Use of Single-Nucleotide Polymorphism Array for Tumor Aberrations in Gene Copy Numbers

  • Kwong-Kwok Wong
Part of the Cancer Drug Discovery and Development™ book series (CDD&D)

Summary

The single nucleotide polymorphism (SNP) array was originally developed to determine the genotypes of a study population for linkage analysis or individual genetic variation analysis. Over the last few years, the number of SNP loci that can be evaluated in a single assay has increased from approximately 1500 to more than 500,000, covering all 22 autosomes and the X chromosome. Because the hybridization signal of each oligonucleotide on the SNP array depends on the amount of target DNA, various statistic algorithms have been developed to estimate the copy number of each SNP locus. Several studies have demonstrated the utility of the SNP array analysis in the detection of gene copy number aberrations in tumor DNA. In this review, we discuss the use of the SNP array analysis in determining tumor aberrations in gene copy numbers, the challenge of using tumor samples in the analysis, and improvements in software for copy number measurement using SNP arrays. The unique ability of the SNP array to determine both the genotype and copy number has uncovered novel DNA amplification events that involve only a single allele.

Key Words

single nucleotide polymorphism array allelic imbalance copy number variation whole-genome amplification formalin-fixed and paraffin-embedded tissue 

References

  1. 1.
    Adams J, Williams SV, Aveyard JS et al. Loss of heterozygosity analysis and DNA copy number measurement on 8p in bladder cancer reveals two mechanisms of allelic loss. Cancer Res 2005;65: 66–75.PubMedGoogle Scholar
  2. 2.
    Bergamaschi A, Kim YH, Wang P et al. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 2006;45:1033–1040.CrossRefPubMedGoogle Scholar
  3. 3.
    Jeon YK, Sung SW, Chung JH et al. Clinicopathologic features and prognostic implications of epidermal growth factor receptor (EGFR) gene copy number and protein expression in non-small cell lung cancer. Lung Cancer 2006;54:387–398.CrossRefPubMedGoogle Scholar
  4. 4.
    Candiotti KA, Birnbach DJ, Lubarsky DA et al. The impact of pharmacogenomics on postoperative nausea and vomiting: do CYP2D6 allele copy number and polymorphisms affect the success or failure of ondansetron prophylaxis? Anesthesiology 2005;102:543–549.CrossRefPubMedGoogle Scholar
  5. 5.
    Ouahchi K, Lindeman N, Lee C. Copy number variants and pharmacogenomics. Pharmacogenomics 2006;7:25–29.CrossRefPubMedGoogle Scholar
  6. 6.
    Cappuzzo F, Varella-Garcia M, Shigematsu H et al. Increased HER2 gene copy number is associated with response to gefitinib therapy in epidermal growth factor receptor-positive non-small-cell lung cancer patients. J Clin Oncol 2005;23:5007–5018.CrossRefPubMedGoogle Scholar
  7. 7.
    Endo K, Sasaki H, Yano M et al. Evaluation of the epidermal growth factor receptor gene mutation and copy number in non-small cell lung cancer with gefitinib therapy. Oncol Rep 2006;16:533–541.PubMedGoogle Scholar
  8. 8.
    Yang SH, Seo MY, Jeong HJ et al. Gene copy number change events at chromosome 20 and their association with recurrence in gastric cancer patients. Clin Cancer Res 2005;11:612–620.PubMedGoogle Scholar
  9. 9.
    Dimova I, Yosifova A, Zaharieva B et al. Association of 20q13.2 copy number changes with the advanced stage of ovarian cancer tissue microarray analysis. Eur J Obstet Gynecol Reprod Biol 2005;118:81–85.CrossRefPubMedGoogle Scholar
  10. 10.
    Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000;100:57–70.CrossRefPubMedGoogle Scholar
  11. 11.
    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;323:643–646.CrossRefPubMedGoogle Scholar
  12. 12.
    Kamb A, Gruis NA, Weaver-Feldhaus J et al. A cell cycle regulator potentially involved in genesis of many tumor types. Science 1994;264:436–440.CrossRefPubMedGoogle Scholar
  13. 13.
    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;275:1943–1947.CrossRefPubMedGoogle Scholar
  14. 14.
    Little CD, Nau MM, Carney DN et al. Amplification and expression of the c-Myc oncogene in human lung cancer cell lines. Nature 1983;306:194–196.CrossRefPubMedGoogle Scholar
  15. 15.
    Lin CR, Chen WS, Kruiger W et al. Expression cloning of human EGF receptor complementary DNA: gene amplification and three related messenger RNA products in A431 cells. Science 1984;224: 843–848.CrossRefPubMedGoogle Scholar
  16. 16.
    Gilbertson RJ, Hill DA, Hernan R et al. ERBB1 is amplified and over-expressed in high-grade diffusely infiltrative pediatric brain stem glioma. Clin Cancer Res 2003;9:3620–3624.PubMedGoogle Scholar
  17. 17.
    Ueda M, Hung YC, Terai Y et al. Glutathione S-transferase GSTM1, GSTT1 and p53 codon 72 polymorphisms in human tumor cells. Hum Cell 2003;16:241–251.CrossRefPubMedGoogle Scholar
  18. 18.
    Wang VW, Bell DA, Berkowitz RS et al. Whole-genome amplification and high-throughput allelotyping identified five distinct deletion regions on chromosomes 5 and 6 in microdissected early-stage ovarian tumors. Cancer Res 2001;61:4169–4174.PubMedGoogle Scholar
  19. 19.
    Kallioniemi A, Kallioniemi OP, Sudar D et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992;258:818–821.CrossRefPubMedGoogle Scholar
  20. 20.
    Lastowska M, Cotterill S, Pearson AD et al. Gain of chromosome arm 17q predicts unfavourable outcome in neuroblastoma patients. U.K. Children's Cancer Study Group and the U.K. Cancer Cytogenetics Group. Eur J Cancer 1997;33:1627–1633.CrossRefPubMedGoogle Scholar
  21. 21.
    Sherry ST, Ward MH, Kholodov M et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001;29:308–311.CrossRefPubMedGoogle Scholar
  22. 22.
    Matsuzaki H, Dong S, Loi H et al. Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods 2004;1:109–111.CrossRefPubMedGoogle Scholar
  23. 23.
    Matsuzaki H, Loi H, Dong S et al. Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res 2004;14:414–425.CrossRefPubMedGoogle Scholar
  24. 24.
    Przeworski M, Hudson RR, Di Rienzo A. Adjusting the focus on human variation. Trends Genet 2000;16:296–302.CrossRefPubMedGoogle Scholar
  25. 25.
    Reich DE, Schaffner SF, Daly MJ et al. Human genome sequence variation and the influence of gene history, mutation and recombination. Nat Genet 2002;32:135–142.CrossRefPubMedGoogle Scholar
  26. 26.
    Di X, Matsuzaki H, Webster TA et al. Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays. Bioinformatics 2005;21:1958–1963.CrossRefPubMedGoogle Scholar
  27. 27.
    Liu WM, Di X, Yang G et al. Algorithms for large-scale genotyping microarrays. Bioinformatics 2003;19:2397–2403.CrossRefPubMedGoogle Scholar
  28. 28.
    Kennedy GC, Matsuzaki H, Dong S et al. Large-scale genotyping of complex DNA. Nat Biotechnol 2003;21:1233–1237.CrossRefPubMedGoogle Scholar
  29. 29.
    Komura D, Shen F, Ishikawa S et al. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res 2006;16:1575–1584.CrossRefPubMedGoogle Scholar
  30. 30.
    Wong KK, Tsang YT, Shen J et al. Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA. Nucleic Acids Res 2004;32:e69.CrossRefPubMedGoogle Scholar
  31. 31.
    Beroukhim R, Lin M, Park Y et al. Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol 2006;2:e41.CrossRefPubMedGoogle Scholar
  32. 32.
    Li LH, Ho SF, Chen CH et al. Long contiguous stretches of homozygosity in the human genome. Hum Mutat 2006;27:1115–1121.CrossRefPubMedGoogle Scholar
  33. 33.
    Huang J, Wei W, Zhang J et al. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics 2004;1:287–299.PubMedGoogle Scholar
  34. 34.
    Nannya Y, Sanada M, Nakazaki K et al. A robust algorithm for copy number detection using high-density oligonucleotide single-nucleotide polymorphism genotyping arrays. Cancer Res 2005;65:6071–6079.CrossRefPubMedGoogle Scholar
  35. 35.
    Laframboise T, Harrington D, Weir BA. PLASQ: a generalized linear model–based procedure to determine allelic dosage in cancer cells from SNP array data. Biostatistics 2007;8:323–336.CrossRefPubMedGoogle Scholar
  36. 36.
    Lai Y, Zhao H. A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array–based CGH data. Comput Biol Chem 2005;29:47–54.CrossRefPubMedGoogle Scholar
  37. 37.
    Janne 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;23:2716–2726.CrossRefPubMedGoogle Scholar
  38. 38.
    Bignell GR, Huang J, Greshock J et al. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 2004;14:287–295.CrossRefPubMedGoogle Scholar
  39. 39.
    Hoque MO, Lee J, Begum S et al. High-throughput molecular analysis of urine sediment for the detection of bladder cancer by high-density single-nucleotide polymorphism array. Cancer Res 2003;63:5723–5726.PubMedGoogle Scholar
  40. 40.
    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;63:4781–4785.PubMedGoogle Scholar
  41. 41.
    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;18:1001–1005.CrossRefPubMedGoogle Scholar
  42. 42.
    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;10:1126–1137.CrossRefPubMedGoogle Scholar
  43. 43.
    Zhao X, Li C, Paez JG et al. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 2004;64:3060–3071.CrossRefPubMedGoogle Scholar
  44. 44.
    Lin M, Wei LJ, Sellers WR et al. dChipSNP: significance curve and clustering of SNP-array–based loss-of-heterozygosity data. Bioinformatics 2004;20:1233–1240.CrossRefPubMedGoogle Scholar
  45. 45.
    Lam CW, To KF, Tong SF. Genome-wide detection of allelic imbalance in renal cell carcinoma using high-density single-nucleotide polymorphism microarrays. Clin Biochem 2006;39:187–190.CrossRefPubMedGoogle Scholar
  46. 46.
    Koed K, Wiuf C, Christensen LL et al. High-density single nucleotide polymorphism array defines novel stage and location-dependent allelic imbalances in human bladder tumors. Cancer Res 2005;65:34–45.PubMedGoogle Scholar
  47. 47.
    Zhou X, Mok SC, Chen Z et al. Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10 K SNP mapping array. Hum Genet 2004;115:327–330.CrossRefPubMedGoogle Scholar
  48. 48.
    Pfeifer D, Pantic M, Skatulla I et al. Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays. Blood 2007;109:1202–1210.CrossRefPubMedGoogle Scholar
  49. 49.
    Wong KK, Tsang YT, Chang YM et al. Genome-wide allelic imbalance analysis of pediatric gliomas by single nucleotide polymorphic allele array. Cancer Res 2006;66:11172–11178.CrossRefPubMedGoogle Scholar
  50. 50.
    LaFramboise T, Weir BA, Zhao X et al. Allele-specific amplification in cancer revealed by SNP array analysis. PLoS Comput Biol 2005;1:e65.CrossRefPubMedGoogle Scholar
  51. 51.
    Rook MS, Delach SM, Deyneko G et al. Whole genome amplification of DNA from laser capture-microdissected tissue for high-throughput single nucleotide polymorphism and short tandem repeat genotyping. Am J Pathol 2004;164:23–33.CrossRefPubMedGoogle Scholar
  52. 52.
    Dean FB, Hosono S, Fang L et al. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 2002;99:5261–5266.CrossRefPubMedGoogle Scholar
  53. 53.
    Paez JG, Lin M, Beroukhim R et al. Genome coverage and sequence fidelity of phi29 polymerase–based multiple strand displacement whole genome amplification. Nucleic Acids Res 2004;32:e71.CrossRefPubMedGoogle Scholar
  54. 54.
    Wang ZC, Buraimoh A, Iglehart JD et al. Genome-wide analysis for loss of heterozygosity in primary and recurrent phyllodes tumor and fibroadenoma of breast using single nucleotide polymorphism arrays. Breast Cancer Res Treat 2006;97:301–309.CrossRefPubMedGoogle Scholar
  55. 55.
    Thompson ER, Herbert SC, Forrest SM et al. Whole genome SNP arrays using DNA derived from formalin-fixed, paraffin-embedded ovarian tumor tissue. Hum Mutat 2005;26:384–389.CrossRefPubMedGoogle Scholar
  56. 56.
    Walker BA, Leone PE, Jenner MW et al. Integration of global SNP–based mapping and expression arrays reveals key regions, mechanisms, and genes important in the pathogenesis of multiple myeloma. Blood 2006;108:1733–1743.CrossRefPubMedGoogle Scholar
  57. 57.
    Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000;132:365–386.PubMedGoogle Scholar
  58. 58.
    Garraway LA, Widlund HR, Rubin MA et al. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 2005;436:117–122.CrossRefPubMedGoogle Scholar
  59. 59.
    Stordal B, Peters G, Davey R. Similar chromosomal changes in cisplatin- and oxaliplatin-resistant sublines of the H69 SCLC cell line are not associated with platinum resistance. Genes Chromosomes Cancer 2006;45:1094–1105.CrossRefPubMedGoogle Scholar
  60. 60.
    Wang Y, Makedon F, Pearlman J. Tumor classification based on DNA copy number aberrations determined using SNP arrays. Oncol Rep 2006;15 Spec no.:1057–1059.PubMedGoogle Scholar
  61. 61.
    Yuan E, Haghighi F, White S et al. A single nucleotide polymorphism chip–based method for combined genetic and epigenetic profiling: validation in decitabine therapy and tumor/normal comparisons. Cancer Res 2006;66:3443–3351.CrossRefPubMedGoogle Scholar
  62. 62.
    Zorn KK, Jazaeri AA, Awtrey CS et al. Choice of normal ovarian control influences determination of differentially expressed genes in ovarian cancer expression profiling studies. Clin Cancer Res 2003;9:4811–4818.PubMedGoogle Scholar
  63. 63.
    Conrad DF, Andrews TD, Carter NP et al. A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 2006;38:75–81.CrossRefPubMedGoogle Scholar
  64. 64.
    McCarroll SA, Hadnott TN, Perry GH et al. Common deletion polymorphisms in the human genome. Nat Genet 2006;38:86–92.CrossRefPubMedGoogle Scholar
  65. 65.
    Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet 2006; 7:85–97.CrossRefPubMedGoogle Scholar
  66. 66.
    Freeman JL, Perry GH, Feuk L et al. Copy number variation: new insights in genome diversity. Genome Res 2006;16:949–961.CrossRefPubMedGoogle Scholar
  67. 67.
    Goidts V, Cooper DN, Armengol L et al. Complex patterns of copy number variation at sites of segmental duplications: an important category of structural variation in the human genome. Hum Genet 2006;120:270–284.CrossRefPubMedGoogle Scholar
  68. 68.
    Sebat J, Lakshmi B, Troge J et al. Large-scale copy number polymorphism in the human genome. Science 2004;305:525–528.CrossRefPubMedGoogle Scholar
  69. 69.
    Sharp AJ, Cheng Z, Eichler EE. Structural variation of the human genome. Annu Rev Genomics Hum Genet 2006;7:407–442.CrossRefPubMedGoogle Scholar
  70. 70.
    Oliphant A, Barker DL, Stuelpnagel JR, Chee MS. BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques 2002;Suppl 56–58:60–61.Google Scholar
  71. 71.
    Lips EH, Dierssen JW, van Eijk R et al. Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single-nucleotide polymorphism arrays. Cancer Res 2005;65:10188–10191.CrossRefPubMedGoogle Scholar
  72. 72.
    Shen R, Fan JB, Campbell D et al. High-throughput SNP genotyping on universal bead arrays. Mutat Res 2005;573:70–82.PubMedGoogle Scholar
  73. 73.
    Gunderson KL, Kuhn KM, Steemers FJ et al. Whole-genome genotyping of haplotype tag single nucleotide polymorphisms. Pharmacogenomics 2006;7:641–648.CrossRefPubMedGoogle Scholar
  74. 74.
    Peiffer DA, Le JM, Steemers FJ et al. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res 2006;16:1136–1148.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Kwong-Kwok Wong
    • 1
  1. 1.Department of Gynecologic OncologyThe University of Texas, M.D. Anderson Cancer CenterHoustonUSA

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