Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavare S, Deloukas P, Hurles ME, Dermitzakis ET: Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 2007, 315 (5813): 848-853. 10.1126/science.1136678.
Article
CAS
PubMed Central
PubMed
Google Scholar
Korbel JO, Tirosh-Wagner T, Urban AE, Chen XN, Kasowski M, Dai L, Grubert F, Erdman C, Gao MC, Lange K, Sobel EM, Barlow GM, Aylsworth AS, Carpenter NJ, Clark RD, Cohen MY, Doran E, Falik-Zaccai T, Lewin SO, Lott IT, McGillivray BC, Moeschler JB, Pettenati MJ, Pueschel SM, Rao KW, Shaffer LG, Shohat M, Van Riper AJ, Warburton D, Weissman S, et al: The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proc Natl Acad Sci U S A. 2009, 106 (29): 12031-12036. 10.1073/pnas.0813248106.
Article
CAS
PubMed Central
PubMed
Google Scholar
Zhang F, Gu W, Hurles ME, Lupski JR: Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet. 2009, 10: 451-481. 10.1146/annurev.genom.9.081307.164217.
Article
CAS
PubMed Central
PubMed
Google Scholar
Campbell PJ, Stephens PJ, Pleasance ED, O’Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, Teague JW, Menzies A, Goodhead I, Turner DJ, Clee CM, Quail MA, Cox A, Brown C, Durbin R, Hurles ME, Edwards PA, Bignell GR, Stratton MR, Futreal PA: Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet. 2008, 40 (6): 722-729. 10.1038/ng.128.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z: Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009, 25 (21): 2865-2871. 10.1093/bioinformatics/btp394.
Article
CAS
PubMed Central
PubMed
Google Scholar
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Genomes P, Eichler EE: Diversity of human copy number variation and multicopy genes. Science. 2010, 330 (6004): 641-646. 10.1126/science.1197005.
Article
CAS
PubMed Central
PubMed
Google Scholar
Rausch T, Zichner T, Schlattl A, Stutz AM, Benes V, Korbel JO: DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012, 28 (18): i333-i339. 10.1093/bioinformatics/bts378.
Article
CAS
PubMed Central
PubMed
Google Scholar
Wu J, Grzeda KR, Stewart C, Grubert F, Urban AE, Snyder MP, Marth GT: Copy Number Variation detection from 1000 Genomes project exon capture sequencing data. BMC Bioinformatics. 2012, 13 (1): 305-10.1186/1471-2105-13-305.
Article
CAS
PubMed Central
PubMed
Google Scholar
Handsaker RE, Korn JM, Nemesh J, McCarroll SA: Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat Genet. 2011, 43 (3): 269-276. 10.1038/ng.768.
Article
CAS
PubMed
Google Scholar
de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD: Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011, 7 (12): e1002384-10.1371/journal.pgen.1002384.
Article
CAS
PubMed Central
PubMed
Google Scholar
Deininger PL, Batzer MA, Hutchison CA, Edgell MH: Master genes in mammalian repetitive DNA amplification. Trends Genet. 1992, 8 (9): 307-311. 10.1016/0168-9525(92)90262-3.
Article
CAS
PubMed
Google Scholar
Cordaux R, Batzer MA: The impact of retrotransposons on human genome evolution. Nat Rev Genet. 2009, 10 (10): 691-703. 10.1038/nrg2640.
Article
CAS
PubMed Central
PubMed
Google Scholar
Konkel MK, Batzer MA: A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome. Semin Cancer Biol. 2010, 20 (4): 211-221. 10.1016/j.semcancer.2010.03.001.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kazazian HH, Wong C, Youssoufian H, Scott AF, Phillips DG, Antonarakis SE: Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature. 1988, 332 (6160): 164-166. 10.1038/332164a0.
Article
CAS
PubMed
Google Scholar
Kazazian HH: Mobile elements: drivers of genome evolution. Science. 2004, 303 (5664): 1626-1632. 10.1126/science.1089670.
Article
CAS
PubMed
Google Scholar
Pace JK, Feschotte C: The evolutionary history of human DNA transposons: evidence for intense activity in the primate lineage. Genome Res. 2007, 17 (4): 422-432. 10.1101/gr.5826307.
Article
CAS
PubMed Central
PubMed
Google Scholar
Xing J, Witherspoon DJ, Ray DA, Batzer MA, Jorde LB: Mobile DNA elements in primate and human evolution. Am J Phys Anthropol. 2007, 134 (Suppl 45): 2-19.
Article
Google Scholar
Belancio VP, Hedges DJ, Deininger P: Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. Genome Res. 2008, 18 (3): 343-358. 10.1101/gr.5558208.
Article
CAS
PubMed
Google Scholar
Wang H, Xing J, Grover D, Hedges DJ, Han K, Walker JA, Batzer MA: SVA elements: a hominid-specific retroposon family. J Mol Biol. 2005, 354 (4): 994-1007. 10.1016/j.jmb.2005.09.085.
Article
CAS
PubMed
Google Scholar
Mills RE, Bennett EA, Iskow RC, Luttig CT, Tsui C, Pittard WS, Devine SE: Recently mobilized transposons in the human and chimpanzee genomes. Am J Hum Genet. 2006, 78 (4): 671-679. 10.1086/501028.
Article
CAS
PubMed Central
PubMed
Google Scholar
Khan H, Smit A, Boissinot S: Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 2006, 16 (1): 78-87.
Article
CAS
PubMed Central
PubMed
Google Scholar
Britten RJ: Evidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago. Proc Natl Acad Sci U S A. 1994, 91 (13): 6148-6150. 10.1073/pnas.91.13.6148.
Article
CAS
PubMed Central
PubMed
Google Scholar
McCarroll SA, Huett A, Kuballa P, Chilewski SD, Landry A, Goyette P, Zody MC, Hall JL, Brant SR, Cho JH, Duerr RH, Silverberg MS, Taylor KD, Rioux JD, Altshuler D, Daly MJ, Xavier RJ: Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn’s disease. Nat Genet. 2008, 40 (9): 1107-1112. 10.1038/ng.215.
Article
CAS
PubMed Central
PubMed
Google Scholar
Miki Y, Katagiri T, Kasumi F, Yoshimoto T, Nakamura Y: Mutation analysis in the BRCA2 gene in primary breast cancers. Nat Genet. 1996, 13 (2): 245-247. 10.1038/ng0696-245.
Article
CAS
PubMed
Google Scholar
Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ, Cancer Genome Atlas Research N: Landscape of somatic retrotransposition in human cancers. Science. 2012, 337 (6097): 967-971. 10.1126/science.1222077.
Article
CAS
PubMed Central
PubMed
Google Scholar
Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA, Genomes Project C: A map of human genome variation from population-scale sequencing. Nature. 2010, 467 (7319): 1061-1073. 10.1038/nature09534.
Article
PubMed
Google Scholar
Stewart C, Kural D, Stromberg MP, Walker JA, Konkel MK, Stutz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO, Marth GT, Genomes P: A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet. 2011, 7 (8): e1002236-10.1371/journal.pgen.1002236.
Article
CAS
PubMed Central
PubMed
Google Scholar
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, et al: Mapping copy number variation by population-scale genome sequencing. Nature. 2011, 470 (7332): 59-65. 10.1038/nature09708.
Article
CAS
PubMed Central
PubMed
Google Scholar
Keane TM, Wong K, Adams DJ: RetroSeq: Transposable element discovery from Illumina paired-end sequencing data. Bioinformatics. 2012, 29 (3): 389-390.
Article
PubMed Central
PubMed
Google Scholar
Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler EE, Sahinalp SC: Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics. 2010, 26 (12): i350-i357. 10.1093/bioinformatics/btq216.
Article
CAS
PubMed Central
PubMed
Google Scholar
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, Genomes Project Analysis G: The variant call format and VCFtools. Bioinformatics. 2011, 27 (15): 2156-2158. 10.1093/bioinformatics/btr330.
Article
CAS
PubMed Central
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009, 25 (16): 2078-2079. 10.1093/bioinformatics/btp352.
Article
PubMed Central
PubMed
Google Scholar
Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT: MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One. 2014, 9 (3): e90581-10.1371/journal.pone.0090581.
Article
PubMed Central
PubMed
Google Scholar
Myers JS, Vincent BJ, Udall H, Watkins WS, Morrish TA, Kilroy GE, Swergold GD, Henke J, Henke L, Moran JV, Jorde LB, Batzer MA: A comprehensive analysis of recently integrated human Ta L1 elements. Am J Hum Genet. 2002, 71 (2): 312-326. 10.1086/341718.
Article
CAS
PubMed Central
PubMed
Google Scholar
Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA, Genomes Project C: An integrated map of genetic variation from 1,092 human genomes. Nature. 2012, 491 (7422): 56-65. 10.1038/nature11632.
Article
PubMed
Google Scholar
Le SQ, Durbin R: SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res. 2011, 21 (6): 952-960. 10.1101/gr.113084.110.
Article
CAS
PubMed Central
PubMed
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20 (9): 1297-1303. 10.1101/gr.107524.110.
Article
CAS
PubMed Central
PubMed
Google Scholar
Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, Zhou Q, Kirkness EF, Levy S, Batzer MA, Jorde LB: Mobile elements create structural variation: analysis of a complete human genome. Genome Res. 2009, 19 (9): 1516-1526. 10.1101/gr.091827.109.
Article
CAS
PubMed Central
PubMed
Google Scholar
Huang CR, Schneider AM, Lu Y, Niranjan T, Shen P, Robinson MA, Steranka JP, Valle D, Civin CI, Wang T, Wheelan SJ, Ji H, Boeke JD, Burns KH: Mobile interspersed repeats are major structural variants in the human genome. Cell. 2010, 141 (7): 1171-1182. 10.1016/j.cell.2010.05.026.
Article
CAS
PubMed Central
PubMed
Google Scholar
Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE: Natural mutagenesis of human genomes by endogenous retrotransposons. Cell. 2010, 141 (7): 1253-1261. 10.1016/j.cell.2010.05.020.
Article
CAS
PubMed Central
PubMed
Google Scholar
Witherspoon DJ, Xing J, Zhang Y, Watkins WS, Batzer MA, Jorde LB: Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. BMC Genomics. 2010, 11: 410-10.1186/1471-2164-11-410.
Article
PubMed Central
PubMed
Google Scholar
Beck CR, Garcia-Perez JL, Badge RM, Moran JV: LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet. 2011, 12: 187-215. 10.1146/annurev-genom-082509-141802.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ewing AD, Kazazian HH: Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans. Genome Res. 2011, 21 (6): 985-990. 10.1101/gr.114777.110.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, Malig M, Hach F, Yorukoglu D, Dao P, Bakhshi M, Sahinalp SC, Eichler EE: Alu repeat discovery and characterization within human genomes. Genome Res. 2011, 21 (6): 840-849. 10.1101/gr.115956.110.
Article
CAS
PubMed Central
PubMed
Google Scholar
Wang J, Song L, Grover D, Azrak S, Batzer MA, Liang P: dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. Hum Mutat. 2006, 27 (4): 323-329. 10.1002/humu.20307.
Article
PubMed Central
PubMed
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10 (3): R25-10.1186/gb-2009-10-3-r25.
Article
PubMed Central
PubMed
Google Scholar
Kohany O, Gentles AJ, Hankus L, Jurka J: Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics. 2006, 7: 474-10.1186/1471-2105-7-474.
Article
PubMed Central
PubMed
Google Scholar
Knuth DE: The Art of Computer Programming. 1968, Reading, Mass: Addison-Wesley Pub. Co
Google Scholar
Youssef S: Clustering with local equivalence relations. Comput Phys Commun. 1987, 45 (1–3): 423-426.
Article
CAS
Google Scholar
Bentley JL: Programming Pearls. 2000, Reading, Mass: Addison-Wesley, 2
Google Scholar
Smit AFA, Hubley R, Green P: RepeatMasker Open-3.0. 1996-2010. http://www.repeatmasker.org/,
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Res. 2002, 12 (6): 996-1006. 10.1101/gr.229102. Article published online before print in May 2002.
Article
CAS
PubMed Central
PubMed
Google Scholar
Holtgrewe M: Mason – a read simulator for second generation sequencing data. Technical Report TR-B-10-06. 2010
Google Scholar
Barnett DW, Garrison EK, Quinlan AR, Stromberg MP, Marth GT: BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics. 2011, 27 (12): 1691-1692. 10.1093/bioinformatics/btr174.
Article
CAS
PubMed Central
PubMed
Google Scholar
Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324.
Article
CAS
PubMed Central
PubMed
Google Scholar
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A: Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005, 15 (10): 1451-1455. 10.1101/gr.4086505.
Article
CAS
PubMed Central
PubMed
Google Scholar
Goecks J, Nekrutenko A, Taylor J, Galaxy T: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010, 11 (8): R86-10.1186/gb-2010-11-8-r86.
Article
PubMed Central
PubMed
Google Scholar
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J: Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010, Chapter 19: Unit 19 10 11-21-
Google Scholar
You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD: BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics. 2008, 9: 253-10.1186/1471-2105-9-253.
Article
PubMed Central
PubMed
Google Scholar
Kent WJ: BLAT–the BLAST-like alignment tool. Genome Res. 2002, 12 (4): 656-664. 10.1101/gr.229202. Article published online before March 2002.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999, 41: 95-98.
CAS
Google Scholar
Rozen S, Skaletsky H: Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 2000, 132: 365-386.
CAS
PubMed
Google Scholar