chen; Anthony J Cox; Sarah Edkins; Paula I Kokko-Gonzales; Niall A Gormley; Russell J Grocock; Christian D Haudenschild; Matthew M Hims; Terena James; Mingming Jia; Zoya Kingsbury; Catherine Leroy; John Marshall; Andrew Menzies; Laura J Mudie; Zemin Ning; Tom Royce; Ole B Schulz-Trieglaff; Anastassia Spiridou; Lucy A Stebbings; Lukasz Szajkowski; Jon Teague; David Williamson; Lynda Chin; Mark T Ross; Peter J Campbell; David R Bentley; P Andrew Futreal; Michael R Stratton Journal: Nature Date: 2009-12-16 Impact factor: 49.962
Authors: Rodrigo Goya; Mark G F Sun; Ryan D Morin; Gillian Leung; Gavin Ha; Kimberley C Wiegand; Janine Senz; Anamaria Crisan; Marco A Marra; Martin Hirst; David Huntsman; Kevin P Murphy; Sam Aparicio; Sohrab P Shah Journal: Bioinformatics Date: 2010-02-03 Impact factor: 6.937
Authors: Li Ding; Matthew J Ellis; Shunqiang Li; David E Larson; Ken Chen; John W Wallis; Christopher C Harris; Michael D McLellan; Robert S Fulton; Lucinda L Fulton; Rachel M Abbott; Jeremy Hoog; David J Dooling; Daniel C Koboldt; Heather Schmidt; Joelle Kalicki; Qunyuan Zhang; Lei Chen; Ling Lin; Michael C Wendl; Joshua F McMichael; Vincent J Magrini; Lisa Cook; Sean D McGrath; Tammi L Vickery; Elizabeth Appelbaum; Katherine Deschryver; Sherri Davies; Therese Guintoli; Li Lin; Robert Crowder; Yu Tao; Jacqueline E Snider; Scott M Smith; Adam F Dukes; Gabriel E Sanderson; Craig S Pohl; Kim D Delehaunty; Catrina C Fronick; Kimberley A Pape; Jerry S Reed; Jody S Robinson; Jennifer S Hodges; William Schierding; Nathan D Dees; Dong Shen; Devin P Locke; Madeline E Wiechert; James M Eldred; Josh B Peck; Benjamin J Oberkfell; Justin T Lolofie; Feiyu Du; Amy E Hawkins; Michelle D O'Laughlin; Kelly E Bernard; Mark Cunningham; Glendoria Elliott; Mark D Mason; Dominic M Thompson; Jennifer L Ivanovich; Paul J Goodfellow; Charles M Perou; George M Weinstock; Rebecca Aft; Mark Watson; Timothy J Ley; Richard K Wilson; Elaine R Mardis Journal: Nature Date: 2010-04-15 Impact factor: 49.962
Authors: Elaine R Mardis; Li Ding; David J Dooling; David E Larson; Michael D McLellan; Ken Chen; Daniel C Koboldt; Robert S Fulton; Kim D Delehaunty; Sean D McGrath; Lucinda A Fulton; Devin P Locke; Vincent J Magrini; Rachel M Abbott; Tammi L Vickery; Jerry S Reed; Jody S Robinson; Todd Wylie; Scott M Smith; Lynn Carmichael; James M Eldred; Christopher C Harris; Jason Walker; Joshua B Peck; Feiyu Du; Adam F Dukes; Gabriel E Sanderson; Anthony M Brummett; Eric Clark; Joshua F McMichael; Rick J Meyer; Jonathan K Schindler; Craig S Pohl; John W Wallis; Xiaoqi Shi; Ling Lin; Heather Schmidt; Yuzhu Tang; Carrie Haipek; Madeline E Wiechert; Jolynda V Ivy; Joelle Kalicki; Glendoria Elliott; Rhonda E Ries; Jacqueline E Payton; Peter Westervelt; Michael H Tomasson; Mark A Watson; Jack Baty; Sharon Heath; William D Shannon; Rakesh Nagarajan; Daniel C Link; Matthew J Walter; Timothy A Graubert; John F DiPersio; Richard K Wilson; Timothy J Ley Journal: N Engl J Med Date: 2009-08-05 Impact factor: 91.245
Authors: Sohrab P Shah; Ryan D Morin; Jaswinder Khattra; Leah Prentice; Trevor Pugh; Angela Burleigh; Allen Delaney; Karen Gelmon; Ryan Guliany; Janine Senz; Christian Steidl; Robert A Holt; Steven Jones; Mark Sun; Gillian Leung; Richard Moore; Tesa Severson; Greg A Taylor; Andrew E Teschendorff; Kane Tse; Gulisa Turashvili; Richard Varhol; René L Warren; Peter Watson; Yongjun Zhao; Carlos Caldas; David Huntsman; Martin Hirst; Marco A Marra; Samuel Aparicio Journal: Nature Date: 2009-10-08 Impact factor: 49.962
Authors: Erin D Pleasance; Philip J Stephens; Sarah O'Meara; David J McBride; Alison Meynert; David Jones; Meng-Lay Lin; David Beare; King Wai Lau; Chris Greenman; Ignacio Varela; Serena Nik-Zainal; Helen R Davies; Gonzalo R Ordoñez; Laura J Mudie; Calli Latimer; Sarah Edkins; Lucy Stebbings; Lina Chen; Mingming Jia; Catherine Leroy; John Marshall; Andrew Menzies; Adam Butler; Jon W Teague; Jonathon Mangion; Yongming A Sun; Stephen F McLaughlin; Heather E Peckham; Eric F Tsung; Gina L Costa; Clarence C Lee; John D Minna; Adi Gazdar; Ewan Birney; Michael D Rhodes; Kevin J McKernan; Michael R Stratton; P Andrew Futreal; Peter J Campbell Journal: Nature Date: 2009-12-16 Impact factor: 49.962
Authors: Daniel C Koboldt; Qunyuan Zhang; David E Larson; Dong Shen; Michael D McLellan; Ling Lin; Christopher A Miller; Elaine R Mardis; Li Ding; Richard K Wilson Journal: Genome Res Date: 2012-02-02 Impact factor: 9.043
Authors: Andrew Roth; Jiarui Ding; Ryan Morin; Anamaria Crisan; Gavin Ha; Ryan Giuliany; Ali Bashashati; Martin Hirst; Gulisa Turashvili; Arusha Oloumi; Marco A Marra; Samuel Aparicio; Sohrab P Shah Journal: Bioinformatics Date: 2012-01-27 Impact factor: 6.937
Authors: Xiuli Zhang; Samuel Kim; Jasreet Hundal; John M Herndon; Shunqiang Li; Allegra A Petti; Savas D Soysal; Lijin Li; Mike D McLellan; Jeremy Hoog; Tina Primeau; Nancy Myers; Tammi L Vickery; Mark Sturmoski; Ian S Hagemann; Chris A Miller; Matthew J Ellis; Elaine R Mardis; Ted Hansen; Timothy P Fleming; S Peter Goedegebuure; William E Gillanders Journal: Cancer Immunol Res Date: 2017-06-15 Impact factor: 11.151
Authors: Christopher R Cabanski; Vincent Magrini; Malachi Griffith; Obi L Griffith; Sean McGrath; Jin Zhang; Jason Walker; Amy Ly; Ryan Demeter; Robert S Fulton; Winnie W Pong; David H Gutmann; Ramaswamy Govindan; Elaine R Mardis; Christopher A Maher Journal: J Mol Diagn Date: 2014-05-09 Impact factor: 5.568
Authors: Jeremy Chien; Hugues Sicotte; Jian-Bing Fan; Sean Humphray; Julie M Cunningham; Kimberly R Kalli; Ann L Oberg; Steven N Hart; Ying Li; Jaime I Davila; Saurabh Baheti; Chen Wang; Sabine Dietmann; Elizabeth J Atkinson; Yan W Asmann; Debra A Bell; Takayo Ota; Yaman Tarabishy; Rui Kuang; Marina Bibikova; R Keira Cheetham; Russell J Grocock; Elizabeth M Swisher; John Peden; David Bentley; Jean-Pierre A Kocher; Scott H Kaufmann; Lynn C Hartmann; Viji Shridhar; Ellen L Goode Journal: Nucleic Acids Res Date: 2015-04-27 Impact factor: 16.971
Authors: J Zachary Sanborn; Jongsuk Chung; Elizabeth Purdom; Nicholas J Wang; Hojabr Kakavand; James S Wilmott; Timothy Butler; John F Thompson; Graham J Mann; Lauren E Haydu; Robyn P M Saw; Klaus J Busam; Roger S Lo; Eric A Collisson; Joe S Hur; Paul T Spellman; James E Cleaver; Joe W Gray; Nam Huh; Rajmohan Murali; Richard A Scolyer; Boris C Bastian; Raymond J Cho Journal: Proc Natl Acad Sci U S A Date: 2015-08-18 Impact factor: 11.205