A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data

Genome Biology

Volumn 11, Issue 9, 2010, Pages

  Yau, Christopher ^a   Mouradov, Dmitri ^b   Jorissen, Robert N ^b   Colella, Stefano ^c,f   Mirza, Ghazala ^c   Steers, Graham ^d   Harris, Adrian ^d   Ragoussis, Jiannis ^c   Sieber, Oliver ^b   Holmes, Christopher C ^a,e  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b ROYAL MELBOURNE HOSPITAL   (Australia)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF OXFORD   (United Kingdom)

^e MRC MAMMALIAN GENETICS UNIT   (United Kingdom)

^f UA INRA 203   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER CELL CULTURE; COMPARATIVE GENOMIC HYBRIDIZATION; CONCEPTUAL FRAMEWORK; COPY NUMBER VARIATION; GENE AMPLIFICATION; GENE DELETION; GENE FREQUENCY; GENE REARRANGEMENT; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOME; GENOTYPE; HETEROZYGOSITY LOSS; HOMOZYGOSITY; HUMAN; KARYOTYPE; LYMPHOBLASTOID CELL LINE; POLYPLOIDY; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; ALGORITHM; BAYES THEOREM; BIOLOGICAL MODEL; DNA CONTAMINATION; GENETICS; HUMAN GENOME; MICROARRAY ANALYSIS; MUTATION; NEOPLASM; TUMOR CELL LINE;

ALGORITHMS; BAYES THEOREM; CELL LINE, TUMOR; DATA INTERPRETATION, STATISTICAL; DNA CONTAMINATION; DNA COPY NUMBER VARIATIONS; GENETIC HETEROGENEITY; GENOME, HUMAN; GENOTYPE; HUMANS; MICROARRAY ANALYSIS; MODELS, GENETIC; MUTATION; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE; POLYPLOIDY;

EID: 77956690576     PISSN: None     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2010-11-9-r92     Document Type: Article

References (45)

1. Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D, Vivanco I, Lee JC, Huang JH, Alexander S, Du J, Kau T, Thomas RK, Shah K, Soto H, Perner S, Prensner J, Debiasi RM, Demichelis F, Hatton C, Rubin MA, Garraway LA, Nelson SF, Liau L, Mischel PS, Cloughesy TF, Meyerson M, Golub TA, Lander ES, Mellinghoff IK, et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci USA 2007, 104:20007-20012. 10.1073/pnas.0710052104, 2148413, 18077431.
2. Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson LA, Shah K, Sato M, Thomas RK, Barletta JA, Borecki IB, Broderick S, Chang AC, Chiang DY, Chirieac LR, Cho J, Fujii Y, Gazdar AF, Giordano T, Greulich H, Hanna M, Johnson BE, Kris MG, Lash A, Lin L, Lindeman N, et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 2007, 450:893-898. 10.1038/nature06358, 2538683, 17982442.
3. Caren H, Kryh H, Nethander M, Sjoberg RM, Trager C, Nilsson S, Abrahamsson J, Kogner P, Martinsson T. High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset. Proc Natl Acad Sci USA 2010, 107:4323-4328. 10.1073/pnas.0910684107, 2840092, 20145112.
4. Waddell N, Arnold J, Cocciardi S, da Silva L, Marsh A, Riley J, Johnstone CN, Orloff M, Assie G, Eng C, Reid L, Keith P, Yan M, Fox S, Devilee P, Godwin AK, Hogervorst FB, Couch F, Grimmond S, Flanagan JM, Khanna K, Simpson PT, Lakhani SR, Chenevix-Trench G. Subtypes of familial breast tumours revealed by expression and copy number profiling. Breast Cancer Res Treat 2010, 123:661-677. 10.1007/s10549-009-0653-1, 19960244.
5. Bignell GR, Greenman CD, Davies H, Butler AP, Edkins S, Andrews JM, Buck G, Chen L, Beare D, Latimer C, Widaa S, Hinton J, Fahey C, Fu B, Swamy S, Dalgliesh GL, Teh BT, Deloukas P, Yang F, Campbell PJ, Futreal PA, Stratton MR. Signatures of mutation and selection in the cancer genome. Nature 2010, 463:893-898. 10.1038/nature08768, 20164919.
6. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir BA, Tanaka KE, Chiang DY, Bass AJ, Loo A, Hoffman C, Prensner J, Liefeld T, Gao Q, Yecies D, Signoretti S, et al. The landscape of somatic copy-number alteration across human cancers. Nature 2010, 463:899-905. 10.1038/nature08822, 2826709, 20164920.
7. Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, Hangaishi A, Kurokawa M, Chiba S, Bailey DK, Kennedy GC, Ogawa S. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 2005, 65:6071-6079. 10.1158/0008-5472.CAN-05-0465, 16024607.
8. Komura D, Shen F, Ishikawa S, Fitch KR, Chen W, Zhang J, Liu G, Ihara S, Nakamura H, Hurles ME, Lee C, Scherer SW, Jones KW, Shapero MH, Huang J, Aburatani H. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res 2006, 16:1575-1584. 10.1101/gr.5629106, 1665641, 17122084.
9. Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J. QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res 2007, 35:2013-2025. 10.1093/nar/gkm076, 1874617, 17341461.
10. Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 2007, 17:1665-1674. 10.1101/gr.6861907, 2045149, 17921354.
11. Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, Lee C, Nizzari MM, Gabriel SB, Purcell S, Daly MJ, Altshuler D. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet 2008, 40:1253-1260. 10.1038/ng.237, 2756534, 18776909.
12. Lindblad-Toh K, Tanenbaum DM, Daly MJ, Winchester E, Lui WO, Villapakkam A, Stanton SE, Larsson C, Hudson TJ, Johnson BE, Lander ES, Meyerson M. Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat Biotechnol 2000, 18:1001-1005. 10.1038/79269, 10973224.
13. Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, Girard L, Minna J, Christiani D, Leo C, Gray JW, Sellers WR, Meyerson M. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 2004, 64:3060-3071. 10.1158/0008-5472.CAN-03-3308, 15126342.
14. LaFramboise T, Weir BA, Zhao X, Beroukhim R, Li C, Harrington D, Sellers WR, Meyerson M. Allele-specific amplification in cancer revealed by SNP array analysis. PLoS Comput Biol 2005, 1:e65. 10.1371/journal.pcbi.0010065, 1289392, 16322765.
15. Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K. Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res 2008, 36:e126. 10.1093/nar/gkn556, 2577347, 18784189.
16. Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F, Haden K, Li J, Shaw CA, Belmont J, Cheung SW, Shen RM, Barker DL, Gunderson KL. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res 2006, 16:1136-1148. 10.1101/gr.5402306, 1557768, 16899659.
17. Attiyeh EF, Diskin SJ, Attiyeh MA, Mosse YP, Hou C, Jackson EM, Kim C, Glessner J, Hakonarson H, Biegel JA, Maris JM. Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy. Genome Res 2009, 19:276-283. 10.1101/gr.075671.107, 2652209, 19141597.
18. Bengtsson H, Irizarry R, Carvalho B, Speed TP. Estimation and assessment of raw copy numbers at the single locus level. Bioinformatics 2008, 24:759-767. 10.1093/bioinformatics/btn016, 18204055.
19. Bengtsson H, Neuvial P, Speed TP. TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC Bioinformatics 2010, 11:245. 10.1186/1471-2105-11-245, 2894037, 20462408.
20. Goransson H, Edlund K, Rydaker M, Rasmussen M, Winquist J, Ekman S, Bergqvist M, Thomas A, Lambe M, Rosenquist R, Holmberg L, Micke P, Botling J, Isaksson A. Quantification of normal cell fraction and copy number neutral LOH in clinical lung cancer samples using SNP array data. PLoS One 2009, 4:e6057. 10.1371/journal.pone.0006057, 2699026, 19557126.
21. Greenman CD, Bignell G, Butler A, Edkins S, Hinton J, Beare D, Swamy S, Santarius T, Chen L, Widaa S, Futreal PA, Stratton MR. PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics 2010, 11:164-175. 10.1093/biostatistics/kxp045, 2800165, 19837654.
22. Lamy P, Andersen CL, Dyrskjot L, Torring N, Wiuf C. A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays. BMC Bioinformatics 2007, 8:434. 10.1186/1471-2105-8-434, 2206057, 17996079.
23. Popova T, Manie E, Stoppa-Lyonnet D, Rigaill G, Barillot E, Stern MH. Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol 2009, 10:R128. 10.1186/gb-2009-10-11-r128, 2810663, 19903341.
24. Staaf J, Lindgren D, Vallon-Christersson J, Isaksson A, Goransson H, Juliusson G, Rosenquist R, Hoglund M, Borg A, Ringner M. Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays. Genome Biol 2008, 9:R136. 10.1186/gb-2008-9-9-r136, 2592714, 18796136.
25. Sun W, Wright FA, Tang Z, Nordgard SH, Van Loo P, Yu T, Kristensen VN, Perou CM. Integrated study of copy number states and genotype calls using high-density SNP arrays. Nucleic Acids Res 2009, 37:5365-5377. 10.1093/nar/gkp493, 2935461, 19581427.
26. Wang K, Li J, Li S, Bolund L, Wiuf C. Estimation of tumor heterogeneity using CGH array data. BMC Bioinformatics 2009, 10:12. 10.1186/1471-2105-10-12, 2640360, 19134174.
27. Yamamoto G, Nannya Y, Kato M, Sanada M, Levine RL, Kawamata N, Hangaishi A, Kurokawa M, Chiba S, Gilliland DG, Koeffler HP, Ogawa S. Highly sensitive method for genomewide detection of allelic composition in nonpaired, primary tumor specimens by use of affymetrix single-nucleotide-polymorphism genotyping microarrays. Am J Hum Genet 2007, 81:114-126. 10.1086/518809, 1950910, 17564968.
28. Yau C, Holmes CC. CNV discovery using SNP genotyping arrays. Cytogenet Genome Res 2008, 123:307-312. 10.1159/000184722, 19287169.
29. LaFramboise T. Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res 2009, 37:4181-4193. 10.1093/nar/gkp552, 2715261, 19570852.
30. Ragoussis J. Genotyping technologies for genetic research. Annu Rev Genomics Hum Genet 2009, 10:117-133. 10.1146/annurev-genom-082908-150116, 19453250.
31. Winchester L, Yau C, Ragoussis J. Comparing CNV detection methods for SNP arrays. Brief Funct Genomic Proteomic 2009, 8:353-366. 10.1093/bfgp/elp017, 19737800.
32. Pfeifer D, Pantic M, Skatulla I, Rawluk J, Kreutz C, Martens UM, Fisch P, Timmer J, Veelken H. Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays. Blood 2007, 109:1202-1210. 10.1182/blood-2006-07-034256, 17053054.
33. Staaf J, Vallon-Christersson J, Lindgren D, Juliusson G, Rosenquist R, Hoglund M, Borg A, Ringner M. Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics 2008, 9:409. 10.1186/1471-2105-9-409, 2572624, 18831757.
34. Gardina PJ, Lo KC, Lee W, Cowell JK, Turpaz Y. Ploidy status and copy number aberrations in primary glioblastomas defined by integrated analysis of allelic ratios, signal ratios and loss of heterozygosity using 500K SNP Mapping Arrays. BMC Genomics 2008, 9:489. 10.1186/1471-2164-9-489, 2576260, 18928532.
35. Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, Andrews TD, Stranger BE, Lynch AG, Dermitzakis ET, Carter NP, Tavare S, Hurles ME. Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biol 2007, 8:R228. 10.1186/gb-2007-8-10-r228, 2246302, 17961237.
36. Abdel-Rahman WM, Katsura K, Rens W, Gorman PA, Sheer D, Bicknell D, Bodmer WF, Arends MJ, Wyllie AH, Edwards PA. Spectral karyotyping suggests additional subsets of colorectal cancers characterized by pattern of chromosome rearrangement. Proc Natl Acad Sci USA 2001, 98:2538-2543. 10.1073/pnas.041603298, 30173, 11226274.
37. Liang JC, Ning Y, Wang RY, Padilla-Nash HM, Schrock E, Soenksen D, Nagarajan L, Ried T. Spectral karyotypic study of the HL-60 cell line: detection of complex rearrangements involving chromosomes 5, 7, and 16 and delineation of critical region of deletion on 5q31.1. Cancer Genet Cytogenet 1999, 113:105-109. 10.1016/S0165-4608(99)00030-8, 10484974.
38. Rowan A, Halford S, Gaasenbeek M, Kemp Z, Sieber O, Volikos E, Douglas E, Fiegler H, Carter N, Talbot I, Silver A, Tomlinson I. Refining molecular analysis in the pathways of colorectal carcinogenesis. Clin Gastroenterol Hepatol 2005, 3:1115-1123. 10.1016/S1542-3565(05)00618-X, 16271343.
39. Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 2009, 6:99-103. 10.1038/nmeth.1276, 2630795, 19043412.
40. Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin ML, Beare D, Lau KW, Greenman C, Varela I, Nik-Zainal S, Davies HR, Ordonez GR, Mudie LJ, Latimer C, Edkins S, Stebbings L, Chen L, Jia M, Leroy C, Marshall J, Menzies A, Butler A, Teague JW, Mangion J, Sun YA, McLaughlin SF, Peckham HE, Tsung EF, et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 2010, 463:184-190. 10.1038/nature08629, 2880489, 20016488.
41. Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT, Stebbings LA, Leroy C, Edkins S, Mudie LJ, Greenman CD, Jia M, Latimer C, Teague JW, Lau KW, Burton J, Quail MA, Swerdlow H, Churcher C, Natrajan R, Sieuwerts AM, Martens JW, Silver DP, Langerod A, Russnes HE, Foekens JA, Reis-Filho JS, van't Veer L, Richardson AL, Borresen-Dale AL, et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 2009, 462:1005-1010. 10.1038/nature08645, 20033038.
42. Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, Schmidt H, Kalicki J, Zhang Q, Chen L, Lin L, Wendl MC, McMichael JF, Magrini VJ, Cook L, McGrath SD, Vickery TL, Appelbaum E, Deschryver K, Davies S, Guintoli T, Lin L, et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 2010, 464:999-1005. 10.1038/nature08989, 20393555.
43. GAP. , http://bioinfo-out.curie.fr/projects/snp_gap/
44. GenoCN. , http://www.bios.unc.edu/~wsun/software/genoCN.htm
45. OncoSNP. , https://sites.google.com/site/oncosnp/