Seminars in Oncology
Volume 34 , Pages S21-S24 , April 2007

Population Genetic Tools: Application to Cancer

  • Stacey Gabriel

      Affiliations

    • Corresponding Author InformationAddress reprint requests to Stacey Gabriel, PhD, Broad Institute of MIT and Harvard, Building #300 1 Kendall Square, Cambridge, MA 02139.

References 

  1. Hall JM, Lee MK, Newman B, et al. Linkage of early-onset familial breast cancer to chromosome 17q21. Science. 1990;250:1684–1689
  2. Groden J, Thliveris A, Samowitz W, et al. Identification and characterization of the familial adenomatous polyposis coli gene. Cell. 1991;66:589–600
  3. Wooster R, Bignell G, Lancaster J, et al. Identification of the breast cancer susceptibility gene BRCA2. Nature. 1995;378:789–792
  4. Houlston RS, Peto J. In:  Eeles RA,  Ponder BA, et al. editor. Genetic predisposition to cancer. London: Chapman & Hall; 1996;p. 208–226
  5. Lichtenstein P, Holm NV, Verkasalo PK, et al. Environmental and heritable factors in the causation of cancer–Analyses of cohorts of twins from Sweden, Denmark, and Finland. N Engl J Med. 2000;343:78–85
  6. Risch N, Merikangas K. The future of genetic studies of complex human diseases. Science. 1996;273:1516–1517
  7. Dunning AM, Healey CS, Pharoah PD, et al. A systematic review of genetic polymorphisms and breast cancer risk. Cancer Epidemiol Biomarkers Prev. 1999;8:843–854
  8. Hirschhorn JN, Lohmueller K, Byrne E, et al. A comprehensive review of genetic association studies. Genet Med. 2002;4:45–61
  9. Simard J, Dumont M, Labuda D, et al. Prostate cancer susceptibility genes: Lessons learned and challenges posed. Endocr Relat Cancer. 2003;10:225–259
  10. Freedman ML, Pearce CL, Penney KL, et al. Systematic evaluation of genetic variation at the androgen receptor locus and risk of prostate cancer in a multiethnic cohort study. Am J Hum Genet. 2005;76:82–90
  11. Cargill M, Altshuler D, Ireland J, et al. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet. 1999;22:231–238
  12. Halushka MK, Mathews DJ, Bailey JA, et al. GIST: A web tool for collecting gene information. Physiol Genomics. 1999;1:75–81
  13. Sachidanandam R, Weissman D, Schmidt SC, et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature. 2001;409:928–933
  14. Gabriel SB, Schaffner SF, Nguyen H, et al. The structure of haplotype blocks in the human genome. Science. 2002;296:2225–2229
  15. Kruglyak L, Nickerson DA. Variation is the spice of life. Nat Genet. 2001;27:234–236
  16. Reich DE, Gabriel SB, Altshuler D. Quality and completeness of SNP databases. Nat Genet. 2003;33:457–458
  17. Strittmatter WJ, Roses AD. Apolipoprotein E and Alzheimer disease. Proc Natl Acad Sci U S A. 1995;92:4725–4727
  18. Dahlback B. Resistance to activated protein C caused by the factor VR506Q mutation is a common risk factor for venous thrombosis. Thromb Haemost. 1997;78:483–488
  19. Altshuler D, Hirschhorn JN, Klannemark M, et al. The common PPARgamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nat Genet. 2000;26:76–80
  20. Begovich AB, Carlton VE, Honigberg LA, et al. A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am J Hum Genet. 2004;75:330–337
  21. Nistico L, Buzzetti R, Pritchard LE, et al. The CTLA-4 gene region of chromosome 2q33 is linked to, and associated with, type 1 diabetes (Belgian Diabetes Registry). Hum Mol Genet. 1996;5:1075–1080
  22. Samson M, Libert F, Doranz BJ, et al. Resistance to HIV-1 infection in Caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature. 1996;382:722–725
  23. Klein RJ, Zeiss C, Chew EY, et al. Complement factor H polymorphism in age-related macular degeneration. Science. 2005;308:385–389
  24. Haines JL, Hauser MA, Schmidt S, et al. Complement factor H variant increases the risk of age-related macular degeneration. Science. 2005;308:419–421
  25. Patil N, Berno AJ, Hinds DA, et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science. 2001;294:1719–1723
  26. Dawson E, Abecasis GR, Bumpstead S, et al. A first-generation linkage disequilibrium map of human chromosome 22. Nature. 2002;418:544–548
  27. Carlson CS, Eberle MA, Rieder MJ, et al. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet. 2004;74:106–120
  28. The International HapMap Consortium. Integrating ethics and science in the International HapMap Project. Nature. 2004;426:789–796
  29. Alshuler D, Brooks LD, Chakravarti A, et al. A haplotype map of the human genome. Nature. 2005;437:1299–1320
  30. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics. 2005;21:263–265
  31. Fisher SA, Abecasis GR, Yashar BM, et al. Meta-analysis of genome scans of age-related macular degeneration. Hum Mol Genet. 2005;14:2257–2264
  32. Hunter DJ, Riboli E, Haiman CA, et al. A candidate gene approach to searching for low-penetrance breast and prostate cancer genes. Nat Rev Cancer. 2005;5:977–985
  33. 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
  34. Paez JG, Janne PA, Lee JC, et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science. 2004;304:1497–1500
  35. Lynch TJ, Bell DW, Sordella R, 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;350:2129–2139
  36. Pao W, Miller V, Zakowski M, et al. EGF receptor gene mutations are common in lung cancers from “never smokers” and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc Natl Acad Sci U S A. 2004;101:13306–13311
  37. Stephens P, Edkins S, Davies H, et al. A screen of the complete protein kinase gene family identifies diverse patterns of somatic mutations in human breast cancer. Nat Genet. 2005;37:590–592

PII: S0093-7754(07)00021-8

doi: 10.1053/j.seminoncol.2007.01.008

Seminars in Oncology
Volume 34 , Pages S21-S24 , April 2007