PEMer: A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

Genome Biology

Volumn 10, Issue 2, 2009, Pages

  Korbel, Jan O ^a,b,c   Abyzov, Alexej ^c   Mu, Xinmeng Jasmine ^c   Carriero, Nicholas ^d   Cayting, Philip ^c   Zhang, Zhengdong ^c   Snyder, Michael ^c   Gerstein, Mark B ^c,d  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^c YALE UNIVERSITY   (United States)

^d Yale University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; CONTROLLED STUDY; GENE MAPPING; GENE STRUCTURE; GENETIC VARIABILITY; GENOMIC FRAGMENT; INTERNET; MATHEMATICAL COMPUTING; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SEQUENCE DATABASE; BIOLOGICAL MODEL; BIOLOGY; GENOME; GENOMICS; METHODOLOGY; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENOME; GENOMIC STRUCTURAL VARIATION; GENOMICS; INTERNET; MODELS, GENETIC; SOFTWARE;

EID: 62549131646     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2009-10-2-r23     Document Type: Article

References (47)

1. Pennisi E Breakthrough of the year. Human genetic variation. Science 2007, 318:1842-1843. 10.1126/science.318.5858.1842 18096770
2. Feuk L Carson AR Scherer SW Structural variation in the human genome. Nat Rev Genet 2006, 7:85-97. 10.1038/nrg1767 16418744
3. 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 17122850
4. 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 17289997
5. 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. 2377015 17828263 10.1038/ng2123
6. 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 15637236
7. 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 16482158
8. 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 17363630
9. 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 18369103
10. 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 16468122
11. 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 16327808
12. 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 16327809
13. 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. 1450206 16537408 10.1073/pnas.0511340103
14. 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. 1891248 17551006 10.1073/ pnas.0703834104
15. 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 18304495
16. 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 18438408
17. 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. 1557762 16902084 10.1101/ gr.4565806
18. 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 17115057
19. 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. 1964779 17803354 10.1371/journal.pbio.0050254
20. 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 18421352
21. 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 17901297
22. 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. 2424287 18451855 10.1038/nature06862
23. 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. 2336809 18292219 10.1101/gr.068304.107
24. 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. 2397511 18364049 10.1186/gb-2008-9-3-r59
25. 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. 1950898 17675364 10.1101/gr.6522707
26. 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 18987734
27. PEMer Package http://sv.gersteinlab.org/pemer
28. Li H Ruan J Durbin R Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18:1851-1858. 2577856 18714091 10.1101/gr.078212.108
29. 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 19122651
30. 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 15895083
31. Pop M Salzberg SL Bioinformatics challenges of new sequencing technology. Trends Genet 2008, 24:142-149. 18262676
32. 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 10890397
33. Kent WJ BLAT - the BLAST-like alignment tool. Genome Res 2002, 12:656-664. 187518 11932250
34. 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 15286789
35. 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 17331616
36. 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. 1564156 16934139 10.1186/1471-2105-7-390
37. 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. 1891342 17568001 10.1101/ gr.6018607
38. 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. 2278375 18404202 10.1371/ journal.pcbi.1000051
39. al EPCe Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816. 2212820 17571346 10.1038/nature05874
40. 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 18586745
41. Smith TF Waterman MS Identification of common molecular subsequences. J Mol Biol 1981, 147:195-197. 10.1016/0022-2836(81)90087-5 7265238
42. 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 A, et al second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449:851-861. 10.1038/ nature06258 17943122
43. 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. 1464427 16056220
44. 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. 2532726 18660515 10.1093/nar/gkn425
45. 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 3294162
46. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool. J Mol Biol 1990, 215:403-410. 2231712
47. 1000 Genomes Project http://1000genomes.org