Anna Ritz1, Ali Bashir2, Suzanne Sindi1, David Hsu1, Iman Hajirasouliha1, Benjamin J Raphael2. 1. Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI. 2. Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI Department of Computer Science, Brown University, RI Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY School of Natural Sciences, University of California, Merced, CA Pacific Biosciences, Menlo Park, CA Center for Computational Molecular Biology, Brown University, RI.
Abstract
MOTIVATION: Structural variation is common in human and cancer genomes. High-throughput DNA sequencing has enabled genome-scale surveys of structural variation. However, the short reads produced by these technologies limit the study of complex variants, particularly those involving repetitive regions. Recent 'third-generation' sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates. RESULTS: We present MultiBreak-SV, an algorithm to detect structural variants (SVs) from single molecule sequencing data, paired read sequencing data, or a combination of sequencing data from different platforms. We demonstrate that combining low-coverage third-generation data from Pacific Biosciences (PacBio) with high-coverage paired read data is advantageous on simulated chromosomes. We apply MultiBreak-SV to PacBio data from four human fosmids and show that it detects known SVs with high sensitivity and specificity. Finally, we perform a whole-genome analysis on PacBio data from a complete hydatidiform mole cell line and predict 1002 high-probability SVs, over half of which are confirmed by an Illumina-based assembly.
MOTIVATION: Structural variation is common in human and cancer genomes. High-throughput DNA sequencing has enabled genome-scale surveys of structural variation. However, the short reads produced by these technologies limit the study of complex variants, particularly those involving repetitive regions. Recent 'third-generation' sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates. RESULTS: We present MultiBreak-SV, an algorithm to detect structural variants (SVs) from single molecule sequencing data, paired read sequencing data, or a combination of sequencing data from different platforms. We demonstrate that combining low-coverage third-generation data from Pacific Biosciences (PacBio) with high-coverage paired read data is advantageous on simulated chromosomes. We apply MultiBreak-SV to PacBio data from four human fosmids and show that it detects known SVs with high sensitivity and specificity. Finally, we perform a whole-genome analysis on PacBio data from a complete hydatidiform mole cell line and predict 1002 high-probability SVs, over half of which are confirmed by an Illumina-based assembly.
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Authors: Samuel Levy; Granger Sutton; Pauline C Ng; Lars Feuk; Aaron L Halpern; Brian P Walenz; Nelson Axelrod; Jiaqi Huang; Ewen F Kirkness; Gennady Denisov; Yuan Lin; Jeffrey R MacDonald; Andy Wing Chun Pang; Mary Shago; Timothy B Stockwell; Alexia Tsiamouri; Vineet Bafna; Vikas Bansal; Saul A Kravitz; Dana A Busam; Karen Y Beeson; Tina C McIntosh; Karin A Remington; Josep F Abril; John Gill; Jon Borman; Yu-Hui Rogers; Marvin E Frazier; Stephen W Scherer; Robert L Strausberg; J Craig Venter Journal: PLoS Biol Date: 2007-09-04 Impact factor: 8.029
Authors: Jeffrey M Kidd; Gregory M Cooper; William F Donahue; Hillary S Hayden; Nick Sampas; Tina Graves; Nancy Hansen; Brian Teague; Can Alkan; Francesca Antonacci; Eric Haugen; Troy Zerr; N Alice Yamada; Peter Tsang; Tera L Newman; Eray Tüzün; Ze Cheng; Heather M Ebling; Nadeem Tusneem; Robert David; Will Gillett; Karen A Phelps; Molly Weaver; David Saranga; Adrianne Brand; Wei Tao; Erik Gustafson; Kevin McKernan; Lin Chen; Maika Malig; Joshua D Smith; Joshua M Korn; Steven A McCarroll; David A Altshuler; Daniel A Peiffer; Michael Dorschner; John Stamatoyannopoulos; David Schwartz; Deborah A Nickerson; James C Mullikin; Richard K Wilson; Laurakay Bruhn; Maynard V Olson; Rajinder Kaul; Douglas R Smith; Evan E Eichler Journal: Nature Date: 2008-05-01 Impact factor: 49.962