Association studies for finding cancer-susceptibility genetic variants (original) (raw)
Houlston, R. S. & Peto, J. in Genetic predisposition to cancer (eds Eeles, R. A., Ponder, B. A. J., Easton, D. F. & Horwich, A.) 208–226 (Chapman & Hall, London, 1996). Book Google Scholar
Lichtenstein, P. 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.343, 78–85 (2000). A landmark paper reporting the heritability of the common cancers based on data from over 40,000 twin pairs from Scandinavia. ArticleCASPubMed Google Scholar
Antoniou, A. C. et al. A comprehensive model for familial breast cancer incorporating BRCA1, BRCA2 and other genes. Br. J. Cancer86, 76–83 (2002). ArticleCASPubMedPubMed Central Google Scholar
Risch, N. Searching for genetic determinants in the new millenium. Nature405, 847–856 (2000). An excellent description of the strengths and weaknesses of different methods for gene mapping in complex diseases. ArticleCASPubMed Google Scholar
Cardon, L. R. & Bell, J. I. Association study designs for complex diseases. Nature Rev. Genet.2, 91–99 (2001). ArticleCASPubMed Google Scholar
Chakravarti, A. Population genetics — making sense out of sequence. Nature Genet.21, 56–60 (1999). ArticleCASPubMed Google Scholar
Glober, G. A., Cantrell, E. G., Doll, R. & Peto, R. Interaction between ABO and rhesus blood groups, the site of origin of gastric cancers, and the age and sex of the patient. Gut12, 570–573 (1971). ArticleCASPubMedPubMed Central Google Scholar
Hildesheim, A. et al. Association of HLA class I and II alleles and extended haplotypes with nasopharyngeal carcinoma in Taiwan. J. Natl Cancer Inst.94, 1780–1789 (2002). ArticleCASPubMed Google Scholar
Engel, L. S. et al. Pooled analysis and meta-analysis of glutathione _S_-transferase M1 and bladder cancer: a HuGE review. Am. J. Epidemiol.156, 95–109 (2002). ArticlePubMed Google Scholar
Vineis, P. et al. Current smoking, occupation, _N_-acetyltransferase-2 and bladder cancer: a pooled analysis of genotype-based studies. Cancer Epidemiol. Biomarkers Prev.10, 1249–1252 (2001). CASPubMed Google Scholar
Dunning, A. M. et al. A systematic review of genetic polymorphisms and breast cancer risk. Cancer Epidemiol. Biomarkers Prev.8, 843–854 (1999). CASPubMed Google Scholar
Gonzalez, C. A., Sala, N. & Capella, G. Genetic susceptibility and gastric cancer risk. Int. J. Cancer100, 249–260 (2002). ArticleCASPubMed Google Scholar
Ioannidis, J. P., Ntzani, E. E., Trikalinos, T. A. & Contopoulos-Ioannidis, D. G. Replication validity of genetic association studies. Nature Genet.29, 306–309 (2001). ArticleCASPubMed Google Scholar
Lohmueller, K. E., Pearce, C. L., Pike, M., Lander, E. S. & Hirschhorn, J. N. Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nature Genet.33, 177–182 (2003). ArticleCASPubMed Google Scholar
Tabor, H. K., Risch, N. J. & Myers, R. M. Candidate-gene approaches for studying complex genetic traits: practical considerations. Nature Rev. Genet.3, 391–397 (2002). ArticleCASPubMed Google Scholar
Dahlman, I. et al. Parameters for reliable results in genetic association studies in common disease. Nature Genet.30, 149–150 (2002). ArticleCASPubMed Google Scholar
Colhoun, H. M., McKeigue, P. M. & Davey Smith, G. Problems of reporting genetic associations with complex outcomes. Lancet361, 865–872 (2003). ArticlePubMed Google Scholar
Patil, N. et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science294, 1719–1723 (2001). ArticleCASPubMed Google Scholar
Johnson, G. C. et al. Haplotype tagging for the identification of common disease genes. Nature Genet.29, 233–237 (2001). ArticleCASPubMed Google Scholar
Gabriel, S. B. et al. The structure of haplotype blocks in the human genome. Science296, 2225–2229 (2002). ArticleCASPubMed Google Scholar
Zhang, K., Calabrese, P., Nordborg, M. & Sun, F. Haplotype block structure and its applications to association studies: power and study designs. Am. J. Hum. Genet.71, 1386–1394 (2002). ArticleCASPubMedPubMed Central Google Scholar
Meng, Z., Zaykin, D. V., Xu, C. F., Wagner, M. & Ehm, M. G. Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes. Am. J. Hum. Genet.73, 115–130 (2003). ArticleCASPubMedPubMed Central Google Scholar
Haiman, C. A. et al. A comprehensive haplotype analysis of CYP19 and breast cancer risk: the Multiethnic Cohort. Hum. Mol. Genet.12, 2679–2692 (2003). One of the first studies to use a comprehensive haplotype-tagging approach to examine a gene for common variants associated with breast cancer risk. ArticleCASPubMed Google Scholar
Carlson, C. S. et al. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am. J. Hum. Genet.74, 106–120 (2004). This paper reports the results of re-sequencing 100 genes in 24 African-American and 23 European-American samples. They showed that a tagging-SNP set can comprehensively interrogate for main effects of common variants, but that tagging SNPs should be selected separately for populations of different ancestries. ArticleCASPubMed Google Scholar
Chapman, J. M., Cooper, J. D., Todd, J. A. & Clayton, D. G. Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power. Hum. Hered.56, 18–31 (2003). ArticlePubMed Google Scholar
Zhang, K. & Jin, L. HaploBlockFinder: haplotype block analyses. Bioinformatics19, 1300–1301 (2003). ArticleCASPubMed Google Scholar
Stram, D. O. et al. Choosing haplotype-tagging SNPS based on unphased genotype data using a preliminary sample of unrelated subjects with an example from the Multiethnic Cohort Study. Hum. Hered.55, 27–36 (2003). ArticlePubMed Google Scholar
Ke, X. & Cardon, L. R. Efficient selective screening of haplotype tag SNPs. Bioinformatics19, 287–288 (2003). ArticleCASPubMed Google Scholar
Neale, B. M. & Sham, P. C. The future of association studies: gene-based analysis and replication. Am. J. Hum. Genet.75, 353–362 (2004). ArticleCASPubMedPubMed Central Google Scholar
Marron, M. P. et al. Insulin-dependent diabetes mellitus (IDDM) is associated with CTLA4 polymorphisms in multiple ethnic groups. Hum. Mol. Genet.6, 1275–1282 (1997). ArticleCASPubMed Google Scholar
Hugot, J. P. et al. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature411, 599–603 (2001). ArticleCASPubMed Google Scholar
Boyd, N. F. et al. Heritability of mammographic density, a risk factor for breast cancer. N. Engl. J. Med.347, 886–894 (2002). ArticlePubMed Google Scholar
Lakhani, S. R. et al. Multifactorial analysis of differences between sporadic breast cancers and cancers involving BRCA1 and BRCA2 mutations. J. Natl Cancer Inst.90, 1138–1145 (1998). ArticleCASPubMed Google Scholar
Botstein, D. & Risch, N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nature Genet.33, S228–S237 (2003). Article Google Scholar
Antoniou, A. & Easton, D. F. Polygenic inheritance of breast cancer: implications for design of association studies. Genet. Epidemiol.25, 190–203 (2003). ArticlePubMed Google Scholar
Meijers-Heijboer, H. et al. Low-penetrance susceptibility to breast cancer due to CHEK2(*)1100delC in noncarriers of BRCA1 or BRCA2 mutations. Nature Genet.31, 55–59 (2002). ArticleCASPubMed Google Scholar
Dunning, A. M. et al. The extent of linkage disequilibrium in four populations with distinct demographic histories. Am. J. Hum. Genet.67, 1544–1554 (2000). ArticleCASPubMedPubMed Central Google Scholar
Sham, P., Bader, J. S., Craig, I., O'Donovan, M. & Owen, M. DNA Pooling: a tool for large-scale association studies. Nature Rev. Genet.3, 862–871 (2002). ArticleCASPubMed Google Scholar
Barratt, B. J. et al. Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design. Ann. Hum. Genet.66, 393–405 (2002). ArticleCASPubMed Google Scholar
Risch, N. & Merikangas, K. The future of genetic studies of complex diseases. Science273, 1516–1517 (1996). ArticleCASPubMed Google Scholar
Carlson, C. S., Eberle, M. A., Kruglyak, L. & Nickerson, D. A. Mapping complex disease loci in whole-genome association studies. Nature429, 446–452 (2004). ArticleCASPubMed Google Scholar
Kruglyak, L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genet.22, 139–144 (1999). ArticleCASPubMed Google Scholar
Kuschel, B. et al. Common polymorphisms in CHEK2 (checkpoint kinase 2) are not associated with breast cancer risk. Cancer Epidemiol. Biomarkers Prev.12, 809–812 (2003). CASPubMed Google Scholar
Hastie, T., Tibshirani, R. & Friedman, J. The elements of statistical learning (Springer–Verlag, New York, 2001). Book Google Scholar
Ritchie, M. D. et al. Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am. J. Hum. Genet.69, 138–147 (2001). ArticleCASPubMedPubMed Central Google Scholar
Wacholder, S., Chanock, S., Garcia-Closas, M., El Ghormli, L. & Rothman, N. Assessing the probability that a positive report is false: an approach for molecular epidemiology studies. J. Natl Cancer Inst.96, 434–442 (2004). ArticlePubMedPubMed Central Google Scholar
Thomas, D. C. & Clayton, D. G. Betting odds and genetic associations. J. Natl Cancer Inst.96, 421–423 (2004). ArticlePubMed Google Scholar
Devlin, B. & Roeder, K. Genomic control for association studies. Biometrics55, 997–1004 (1999). ArticleCASPubMed Google Scholar
Pritchard, J. K. & Rosenberg, N. A. The use of unlinked genetic markers to detect population stratification in association studies. Am. J. Hum. Genet.65, 220–228 (1999). ArticleCASPubMedPubMed Central Google Scholar
Cardon, L. R. & Palmer, L. J. Population stratification and spurious allelic association. Lancet361, 598–604 (2003). An excellent review of methods to detect and account for population stratification in genotype–phenotype association studies. ArticlePubMed Google Scholar
Marchini, J., Cardon, L. R., Phillips, M. S. & Donnelly, P. The effects of human population structure on large genetic association studies. Nature Genet.36, 512–517 (2004). ArticleCASPubMed Google Scholar
Freedman, M. L. et al. Assessing the impact of population stratification on genetic association studies. Nature Genet.36, 388–393 (2004). ArticleCASPubMed Google Scholar
Risch, N. The genetic epidemiology of cancer: interpreting family and twin studies and their implications for molecular genetic approaches. Cancer Epidemiol. Biomarkers Prev.10, 733–741 (2001). CASPubMed Google Scholar