Estimation of Copy Number Alterations from Exome Sequencing Data

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Valdés Mas, Rafael ^a   Bea, Silvia ^b   Puente, Diana A ^a   López Otín, Carlos ^a   Puente, Xose S ^a   Wang, Pei ^c  

^a DEPARTAMENTO DE BIOQUÍMICA Y BIOLOGÍA MOLECULAR   (Spain)

^b INSTITUT D INVESTIGACIONS BIOMÈDIQUES AUGUST PI I SUNYER IDIBAPS   (Spain)

^c Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CHROMOSOME ANALYSIS; CHROMOSOME LOSS; CHROMOSOME SUBSTITUTION; CHRONIC LYMPHATIC LEUKEMIA; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER PROGRAM; COPY NUMBER VARIATION; EXOME; FALSE POSITIVE RESULT; GENE DOSAGE; INDEL MUTATION; INTERMETHOD COMPARISON; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS;

COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA COPY NUMBER VARIATIONS; EXOME; FEMALE; HUMANS; MALE; SEQUENCE ANALYSIS, DNA;

EID: 84871290113     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0051422     Document Type: Article

References (42)

1. Lupski JR, Reid JG, Gonzaga-Jauregui C, Rio Deiros D, Chen DC, et al. (2010) Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med 362: 1181-1191.
2. Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, et al. (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328: 636-639.
3. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, et al. (2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456: 66-72.
4. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, et al. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463: 191-196.
5. Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, et al. (2010) A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463: 184-190.
6. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, et al. (2009) Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 361: 1058-1066.
7. Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, et al. (2010) DNMT3A mutations in acute myeloid leukemia. N Engl J Med 363: 2424-2433.
8. Puente XS, Pinyol M, Quesada V, Conde L, Ordonez GR, et al. (2011) Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 475: 101-105.
9. Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, et al. (2011) Initial genome sequencing and analysis of multiple myeloma. Nature 471: 467-472.
10. Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, et al. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27: 182-189.
11. Hodges E, Rooks M, Xuan Z, Bhattacharjee A, Benjamin Gordon D, et al. (2009) Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protoc 4: 960-974.
12. Gilissen C, Hoischen A, Brunner HG, Veltman JA, (2011) Unlocking Mendelian disease using exome sequencing. Genome Biol 12: 228.
13. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, et al. (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461: 272-276.
14. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, et al. (2010) Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 42: 30-35.
15. Varela I, Tarpey P, Raine K, Huang D, Ong CK, et al. (2011) Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 469: 539-542.
16. Bilguvar K, Ozturk AK, Louvi A, Kwan KY, Choi M, et al. (2010) Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature 467: 207-210.
17. Harbour JW, Onken MD, Roberson ED, Duan S, Cao L, et al. (2010) Frequent mutation of BAP1 in metastasizing uveal melanomas. Science 330: 1410-1413.
18. Puente XS, Quesada V, Osorio FG, Cabanillas R, Cadinanos J, et al. (2011) Exome Sequencing and Functional Analysis Identifies BANF1 Mutation as the Cause of a Hereditary Progeroid Syndrome. Am J Hum Genet 88: 650-656.
19. Wang Y, Guo L, Cai SP, Dai M, Yang Q, et al. (2012) Exome Sequencing Identifies Compound Heterozygous Mutations in CYP4V2 in a Pedigree with Retinitis Pigmentosa. PLoS One 7: e33673.
20. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, et al. (2010) The landscape of somatic copy-number alteration across human cancers. Nature 463: 899-905.
21. Akavia UD, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, et al. (2010) An integrated approach to uncover drivers of cancer. Cell 143: 1005-1017.
22. Stratton MR, Campbell PJ, Futreal PA, (2009) The cancer genome. Nature 458: 719-724.
23. Merla G, Brunetti-Pierri N, Micale L, Fusco C, (2010) Copy number variants at Williams-Beuren syndrome 7q11.23 region. Hum Genet 128: 3-26.
24. Mefford HC, Cooper GM, Zerr T, Smith JD, Baker C, et al. (2009) A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease. Genome Res 19: 1579-1585.
25. Link DC, Schuettpelz LG, Shen D, Wang J, Walter MJ, et al. (2011) Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. Jama 305: 1568-1576.
26. Robbins CM, Tembe WA, Baker A, Sinari S, Moses TY, et al. (2010) Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors. Genome Res 21: 47-55.
27. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, et al. (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40: 722-729.
28. Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, Cochran AJ, et al. (2011) Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics 27: 2648-2654.
29. Krumm N, Sudmant PH, Ko A, O'Roak BJ, Malig M, et al. (2012) Copy number variation detection and genotyping from exome sequence data. Genome Res 22: 1525-1532.
30. Li J, Lupat R, Amarasinghe KC, Thompson ER, Doyle MA, et al. (2012) CONTRA: copy number analysis for targeted resequencing. Bioinformatics 28: 1307-1313.
31. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, et al. (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22: 568-576.
32. Lonigro RJ, Grasso CS, Robinson DR, Jing X, Wu YM, et al. (2012) Detection of somatic copy number alterations in cancer using targeted exome capture sequencing. Neoplasia 13: 1019-1025.
33. Li H, Durbin R, (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
34. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
35. Venkatraman ES, Olshen AB, (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663.
36. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
37. Quesada V, Conde L, Villamor N, Ordoñez GR, Jares P, et al. (2011) Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 in chronic lymphocytic leukemia. Nat Genet 44: 47-52.
38. Aqeilan RI, Calin GA, Croce CM, (2010) miR-15a and miR-16-1 in cancer: discovery, function and future perspectives. Cell Death Differ 17: 215-220.
39. Zenz T, Mertens D, Kuppers R, Dohner H, Stilgenbauer S, (2010) From pathogenesis to treatment of chronic lymphocytic leukaemia. Nat Rev Cancer 10: 37-50.
40. Bell D, Berchuck A, Birrer M, Chien J, Cramer DW, et al. (2011) Integrated genomic analyses of ovarian carcinoma. Nature 474: 609-615.
41. Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, et al. (2010) International network of cancer genome projects. Nature 464: 993-998.
42. Meyerson M, Gabriel S, Getz G, (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 11: 685-696.