An Integrated View of Copy Number and Allelic Alterations in the Cancer Genome Using Single Nucleotide Polymorphism Arrays

Cancer Research

Volumn 64, Issue 9, 2004, Pages 3060-3071

  Zhao, Xiaojun ^a,b   Li, Cheng ^a,c   Paez, J Guillermo ^a,b   Chin, Koei ^d   Jänne, Pasi A ^a,b   Chen, Tzu Hsiu ^a   Girard, Luc ^e,f   Minna, John ^e,f   Christiani, David ^c   Leo, Chris ^a   Gray, Joe W ^d   Sellers, William R ^a,b   Meyerson, Matthew ^a,b  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^f UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREAST CARCINOMA; CANCER CELL CULTURE; CANCER GENETICS; CARCINOGENESIS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA DETERMINATION; GENE AMPLIFICATION; GENE DELETION; HEMIZYGOSITY; HETEROZYGOSITY LOSS; HOMOZYGOSITY; HUMAN; HUMAN CELL; LUNG CARCINOMA; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; BREAST NEOPLASMS; DNA, NEOPLASM; GENE DOSAGE; HOMOZYGOTE; HUMANS; LOSS OF HETEROZYGOSITY; LUNG NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 2342453338     PISSN: 00085472     EISSN: None     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-03-3308     Document Type: Article

References (31)

1. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000;100:57-70.
2. Friend SH, Bernards R, Rogelj S, et al. A human DNA segment with properties of the gene that predisposes to retinoblastoma and osteosarcoma. Nature 1986;323:643-6.
3. Kamb A, Gruis NA, Weaver-Feldhaus J, et al. A cell cycle regulator potentially involved in genesis of many tumor types. Science 1994;264:436-40.
4. Li J, Yen C, Liaw D, et al. PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science 1997;275:1943-7.
5. Little CD, Nau MM, Carney DN, Gazdar AF, Minna JD. Amplification and expression of the c-myc oncogene in human lung cancer cell lines. Nature 1983;306:194-6.
6. Di Fiore PP, Pierce JH, Kraus MH, Segatto O, King CR, Aaronson SA. erbB-2 is a potent oncogene when overexpressed in NIH/3T3 cells. Science 1987;237:178-82.
7. Kallioniemi A, Kallioniemi OP, Sudar D, et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992;258:818-21.
8. Pinkel D, Segraves R, Sudar D, et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998;20:207-11.
9. Pollack JR, Perou CM, Alizadeh AA, et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999;23:41-6.
10. Solinas-Toldo S, Lampel S, Stilgenbauer S, et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 1997;20:399-407.
11. Lucito R, West J, Reiner A, et al. Detecting gene copy number fluctuations in tumor cells by microarray analysis of genomic representations. Genome Res 2000;10:1726-36.
12. Lucito R, Healy J, Alexander J, et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res 2003;13:2291-305.
13. Wang DG, Fan JB, Siao CJ, et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome Science 1998;280:1077-82.
14. Mei R, Galipeau PC, Prass C, et al. Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res 2000;10:1126-37.
15. Lindblad-Toh K, Tanenbaum DM, Daly MJ, et al. Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat Biotechnol 2000;18:1001-5.
16. Hoque MO, Lee CC, Cairns P, Schoenberg M, Sidransky D. Genome-wide genetic characterization of bladder cancer: a comparison of high-density single-nucleotide polymorphism arrays and PCR-based microsatellite analysis. Cancer Res 2003;63:2216-22.
17. Lieberfarb ME, Lin M, Lechpammer M, et al. Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP. Cancer Res 2003;63:4781-5.
18. Primdahl H, Wikman FP, von der Maase H, Zhou XG, Wolf H, Orntoft TF. Allelic imbalances in human bladder cancer: genome-wide detection with high-density single-nucleotide polymorphism arrays. J Natl Cancer Inst 2002;94:216-23.
19. Wang ZC, Lin M, Wei L-J, et al. Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers Cancer Res 2004;64:64-71.
20. Jänne PA, Li C, Zhao X, et al. High-resolution single nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines. Oncogene 2004;23:2716-26.
21. Kennedy GC, Matsuzaki H, Dong S, et al. Large-scale genotyping of complex DNA. Nat Biotechnol 2003;21:1233-7.
22. Li C, Hung Wong W. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2001;2:RESEARCH0032.
23. Li C, Wong WH. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 2001;98:31-6.
24. Dugad R, Desai UB. A tutorial on Hidden Markov Models. Technical report, No. SPANN-96.1, 1996.
25. Lange K. Mathematical and Statistical Methods for Genetic Analysis. New York: Springer-Verlag, 2002.
26. Li C, Wang WH. DNA-Chip Analyzer (dChip). In: The Analysis of Gene Expression Data: Methods and Software. Parmigiani G, Garrett ES, Irizarry R, Zeger SL, editors. New York: Springer, 2003. p. 120-41.
27. Wang TL, Maierhofer C, Speicher MR, et al. Digital karyotyping. Proc Natl Acad Sci USA 2002;99:16156-61.
28. Sundaresan V, Chung, Heppell-Parton A, et al. Homozygous deletions at 3p12 in breast and lung cancer. Oncogene 1998;17:1723-9.
29. Albertson DG, Pinkel D. Genomic microarrays in human genetic disease and cancer. Hum Mol Genet 2003;12 Spec No 2:R145-52.
30. Knudson AG, Jr. Mutation and cancer: statistical study of retinoblastoma. Proc Natl Acad Sci USA 1971;68:820-3.
31. Cavenee WK, Dryja TP, Phillips RA, et al. Expression of recessive alleles by chromosomal mechanisms in retinoblastoma. Nature 1983;305:779-84.