Genome-wide identification of significant aberrations in cancer genome

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Yuan, Xiguo ^a,b   Yu, Guoqiang ^b,c   Hou, Xuchu ^b   Shih, Ie Ming ^d,h   Clarke, Robert ^e   Zhang, Junying ^a   Hoffman, Eric P ^f   Wang, Roger R ^g   Zhang, Zhen ^h   Wang, Yue ^b  

^a XIDIAN UNIVERSITY   (China)

^b State University   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e GEORGETOWN UNIVERSITY   (United States)

^f CHILDREN'S NATIONAL MEDICAL CENTER   (United States)

^g Richard Montgomery High School   (United States)

^h DEPARTMENT OF PATHOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ANALYTIC METHOD; ARTICLE; CALCULATION; CONTROLLED STUDY; GENETIC ASSOCIATION; GLIOBLASTOMA; INTERMETHOD COMPARISON; LUNG ADENOCARCINOMA; ONCOGENE; OVARY CANCER; PROSTATE CANCER; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY AND SPECIFICITY; SIGNIFICANT ABERRATION IN CANCER; SIMULATION; TUMOR GENE; TUMOR SUPPRESSOR GENE;

EID: 84864259654     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-342     Document Type: Article

References (36)

1. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, et al. The landscape of somatic copy-number alteration across human cancers. Nature 2010, 463(7283):899-905. 10.1038/nature08822, 2826709, 20164920.
2. Leary RJ, Lin JC, Cummins J, Boca S, Wood LD, Parsons DW, Jones S, Sjoblom T, Park BH, Parsons R, et al. Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl Acad Sci U S A 2008, 105(42):16224-16229. 10.1073/pnas.0808041105, 2571022, 18852474.
3. Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D, Vivanco I, Lee JC, Huang JH, Alexander S, et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A 2007, 104(50):20007-20012. 10.1073/pnas.0710052104, 2148413, 18077431.
4. Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, et al. The genomic landscapes of human breast and colorectal cancers. Science 2007, 318(5853):1108-1113. 10.1126/science.1145720, 17932254.
5. Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, Girard L, Minna J, Christiani D, Leo C, et al. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 2004, 64(9):3060-3071. 10.1158/0008-5472.CAN-03-3308, 15126342.
6. Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat Genet 2005, 37(Suppl):S11-S17.
7. Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson LA, et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 2007, 450(7171):893-898. 10.1038/nature06358, 2538683, 17982442.
8. Liu W, Laitinen S, Khan S, Vihinen M, Kowalski J, Yu G, Chen L, Ewing CM, Eisenberger MA, Carducci MA, et al. Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer. Nat Med 2009, 15(5):559-565. 10.1038/nm.1944, 2839160, 19363497.
9. Walter V, Nobel AB, Wright FA. DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors. Bioinformatics 2011, 27(5):678-685. 10.1093/bioinformatics/btq717, 3042182, 21183584.
10. Shah SP, Lam WL, Ng RT, Murphy KP. Modeling recurrent DNA copy number alterations in array CGH data. Bioinformatics 2007, 23(13):i450-i458. 10.1093/bioinformatics/btm221, 17646330.
11. Rueda OM, Diaz-Uriarte R. Finding recurrent copy number alteration regions: a review of methods. Curr Bioinforma 2010, 5:17.
12. Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ, Weber BL, Maris JM, Grant GR. STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Res 2006, 16(9):1149-1158. 10.1101/gr.5076506, 1557772, 16899652.
13. Ivakhno S, Tavare S. CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data. Bioinformatics 2010, 26(11):1395-1402. 10.1093/bioinformatics/btq145, 20403815.
14. Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol 2011, 12(4):R41. 10.1186/gb-2011-12-4-r41, 3218867, 21527027.
15. Klijn C, Holstege H, de Ridder J, Liu X, Reinders M, Jonkers J, Wessels L. Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data. Nucleic Acids Res 2008, 36(2):e13. 2241875, 18187509.
16. Zhang Q, Ding L, Larson DE, Koboldt DC, McLellan MD, Chen K, Shi X, Kraja A, Mardis ER, Wilson RK, et al. CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. Bioinformatics 2010, 26(4):464-469. 10.1093/bioinformatics/btp708, 2852218, 20031968.
17. Choi H, Qin ZS, Ghosh D. A double-layered mixture model for the joint analysis of DNA copy number and gene expression data. J Comput Biol 2010, 17(2):121-137. 10.1089/cmb.2009.0019, 3148827, 20170400.
18. Yu G, Zhang B, Bova GS, Xu J, Shih IM, Wang Y. BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data. Bioinformatics 2011, 27(11):1473-1480. 10.1093/bioinformatics/btr183, 3102226, 21498400.
19. Fu JC, Johnson BC, Chang Y-M. Approximating the extreme right-hand tail probability for the distribution of the number of patterns in a sequence of multi-state trials. Journal of Statistical Planning and Inference 2011, 142(2):473-480.
20. Li C, Wong WH. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A 2001, 98(1):31-36. 14539, 11134512.
21. Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH, Li C. dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 2004, 20(8):1233-1240. 10.1093/bioinformatics/bth069, 14871870.
22. Venkatraman ES, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 2007, 23(6):657-663. 10.1093/bioinformatics/btl646, 17234643.
23. Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5(4):557-572. 10.1093/biostatistics/kxh008, 15475419.
24. Willenbrock H, Fridlyand J. A comparison study: applying segmentation to array CGH data for downstream analyses. Bioinformatics 2005, 21(22):4084-4091. 10.1093/bioinformatics/bti677, 16159913.
25. Chen L, Yu G, Langefeld CD, Miller DJ, Guy RT, Raghuram J, Yuan X, Herrington DM, Wang Y. Comparative analysis of methods for detecting interacting loci. BMC Genomics 2011, 12:344. 10.1186/1471-2164-12-344, 3161015, 21729295.
26. Kuo KT, Guan B, Feng Y, Mao TL, Chen X, Jinawath N, Wang Y, Kurman RJ, Shih Ie M, Wang TL. Analysis of DNA copy number alterations in ovarian serous tumors identifies new molecular genetic changes in low-grade and high-grade carcinomas. Cancer Res 2009, 69(9):4036-4042. 10.1158/0008-5472.CAN-08-3913, 2782554, 19383911.
27. Kuo KT, Mao TL, Chen X, Feng Y, Nakayama K, Wang Y, Glas R, Ma MJ, Kurman RJ, Shih Ie M, et al. DNA copy numbers profiles in affinity-purified ovarian clear cell carcinoma. Clin Cancer Res 2010, 16(7):1997-2008. 10.1158/1078-0432.CCR-09-2105, 2848895, 20233889.
28. Feng Y, Yu G, Wang T-L, Shih I-M, Wang Y. Analyzing DNA copy number changes using fused margin regression. Intl J of Functional Informatics and Personalized Medicine 2010, 3(1):3-15.
29. Bast RC, Hennessy B, Mills GB. The biology of ovarian cancer: new opportunities for translation. Nat Rev Cancer 2009, 9(6):415-428. 10.1038/nrc2644, 2814299, 19461667.
30. Integrated genomic analyses of ovarian carcinoma. Nature 2011, 474(7353):609-615. 10.1038/nature10166, 3163504, 21720365.
31. Lynch TJ, Bell DW, Sordella R, Gurubhagavatula S, Okimoto RA, Brannigan BW, Harris PL, Haserlat SM, Supko JG, Haluska FG, et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med 2004, 350(21):2129-2139. 10.1056/NEJMoa040938, 15118073.
32. Kotliarov Y, Steed ME, Christopher N, Walling J, Su Q, Center A, Heiss J, Rosenblum M, Mikkelsen T, Zenklusen JC, et al. High-resolution global genomic survey of 178 gliomas reveals novel regions of copy number alteration and allelic imbalances. Cancer Res 2006, 66(19):9428-9436. 10.1158/0008-5472.CAN-06-1691, 17018597.
33. Westfall PH, Young SS. Resampling-based multiple testing : examples and methods for P-value adjustment 1993, New York, Wiley.
34. Shaffer JP. Multiple hypothesis testing. Annu Rev Psychol 1995, 46:24.
35. Shibata D. Cancer. Heterogeneity and tumor history. Science 2012, 336(6079):304-305. 10.1126/science.1222361, 22517848.
36. Marusyk A, Almendro V, Polyak K. Intra-tumour heterogeneity: a looking glass for cancer?. Nat Rev Cancer 2012, 12(5):323-334. 10.1038/nrc3261, 22513401.