Pennisi E: Breakthrough of the year. Human genetic variation. Science. 2007, 318: 1842-1843. 10.1126/science.318.5858.1842.
Article
PubMed
CAS
Google Scholar
Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet. 2006, 7: 85-97. 10.1038/nrg1767.
Article
PubMed
CAS
Google Scholar
Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, et al: Global variation in copy number in the human genome. Nature. 2006, 444: 444-454. 10.1038/nature05329.
Article
PubMed
CAS
PubMed Central
Google Scholar
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: 848-853. 10.1126/science.1136678.
Article
PubMed
CAS
PubMed Central
Google Scholar
Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC: Diet and the evolution of human amylase gene copy number variation. Nat Genet. 2007, 39: 1256-1260. 10.1038/ng2123.
Article
PubMed
CAS
PubMed Central
Google Scholar
Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, Nibbs RJ, Freedman BI, Quinones MP, Bamshad MJ, Murthy KK, Rovin BH, Bradley W, Clark RA, Anderson SA, O'Connell RJ, Agan BK, Ahuja SS, Bologna R, Sen L, Dolan MJ, Ahuja SK: The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science. 2005, 307: 1434-1440. 10.1126/science.1101160.
Article
PubMed
CAS
Google Scholar
Aitman TJ, Dong R, Vyse TJ, Norsworthy PJ, Johnson MD, Smith J, Mangion J, Roberton-Lowe C, Marshall AJ, Petretto E, Hodges MD, Bhangal G, Patel SG, Sheehan-Rooney K, Duda M, Cook PR, Evans DJ, Domin J, Flint J, Boyle JJ, Pusey CD, Cook HT: Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature. 2006, 439: 851-855. 10.1038/nature04489.
Article
PubMed
CAS
Google Scholar
Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee YH, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimaki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra V, Chung W, Warburton D, King MC, Skuse D, Geschwind DH, Gilliam TC, et al: Strong association of de novo copy number mutations with autism. Science. 2007, 316: 445-449. 10.1126/science.1138659.
Article
PubMed
CAS
PubMed Central
Google Scholar
Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, Nord AS, Kusenda M, Malhotra D, Bhandari A, Stray SM, Rippey CF, Roccanova P, Makarov V, Lakshmi B, Findling RL, Sikich L, Stromberg T, Merriman B, Gogtay N, Butler P, Eckstrand K, Noory L, Gochman P, Long R, Chen Z, Davis S, Baker C, Eichler EE, Meltzer PS, et al: Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science. 2008, 320: 539-543. 10.1126/science.1155174.
Article
PubMed
CAS
Google Scholar
McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ, Altshuler DM: Common deletion polymorphisms in the human genome. Nat Genet. 2006, 38: 86-92. 10.1038/ng1696.
Article
PubMed
CAS
Google Scholar
Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK: A high-resolution survey of deletion polymorphism in the human genome. Nat Genet. 2006, 38: 75-81. 10.1038/ng1697.
Article
PubMed
CAS
Google Scholar
Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA: Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet. 2006, 38: 82-85. 10.1038/ng1695.
Article
PubMed
CAS
Google Scholar
Urban AE, Korbel JO, Selzer R, Richmond T, Hacker A, Popescu GV, Cubells JF, Green R, Emanuel BS, Gerstein MB, Weissman SM, Snyder M: High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci USA. 2006, 103: 4534-4539. 10.1073/pnas.0511340103.
Article
PubMed
CAS
PubMed Central
Google Scholar
Korbel JO, Urban AE, Grubert F, Du J, Royce TE, Starr P, Zhong G, Emanuel BS, Weissman SM, Snyder M, Gerstein MB: Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc Natl Acad Sci USA. 2007, 104: 10110-10115. 10.1073/pnas.0703834104.
Article
PubMed
CAS
PubMed Central
Google Scholar
Perry GH, Ben-Dor A, Tsalenko A, Sampras N, Rodriguez-Revenga L, Tran CW, Scheffer A, Steinfeld I, Tsang P, Yamada NA, Park HS, Kim JI, Seo JS, Yakhini Z, Laderman S, Bruhn L, Lee C: The fine-scale and complex architecture of human copy-number variation. Am J Hum Genet. 2008, 82: 685-695. 10.1016/j.ajhg.2007.12.010.
Article
PubMed
CAS
PubMed Central
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: 722-729. 10.1038/ng.128.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE: An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 2006, 16: 1182-1190. 10.1101/gr.4565806.
Article
PubMed
CAS
PubMed Central
Google Scholar
Khaja R, Zhang J, MacDonald JR, He Y, Joseph-George AM, Wei J, Rafiq MA, Qian C, Shago M, Pantano L, Aburatani H, Jones K, Redon R, Hurles M, Armengol L, Estivill X, Mural RJ, Lee C, Scherer SW, Feuk L: Genome assembly comparison identifies structural variants in the human genome. Nat Genet. 2006, 38: 1413-1418. 10.1038/ng1921.
Article
PubMed
CAS
PubMed Central
Google Scholar
Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, et al: The diploid genome sequence of an individual human. PLoS Biol. 2007, 5: e254-10.1371/journal.pbio.0050254.
Article
PubMed
PubMed Central
Google Scholar
Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM: The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008, 452: 872-876. 10.1038/nature06884.
Article
PubMed
CAS
Google Scholar
Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M: Paired-end mapping reveals extensive structural variation in the human genome. Science. 2007, 318: 420-426. 10.1126/science.1149504.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tuzun E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, et al: Mapping and sequencing of structural variation from eight human genomes. Nature. 2008, 453: 56-64. 10.1038/nature06862.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chen J, Kim YC, Jung YC, Xuan Z, Dworkin G, Zhang Y, Zhang MQ, Wang SM: Scanning the human genome at kilobase resolution. Genome Res. 2008, 18: 751-762. 10.1101/gr.068304.107.
Article
PubMed
CAS
PubMed Central
Google Scholar
Raphael BJ, Volik S, Yu P, Wu C, Huang G, Linardopoulou EV, Trask BJ, Waldman F, Costello J, Pienta KJ, Mills GB, Bajsarowicz K, Kobayashi Y, Sridharan S, Paris PL, Tao Q, Aerni SJ, Brown RP, Bashir A, Gray JW, Cheng JF, de Jong P, Nefedov M, Ried T, Padilla-Nash HM, Collins CC: A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol. 2008, 9: R59-10.1186/gb-2008-9-3-r59.
Article
PubMed
PubMed Central
Google Scholar
Bignell GR, Santarius T, Pole JC, Butler AP, Perry J, Pleasance E, Greenman C, Menzies A, Taylor S, Edkins S, Campbell P, Quail M, Plumb B, Matthews L, McLay K, Edwards PA, Rogers J, Wooster R, Futreal PA, Stratton MR: Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res. 2007, 17: 1296-1303. 10.1101/gr.6522707.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bentley D, Balasubramanian S, Swerdlow H, Smith G, Milton J, Brown C, Hall K, Evers D, Barnes C, Bignell H, Boutell J, Bryant J, Carter R: Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008, 456: 53-59. 10.1038/nature07517.
Article
PubMed
CAS
PubMed Central
Google Scholar
PEMer Package. [http://sv.gersteinlab.org/pemer]
Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008, 18: 1851-1858. 10.1101/gr.078212.108.
Article
PubMed
CAS
PubMed Central
Google Scholar
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB: PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 2009, 27: 66-75. 10.1038/nbt.1518.
Article
PubMed
CAS
PubMed Central
Google Scholar
Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE: Fine-scale structural variation of the human genome. Nat Genet. 2005, 37: 727-732. 10.1038/ng1562.
Article
PubMed
CAS
Google Scholar
Pop M, Salzberg SL: Bioinformatics challenges of new sequencing technology. Trends Genet. 2008, 24: 142-149.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zhang Z, Schwartz S, Wagner L, Miller W: A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000, 7: 203-214. 10.1089/10665270050081478.
Article
PubMed
CAS
Google Scholar
Kent WJ: BLAT - the BLAST-like alignment tool. Genome Res. 2002, 12: 656-664.
Article
PubMed
CAS
PubMed Central
Google Scholar
Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C: Detection of large-scale variation in the human genome. Nat Genet. 2004, 36: 949-951. 10.1038/ng1416.
Article
PubMed
CAS
Google Scholar
Mills RE, Bennett EA, Iskow RC, Devine SE: Which transposable elements are active in the human genome?. Trends Genet. 2007, 23: 183-191. 10.1016/j.tig.2007.02.006.
Article
PubMed
CAS
Google Scholar
Chiu KP, Wong CH, Chen Q, Ariyaratne P, Ooi HS, Wei CL, Sung WK, Ruan Y: PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data. BMC Bioinformatics. 2006, 7: 390-10.1186/1471-2105-7-390.
Article
PubMed
PubMed Central
Google Scholar
Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P, Bin WG, Kuznetsov VA, Shahab A, Sung WK, Bourque G, Palanisamy N, Wei CL: Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res. 2007, 17: 828-838. 10.1101/gr.6018607.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bashir A, Volik S, Collins C, Bafna V, Raphael BJ: Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol. 2008, 4: e1000051-10.1371/journal.pcbi.1000051.
Article
PubMed
PubMed Central
Google Scholar
al EPCe: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007, 447: 799-816. 10.1038/nature05874.
Article
Google Scholar
Lee S, Cheran E, Brudno M: A robust framework for detecting structural variations in a genome. Bioinformatics. 2008, 24: i59-67. 10.1093/bioinformatics/btn176.
Article
PubMed
CAS
PubMed Central
Google Scholar
Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol. 1981, 147: 195-197. 10.1016/0022-2836(81)90087-5.
Article
PubMed
CAS
Google Scholar
Consortium TIH, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, et al: A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007, 449: 851-861. 10.1038/nature06258.
Article
Google Scholar
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al: Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005, 437: 376-380.
PubMed
CAS
PubMed Central
Google Scholar
Dohm JC, Lottaz C, Borodina T, Himmelbauer H: Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucl Acids Res. 2008, 36: e105-10.1093/nar/gkn425.
Article
PubMed
PubMed Central
Google Scholar
Lander ES, Waterman MS: Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics. 1988, 2: 231-239. 10.1016/0888-7543(88)90007-9.
Article
PubMed
CAS
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.
Article
PubMed
CAS
Google Scholar
1000 Genomes Project. [http://1000genomes.org]