AIMS: Next-generation sequencing is being implemented in the clinical laboratory environment for the purposes of candidate causal variant discovery in patients affected with a variety of genetic disorders. The successful implementation of this technology for diagnosing genetic disorders requires a rapid, user-friendly method to annotate variants and generate short lists of clinically relevant variants of interest. This report describes Omicia's Opal platform, a new software tool designed for variant discovery and interpretation in a clinical laboratory environment. The software allows clinical scientists to process, analyze, interpret and report on personal genome files. MATERIALS & METHODS: To demonstrate the software, the authors describe the interactive use of the system for the rapid discovery of disease-causing variants using three cases. RESULTS & CONCLUSION: Here, the authors show the features of the Opal system and their use in uncovering variants of clinical significance.
AIMS: Next-generation sequencing is being implemented in the clinical laboratory environment for the purposes of candidate causal variant discovery in patients affected with a variety of genetic disorders. The successful implementation of this technology for diagnosing genetic disorders requires a rapid, user-friendly method to annotate variants and generate short lists of clinically relevant variants of interest. This report describes Omicia's Opal platform, a new software tool designed for variant discovery and interpretation in a clinical laboratory environment. The software allows clinical scientists to process, analyze, interpret and report on personal genome files. MATERIALS & METHODS: To demonstrate the software, the authors describe the interactive use of the system for the rapid discovery of disease-causing variants using three cases. RESULTS & CONCLUSION: Here, the authors show the features of the Opal system and their use in uncovering variants of clinical significance.
Authors: Mark Yandell; Chad Huff; Hao Hu; Marc Singleton; Barry Moore; Jinchuan Xing; Lynn B Jorde; Martin G Reese Journal: Genome Res Date: 2011-06-23 Impact factor: 9.043
Authors: Matthew N Bainbridge; Wojciech Wiszniewski; David R Murdock; Jennifer Friedman; Claudia Gonzaga-Jauregui; Irene Newsham; Jeffrey G Reid; John K Fink; Margaret B Morgan; Marie-Claude Gingras; Donna M Muzny; Linh D Hoang; Shahed Yousaf; James R Lupski; Richard A Gibbs Journal: Sci Transl Med Date: 2011-06-15 Impact factor: 17.956
Authors: Alan F Rope; Kai Wang; Rune Evjenth; Jinchuan Xing; Jennifer J Johnston; Jeffrey J Swensen; W Evan Johnson; Barry Moore; Chad D Huff; Lynne M Bird; John C Carey; John M Opitz; Cathy A Stevens; Tao Jiang; Christa Schank; Heidi Deborah Fain; Reid Robison; Brian Dalley; Steven Chin; Sarah T South; Theodore J Pysher; Lynn B Jorde; Hakon Hakonarson; Johan R Lillehaug; Leslie G Biesecker; Mark Yandell; Thomas Arnesen; Gholson J Lyon Journal: Am J Hum Genet Date: 2011-06-23 Impact factor: 11.025
Authors: Elizabeth A Worthey; Alan N Mayer; Grant D Syverson; Daniel Helbling; Benedetta B Bonacci; Brennan Decker; Jaime M Serpe; Trivikram Dasu; Michael R Tschannen; Regan L Veith; Monica J Basehore; Ulrich Broeckel; Aoy Tomita-Mitchell; Marjorie J Arca; James T Casper; David A Margolis; David P Bick; Martin J Hessner; John M Routes; James W Verbsky; Howard J Jacob; David P Dimmock Journal: Genet Med Date: 2011-03 Impact factor: 8.822
Authors: Mark A DePristo; Eric Banks; Ryan Poplin; Kiran V Garimella; Jared R Maguire; Christopher Hartl; Anthony A Philippakis; Guillermo del Angel; Manuel A Rivas; Matt Hanna; Aaron McKenna; Tim J Fennell; Andrew M Kernytsky; Andrey Y Sivachenko; Kristian Cibulskis; Stacey B Gabriel; David Altshuler; Mark J Daly Journal: Nat Genet Date: 2011-04-10 Impact factor: 38.330
Authors: Ruth L Seal; Susan M Gordon; Michael J Lush; Mathew W Wright; Elspeth A Bruford Journal: Nucleic Acids Res Date: 2010-10-06 Impact factor: 16.971
Authors: Petr Danecek; Adam Auton; Goncalo Abecasis; Cornelis A Albers; Eric Banks; Mark A DePristo; Robert E Handsaker; Gerton Lunter; Gabor T Marth; Stephen T Sherry; Gilean McVean; Richard Durbin Journal: Bioinformatics Date: 2011-06-07 Impact factor: 6.937
Authors: Paul Flicek; Ikhlak Ahmed; M Ridwan Amode; Daniel Barrell; Kathryn Beal; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Laurent Gil; Carlos García-Girón; Leo Gordon; Thibaut Hourlier; Sarah Hunt; Thomas Juettemann; Andreas K Kähäri; Stephen Keenan; Monika Komorowska; Eugene Kulesha; Ian Longden; Thomas Maurel; William M McLaren; Matthieu Muffato; Rishi Nag; Bert Overduin; Miguel Pignatelli; Bethan Pritchard; Emily Pritchard; Harpreet Singh Riat; Graham R S Ritchie; Magali Ruffier; Michael Schuster; Daniel Sheppard; Daniel Sobral; Kieron Taylor; Anja Thormann; Stephen Trevanion; Simon White; Steven P Wilder; Bronwen L Aken; Ewan Birney; Fiona Cunningham; Ian Dunham; Jennifer Harrow; Javier Herrero; Tim J P Hubbard; Nathan Johnson; Rhoda Kinsella; Anne Parker; Giulietta Spudich; Andy Yates; Amonida Zadissa; Stephen M J Searle Journal: Nucleic Acids Res Date: 2012-11-30 Impact factor: 16.971
Authors: Brett Kennedy; Zev Kronenberg; Hao Hu; Barry Moore; Steven Flygare; Martin G Reese; Lynn B Jorde; Mark Yandell; Chad Huff Journal: Curr Protoc Hum Genet Date: 2014-04-24
Authors: Jirair K Bedoyan; Samuel P Yang; Sacha Ferdinandusse; Rhona M Jack; Alexander Miron; George Grahame; Suzanne D DeBrosse; Charles L Hoppel; Douglas S Kerr; Ronald J A Wanders Journal: Mol Genet Metab Date: 2017-02-02 Impact factor: 4.797
Authors: Xiaoping Huang; Jirair K Bedoyan; Didem Demirbas; David J Harris; Alexander Miron; Simone Edelheit; George Grahame; Suzanne D DeBrosse; Lee-Jun Wong; Charles L Hoppel; Douglas S Kerr; Irina Anselm; Gerard T Berry Journal: Mol Genet Metab Date: 2016-11-12 Impact factor: 4.797
Authors: Bushra Gorsi; Edgar Hernandez; Marvin Barry Moore; Mika Moriwaki; Clement Y Chow; Emily Coelho; Elaine Taylor; Claire Lu; Amanda Walker; Philippe Touraine; Lawrence M Nelson; Amber R Cooper; Elaine R Mardis; Aleksander Rajkovic; Mark Yandell; Corrine K Welt Journal: J Clin Endocrinol Metab Date: 2022-02-17 Impact factor: 5.958
Authors: Abdulmoein Eid Al-Agha; Ihab Abdulhamed Ahmed; Esther Nuebel; Mika Moriwaki; Barry Moore; Katherine A Peacock; Tim Mosbruger; Deborah W Neklason; Lynn B Jorde; Mark Yandell; Corrine K Welt Journal: J Clin Endocrinol Metab Date: 2018-02-01 Impact factor: 5.958
Authors: Michelle M Clark; Amber Hildreth; Sergey Batalov; Yan Ding; Shimul Chowdhury; Kelly Watkins; Katarzyna Ellsworth; Brandon Camp; Cyrielle I Kint; Calum Yacoubian; Lauge Farnaes; Matthew N Bainbridge; Curtis Beebe; Joshua J A Braun; Margaret Bray; Jeanne Carroll; Julie A Cakici; Sara A Caylor; Christina Clarke; Mitchell P Creed; Jennifer Friedman; Alison Frith; Richard Gain; Mary Gaughran; Shauna George; Sheldon Gilmer; Joseph Gleeson; Jeremy Gore; Haiying Grunenwald; Raymond L Hovey; Marie L Janes; Kejia Lin; Paul D McDonagh; Kyle McBride; Patrick Mulrooney; Shareef Nahas; Daeheon Oh; Albert Oriol; Laura Puckett; Zia Rady; Martin G Reese; Julie Ryu; Lisa Salz; Erica Sanford; Lawrence Stewart; Nathaly Sweeney; Mari Tokita; Luca Van Der Kraan; Sarah White; Kristen Wigby; Brett Williams; Terence Wong; Meredith S Wright; Catherine Yamada; Peter Schols; John Reynders; Kevin Hall; David Dimmock; Narayanan Veeraraghavan; Thomas Defay; Stephen F Kingsmore Journal: Sci Transl Med Date: 2019-04-24 Impact factor: 19.319
Authors: Catherine A Brownstein; Alan H Beggs; Nils Homer; Barry Merriman; Timothy W Yu; Katherine C Flannery; Elizabeth T DeChene; Meghan C Towne; Sarah K Savage; Emily N Price; Ingrid A Holm; Lovelace J Luquette; Elaine Lyon; Joseph Majzoub; Peter Neupert; David McCallie; Peter Szolovits; Huntington F Willard; Nancy J Mendelsohn; Renee Temme; Richard S Finkel; Sabrina W Yum; Livija Medne; Shamil R Sunyaev; Ivan Adzhubey; Christopher A Cassa; Paul I W de Bakker; Hatice Duzkale; Piotr Dworzyński; William Fairbrother; Laurent Francioli; Birgit H Funke; Monica A Giovanni; Robert E Handsaker; Kasper Lage; Matthew S Lebo; Monkol Lek; Ignaty Leshchiner; Daniel G MacArthur; Heather M McLaughlin; Michael F Murray; Tune H Pers; Paz P Polak; Soumya Raychaudhuri; Heidi L Rehm; Rachel Soemedi; Nathan O Stitziel; Sara Vestecka; Jochen Supper; Claudia Gugenmus; Bernward Klocke; Alexander Hahn; Max Schubach; Mortiz Menzel; Saskia Biskup; Peter Freisinger; Mario Deng; Martin Braun; Sven Perner; Richard J H Smith; Janeen L Andorf; Jian Huang; Kelli Ryckman; Val C Sheffield; Edwin M Stone; Thomas Bair; E Ann Black-Ziegelbein; Terry A Braun; Benjamin Darbro; Adam P DeLuca; Diana L Kolbe; Todd E Scheetz; Aiden E Shearer; Rama Sompallae; Kai Wang; Alexander G Bassuk; Erik Edens; Katherine Mathews; Steven A Moore; Oleg A Shchelochkov; Pamela Trapane; Aaron Bossler; Colleen A Campbell; Jonathan W Heusel; Anne Kwitek; Tara Maga; Karin Panzer; Thomas Wassink; Douglas Van Daele; Hela Azaiez; Kevin Booth; Nic Meyer; Michael M Segal; Marc S Williams; Gerard Tromp; Peter White; Donald Corsmeier; Sara Fitzgerald-Butt; Gail Herman; Devon Lamb-Thrush; Kim L McBride; David Newsom; Christopher R Pierson; Alexander T Rakowsky; Aleš Maver; Luca Lovrečić; Anja Palandačić; Borut Peterlin; Ali Torkamani; Anna Wedell; Mikael Huss; Andrey Alexeyenko; Jessica M Lindvall; Måns Magnusson; Daniel Nilsson; Henrik Stranneheim; Fulya Taylan; Christian Gilissen; Alexander Hoischen; Bregje van Bon; Helger Yntema; Marcel Nelen; Weidong Zhang; Jason Sager; Lu Zhang; Kathryn Blair; Deniz Kural; Michael Cariaso; Greg G Lennon; Asif Javed; Saloni Agrawal; Pauline C Ng; Komal S Sandhu; Shuba Krishna; Vamsi Veeramachaneni; Ofer Isakov; Eran Halperin; Eitan Friedman; Noam Shomron; Gustavo Glusman; Jared C Roach; Juan Caballero; Hannah C Cox; Denise Mauldin; Seth A Ament; Lee Rowen; Daniel R Richards; F Anthony San Lucas; Manuel L Gonzalez-Garay; C Thomas Caskey; Yu Bai; Ying Huang; Fang Fang; Yan Zhang; Zhengyuan Wang; Jorge Barrera; Juan M Garcia-Lobo; Domingo González-Lamuño; Javier Llorca; Maria C Rodriguez; Ignacio Varela; Martin G Reese; Francisco M De La Vega; Edward Kiruluta; Michele Cargill; Reece K Hart; Jon M Sorenson; Gholson J Lyon; David A Stevenson; Bruce E Bray; Barry M Moore; Karen Eilbeck; Mark Yandell; Hongyu Zhao; Lin Hou; Xiaowei Chen; Xiting Yan; Mengjie Chen; Cong Li; Can Yang; Murat Gunel; Peining Li; Yong Kong; Austin C Alexander; Zayed I Albertyn; Kym M Boycott; Dennis E Bulman; Paul M K Gordon; A Micheil Innes; Bartha M Knoppers; Jacek Majewski; Christian R Marshall; Jillian S Parboosingh; Sarah L Sawyer; Mark E Samuels; Jeremy Schwartzentruber; Isaac S Kohane; David M Margulies Journal: Genome Biol Date: 2014-03-25 Impact factor: 13.583
Authors: Lauge Farnaes; Shareef A Nahas; Shimul Chowdhury; James Nelson; Serge Batalov; David M Dimmock; Stephen F Kingsmore Journal: Cold Spring Harb Mol Case Stud Date: 2017-09-01