BACKGROUND: Next-generation sequencing produces high-throughput data, albeit with greater error and shorter reads than traditional Sanger sequencing methods. This complicates the detection of genomic variations, especially, small insertions and deletions. FINDINGS: Here we describe ParMap, a statistical algorithm for the identification of complex genetic variants, such as small insertion and deletions, using partially mapped reads in nextgen sequencing data. CONCLUSIONS: We report ParMap's successful application to the mutation analysis of chromosome X exome-captured leukemia DNA samples.
BACKGROUND: Next-generation sequencing produces high-throughput data, albeit with greater error and shorter reads than traditional Sanger sequencing methods. This complicates the detection of genomic variations, especially, small insertions and deletions. FINDINGS: Here we describe ParMap, a statistical algorithm for the identification of complex genetic variants, such as small insertion and deletions, using partially mapped reads in nextgen sequencing data. CONCLUSIONS: We report ParMap's successful application to the mutation analysis of chromosome X exome-captured leukemia DNA samples.
Authors: Kevin Judd McKernan; Heather E Peckham; Gina L Costa; Stephen F McLaughlin; Yutao Fu; Eric F Tsung; Christopher R Clouser; Cisyla Duncan; Jeffrey K Ichikawa; Clarence C Lee; Zheng Zhang; Swati S Ranade; Eileen T Dimalanta; Fiona C Hyland; Tanya D Sokolsky; Lei Zhang; Andrew Sheridan; Haoning Fu; Cynthia L Hendrickson; Bin Li; Lev Kotler; Jeremy R Stuart; Joel A Malek; Jonathan M Manning; Alena A Antipova; Damon S Perez; Michael P Moore; Kathleen C Hayashibara; Michael R Lyons; Robert E Beaudoin; Brittany E Coleman; Michael W Laptewicz; Adam E Sannicandro; Michael D Rhodes; Rajesh K Gottimukkala; Shan Yang; Vineet Bafna; Ali Bashir; Andrew MacBride; Can Alkan; Jeffrey M Kidd; Evan E Eichler; Martin G Reese; Francisco M De La Vega; Alan P Blanchard Journal: Genome Res Date: 2009-06-22 Impact factor: 9.043
Authors: Pieter Van Vlierberghe; Teresa Palomero; Hossein Khiabanian; Joni Van der Meulen; Mireia Castillo; Nadine Van Roy; Barbara De Moerloose; Jan Philippé; Sara González-García; María L Toribio; Tom Taghon; Linda Zuurbier; Barbara Cauwelier; Christine J Harrison; Claire Schwab; Markus Pisecker; Sabine Strehl; Anton W Langerak; Jozef Gecz; Edwin Sonneveld; Rob Pieters; Elisabeth Paietta; Jacob M Rowe; Peter H Wiernik; Yves Benoit; Jean Soulier; Bruce Poppe; Xiaopan Yao; Carlos Cordon-Cardo; Jules Meijerink; Raul Rabadan; Frank Speleman; Adolfo Ferrando Journal: Nat Genet Date: 2010-03-14 Impact factor: 38.330
Authors: Andreas Gnirke; Alexandre Melnikov; Jared Maguire; Peter Rogov; Emily M LeProust; William Brockman; Timothy Fennell; Georgia Giannoukos; Sheila Fisher; Carsten Russ; Stacey Gabriel; David B Jaffe; Eric S Lander; Chad Nusbaum Journal: Nat Biotechnol Date: 2009-02-01 Impact factor: 54.908
Authors: Stephen M Rumble; Phil Lacroute; Adrian V Dalca; Marc Fiume; Arend Sidow; Michael Brudno Journal: PLoS Comput Biol Date: 2009-05-22 Impact factor: 4.475
Authors: R M Kuhn; D Karolchik; A S Zweig; T Wang; K E Smith; K R Rosenbloom; B Rhead; B J Raney; A Pohl; M Pheasant; L Meyer; F Hsu; A S Hinrichs; R A Harte; B Giardine; P Fujita; M Diekhans; T Dreszer; H Clawson; G P Barber; D Haussler; W J Kent Journal: Nucleic Acids Res Date: 2008-11-07 Impact factor: 16.971
Authors: Pieter Van Vlierberghe; Teresa Palomero; Hossein Khiabanian; Joni Van der Meulen; Mireia Castillo; Nadine Van Roy; Barbara De Moerloose; Jan Philippé; Sara González-García; María L Toribio; Tom Taghon; Linda Zuurbier; Barbara Cauwelier; Christine J Harrison; Claire Schwab; Markus Pisecker; Sabine Strehl; Anton W Langerak; Jozef Gecz; Edwin Sonneveld; Rob Pieters; Elisabeth Paietta; Jacob M Rowe; Peter H Wiernik; Yves Benoit; Jean Soulier; Bruce Poppe; Xiaopan Yao; Carlos Cordon-Cardo; Jules Meijerink; Raul Rabadan; Frank Speleman; Adolfo Ferrando Journal: Nat Genet Date: 2010-03-14 Impact factor: 38.330