Analysis of Single Nucleotide Polymorphisms in Case–Control Studies

Methods in Molecular Biology

Volumn 719, Issue , 2011, Pages 219-234

  Li, Yonghong ^a   Shiffman, Dov ^a   Oberbauer, Rainer ^b  

^a CELERA   (United States)

^b MEDICAL UNIVERSITY OF VIENNA   (Austria)

Author keywords

Case control association studies; Genetic analysis; Genotyping; Linkage disequilibrium; Single nucleotide polymorphism

Indexed keywords

ARTICLE; BIOLOGY; CASE CONTROL STUDY; CHROMOSOME MAP; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENERAL ASPECTS OF DISEASE; GENETICS; GENOTYPE; HUMAN; QUALITY CONTROL; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM;

CASE-CONTROL STUDIES; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DISEASE; GENE FREQUENCY; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS;

EID: 79958248715     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-027-0_10     Document Type: Chapter

References (36)

1. The International HapMap Project. (2003) Nature 426, 789–96.
2. Hindorff, L.A., Sethupathy, P., Junkins, H.A., Ramos, E.M., Mehta, J.P., Collins, F.S., and Manolio, T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106, 9362–7.
3. Li, Y., and Begovich, A.B. (2009) Unraveling the genetics of complex diseases: susceptibility genes for rheumatoid arthritis and psoriasis. Semin Immunol 21, 318–27.
4. Hahn, L.W., Ritchie, M.D., and Moore, J.H. (2003) Multifactor dimensionality reduction software for detecting gene–gene and gene– environment interactions. Bioinformatics 19, 376–82.
5. Torkamani, A., and Schork, N.J. (2009) Pathway and network analysis with high-density allelic association data. Methods Mol Biol 563, 289–301.
6. Vance, J.M. (2006) Collection of biological samples for DNA analysis. Genetic Analysis of Complex Diseases, 2nd edition, Ed. Haines, J.L. & Pericak-Vance, M., Wiley, New York.
7. Germer, S., Holland, M.J., and Higuchi, R. (2000) High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res 10, 258–66.
8. Begovich, A.B., Carlton, V.E., Honigberg, L.A., Schrodi, S.J., Chokkalingam, A.P., Alexander, H.C., Ardlie, K.G., Huang, Q., Smith, A.M., Spoerke, J.M., Conn, M.T., Chang, M., Chang, S.Y., Saiki, R.K., Catanese, J.J., Leong, D.U., Garcia, V.E., McAllister, L.B., Jeffery, D.A., Lee, A.T., Batliwalla, F., Remmers, E., Criswell, L.A., Seldin, M.F., Kastner, D.L., Amos, C.I., Sninsky, J.J., and Gregersen, P.K. (2004) A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am J Hum Genet 75, 330–7.
9. Luke, M.M., Kane, J.P., Liu, D.M., Rowland, C.M., Shiffman, D., Cassano, J., Catanese, J.J., Pullinger, C.R., Leong, D.U., Arellano, A.R., Tong, C.H., Movsesyan, I., Naya-Vigne, J., Noordhof, C., Feric, N.T., Malloy, M.J., Topol, E.J., Koschinsky, M.L., Devlin, J.J., and Ellis, S.G. (2007) A polymorphism in the protease-like domain of apolipoprotein(a) is associated with severe coronary artery disease. Arterioscler Thromb Vasc Biol 27, 2030–6.
10. Shiffman, D., Kane, J.P., Louie, J.Z., Arellano, A.R., Ross, D.A., Catanese, J.J., Malloy, M.J., Ellis, S.G., and Devlin, J.J. (2008) Analysis of 17,576 potentially functional SNPs in three case–control studies of myocardial infarction. PLoS One 3, e2895.
11. Balding, D.J. (2006) A tutorial on statistical methods for population association studies. Nat Rev Genet 7, 781–91.
12. Armitage, P. (1955) Tests for linear trends in proportions and frequencies. Biometrics 26, 535–46.
13. Bonferonni, C.E. (1936) Teoria statistica delle classi e calcolo delle probabilità. Pubblicazioni del R Istituto Superiore di Scienze Economiche e Commerciali di Firenze 8, 3–62.
14. Benjamini, Y., and Hockberg, Y. (1995) Controlling the false discovery rate: a new and powerful approach to multiple testing. J R Stat Soc Ser B 57, 1289–1300.
15. Stephens, M., and Balding, D.J. (2009) Bayesian statistical methods for genetic association studies. Nat Rev Genet 10, 681–90.
16. Mantel, N., and Haenszel, W. (1959) Statistical aspects of the analysis of data from retrospective studies of disease. J Natl Cancer Inst 22, 719–48.
17. Rothman, K., and Greenland, S. (1998) Modern Epidemiology, 2nd edition, Lippincott Williams and Wilkins, Philadelphia, PA.
18. Chang, M., Li, Y., Yan, C., Callis, K., Matsunami, N., Garcia, V., Cargill, M., Civello, D., Bui, N., Catanese, J., Leppert, M., Krueger, G., Begovich, A., and Schrodi, S. (2008) Variants in the 5q31 cytokine gene cluster are associated with psoriasis. Genes Immun 9, 176–81.
19. Li, Y., Chang, M., Schrodi, S., Callis-Duffin, K., Matsunami, N., Civello, D., Bui, N., Catanese, J., Leppert, M.F., Krueger, G.G., and Begovich, A. (2008) The 5q31 variants associated with psoriasis and Crohn’s disease are distinct. Hum Mol Genet 17, 2978–85.
20. Cargill, M., Schrodi, S.J., Chang, M., Garcia, V.E., Brandon, R., Callis, K.P., Matsunami, N., Ardlie, K.G., Civello, D., Catanese, J.J., Leong, D.U., Panko, J.M., McAllister, L.B., Hansen, C.B., Papenfuss, J., Prescott, S.M., White, T.J., Leppert, M.F., Krueger, G.G., and Begovich, A.B. (2007) A large-scale genetic association study confirms IL12B and leads to the identification of IL23R as psoriasis-risk genes. Am J Hum Genet 80, 273–90.
21. Niu, T. (2004) Algorithms for inferring hap-lotypes. Genet Epidemiol 27, 334–47.
22. Romeo, S., Kozlitina, J., Xing, C., Pertsemlidis, A., Cox, D., Pennacchio, L.A., Boerwinkle, E., Cohen, J.C., and Hobbs, H.H. (2008) Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. Nat Genet 40, 1461–5.
23. Bottini, N., Musumeci, L., Alonso, A., Rahmouni, S., Nika, K., Rostamkhani, M., MacMurray, J., Meloni, G.F., Lucarelli, P., Pellecchia, M., Eisenbarth, G.S., Comings, D., and Mustelin, T. (2004) A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes. Nat Genet 36, 337–8.
24. Vang, T., Congia, M., Macis, M.D., Musumeci, L., Orru, V., Zavattari, P., Nika, K., Tautz, L., Tasken, K., Cucca, F., Mustelin, T., and Bottini, N. (2005) Autoimmune-associated lymphoid tyrosine phosphatase is a gain-of-function variant. Nat Genet 37, 1317–9.
25. Cameron, L., Webster, R.B., Strempel, J.M., Kiesler, P., Kabesch, M., Ramachandran, H., Yu, L., Stern, D.A., Graves, P.E., Lohman, I.C., Wright, A.L., Halonen, M., Klimecki, W.T., and Vercelli, D. (2006) Th2 cell-selective enhancement of human IL13 transcription by IL13-1112C > T, a polymorphism associated with allergic inflammation. J Immunol 177, 8633–42.
26. Skol, A.D., Scott, L.J., Abecasis, G.R., and Boehnke, M. (2006) Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet 38, 209–13.
27. Wellcome Trust Case Control Consortium. (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661–78.
28. Tobin, M.D., Sheehan, N.A., Scurrah, K.J., and Burton, P.R. (2005) Adjusting for treatment effects in studies of quantitative traits: antihypertensive therapy and systolic blood pressure. Stat Med 24, 2911–35.
29. Johnson, A.D. (2009) Single-nucleotide polymorphism bioinformatics: a comprehensive review of resources. Circ Cardiovasc Genet 2, 530–6.
30. Little, J., Higgins, J.P., Ioannidis, J.P., Moher, D., Gagnon, F., von Elm, E., Khoury, M.J., Cohen, B., Davey-Smith, G., Grimshaw, J., Scheet, P., Gwinn, M., Williamson, R.E., Zou, G.Y., Hutchings, K., Johnson, C.Y., Tait, V., Wiens, M., Golding, J., van Duijn, C., McLaughlin, J., Paterson, A., Wells, G., Fortier, I., Freedman, M., Zecevic, M., King, R., Infante-Rivard, C., Stewart, A., and Birkett, N. (2009) Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE statement. Eur J Epidemiol 24, 37–55.
31. Cardon, L.R., and Bell, J.I. (2001) Association study designs for complex diseases. Nat Rev Genet 2, 91–9.
32. Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A., and Reich, D. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38, 904–9.
33. Manolio, T.A., Collins, F.S., Cox, N.J., Goldstein, D.B., Hindorff, L.A., Hunter, D.J., McCarthy, M.I., Ramos, E.M., Cardon, L.R., Chakravarti, A., Cho, J.H., Guttmacher, A.E., Kong, A., Kruglyak, L., Mardis, E., Rotimi, C.N., Slatkin, M., Valle, D., Whittemore, A.S., Boehnke, M., Clark, A.G., Eichler, E.E., Gibson, G., Haines, J.L., Mackay, T.F., McCarroll, S.A., and Visscher, P.M. (2009) Finding the missing heritability of complex diseases. Nature 461, 747–53.
34. Wain, L.V., Armour, J.A., and Tobin, M.D. (2009) Genomic copy number variation, human health, and disease. Lancet 374, 340–50.
35. Ionita-Laza, I., Rogers, A.J., Lange, C., Raby, B.A., and Lee, C. (2009) Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis. Genomics 93, 22–6.
36. McCarthy, M.I., Abecasis, G.R., Cardon, L.R., Goldstein, D.B., Little, J., Ioannidis, J.P., and Hirschhorn, J.N. (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9, 356–69.