MOTIVATION: In the past few years, human genome structural variation discovery has enjoyed increased attention from the genomics research community. Many studies were published to characterize short insertions, deletions, duplications and inversions, and associate copy number variants (CNVs) with disease. Detection of new sequence insertions requires sequence data, however, the 'detectable' sequence length with read-pair analysis is limited by the insert size. Thus, longer sequence insertions that contribute to our genetic makeup are not extensively researched. RESULTS: We present NovelSeq: a computational framework to discover the content and location of long novel sequence insertions using paired-end sequencing data generated by the next-generation sequencing platforms. Our framework can be built as part of a general sequence analysis pipeline to discover multiple types of genetic variation (SNPs, structural variation, etc.), thus it requires significantly less-computational resources than de novo sequence assembly. We apply our methods to detect novel sequence insertions in the genome of an anonymous donor and validate our results by comparing with the insertions discovered in the same genome using various sources of sequence data. AVAILABILITY: The implementation of the NovelSeq pipeline is available at http://compbio.cs.sfu.ca/strvar.htm CONTACT: eee@gs.washington.edu; cenk@cs.sfu.ca
MOTIVATION: In the past few years, human genome structural variation discovery has enjoyed increased attention from the genomics research community. Many studies were published to characterize short insertions, deletions, duplications and inversions, and associate copy number variants (CNVs) with disease. Detection of new sequence insertions requires sequence data, however, the 'detectable' sequence length with read-pair analysis is limited by the insert size. Thus, longer sequence insertions that contribute to our genetic makeup are not extensively researched. RESULTS: We present NovelSeq: a computational framework to discover the content and location of long novel sequence insertions using paired-end sequencing data generated by the next-generation sequencing platforms. Our framework can be built as part of a general sequence analysis pipeline to discover multiple types of genetic variation (SNPs, structural variation, etc.), thus it requires significantly less-computational resources than de novo sequence assembly. We apply our methods to detect novel sequence insertions in the genome of an anonymous donor and validate our results by comparing with the insertions discovered in the same genome using various sources of sequence data. AVAILABILITY: The implementation of the NovelSeq pipeline is available at http://compbio.cs.sfu.ca/strvar.htm CONTACT: eee@gs.washington.edu; cenk@cs.sfu.ca
Authors: Eray Tuzun; Andrew J Sharp; Jeffrey A Bailey; Rajinder Kaul; V Anne Morrison; Lisa M Pertz; Eric Haugen; Hillary Hayden; Donna Albertson; Daniel Pinkel; Maynard V Olson; Evan E Eichler Journal: Nat Genet Date: 2005-05-15 Impact factor: 38.330
Authors: Jared T Simpson; Kim Wong; Shaun D Jackman; Jacqueline E Schein; Steven J M Jones; Inanç Birol Journal: Genome Res Date: 2009-02-27 Impact factor: 9.043
Authors: Jeffrey M Kidd; Nick Sampas; Francesca Antonacci; Tina Graves; Robert Fulton; Hillary S Hayden; Can Alkan; Maika Malig; Mario Ventura; Giuliana Giannuzzi; Joelle Kallicki; Paige Anderson; Anya Tsalenko; N Alice Yamada; Peter Tsang; Rajinder Kaul; Richard K Wilson; Laurakay Bruhn; Evan E Eichler Journal: Nat Methods Date: 2010-05 Impact factor: 28.547
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: Can Alkan; Jeffrey M Kidd; Tomas Marques-Bonet; Gozde Aksay; Francesca Antonacci; Fereydoun Hormozdiari; Jacob O Kitzman; Carl Baker; Maika Malig; Onur Mutlu; S Cenk Sahinalp; Richard A Gibbs; Evan E Eichler Journal: Nat Genet Date: 2009-08-30 Impact factor: 38.330
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
Authors: Fereydoun Hormozdiari; Iman Hajirasouliha; Andrew McPherson; Evan E Eichler; S Cenk Sahinalp Journal: Genome Res Date: 2011-11-02 Impact factor: 9.043