Block-based Bayesian epistasis association mapping with application to WTCCC type 1 diabetes data

Annals of Applied Statistics

Volumn 5, Issue 3, 2011, Pages 2052-2077

  Zhang, Yu ^a   Zhang, Jing ^a   Liu, Jun S ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Bayesian methods; Disease association study; Epistasis; LD block

Indexed keywords

EID: 84859103409     PISSN: 19326157     EISSN: 19417330     Source Type: Journal    
DOI: 10.1214/11-AOAS469     Document Type: Article

References (35)

1. Anderson, E. C. and Slatkin, M. (2004). Population-genetic basis of haplotype blocks in the 5q31 region. Am. J. Hum. Genet. 74 40-49.
2. Barrett, J. C., Fry, B., Maller, J. and Daly, M. J. (2005). Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics 21 263-265.
3. de Bakker, P. I., Yelensky, R., Pe'er, I., Gabriel, S. B., Daly, M. J. and Altshuler, D. (2005). Efficiency and power in genetic association studies. Nat. Genet. 37 1217-1223.
4. Friedman, J., Hastie, T. and Tibshirani, R. (2010). A note on the group lasso and a sparse group lasso. Technical report, Stanford Univ.
5. Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S. N., Rotimi, C., Adeyemo, A., Cooper, R., Ward, R., Lander, E. S., Daly, M. J. and Altshuler, D. (2002). The structure of haplotype blocks in the human genome. Science 296 2225-2229.
6. Heckerman, D., Geiger, D. and Chickering, D. (1995). Learning Bayesian networks: The combination of knowledge and statistical data. Mach. Learn. 20 197-243.
7. The International HapMap Consortium (2005). A haplotype map of the human genome. Nature 437 1299-1320.
8. Jeffreys, A. J., Kauppi, L. and Neumann, R. (2001). Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29 217-222.
9. Jeffreys, A. J., Ritchie, A. and Neumann, R. (2000). High resolution analysis of haplotype diversity and meiotic crossover in the human TAP2 recombination hotspot. Hum. Mol. Genet. 9 725-733.
10. Johnson, G. C., Esposito, L., Barratt, B. J., Smith, A. N., Heward, J., Genova, G. D., Ueda, H., Cordell, H. J., Eaves, I. A., Dudbridge, F., Twells, R. C., Payne, F., Hughes, W., Nutland, S., Stevens, H., Carr, P., Tuomilehto-Wolf, E., Tuomilehto, J., Gough, S. C., Clayton, D. G. and Todd, J. A. (2001). Haplotype tagging for the identification of common disease genes. Nat. Genet. 29 233-237.
11. Kuno, S.-I., Taniguchi, A., Saito, A., Tsuchida-Otsuka, S. and Kamatani, N. (2004). Comparison between various strategies for the disease-gene mapping using linkage disequilibrium analyses: Studies on adenine phosphoribosyltransferase deficiency used as an example. J. Hum. Genet. 49 463-473.
12. Liu, J. S. (2001). Monte Carlo Strategies in Scientific Computing. Springer, New York.
13. Marchini, J., Donnelly, P. and Cardon, L. R. (2005). Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat. Genet. 37 413-417.
14. Marchini, J., Howie, B., Myers, S., McVean, G. and Donnelly, P. (2007). A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39 906-913.
15. Nejentsev, S., Howson, J. M. M., Walker, N. M., Szeszko, J., Field, S. F., Stevens, H. E., Reynolds, P., Hardy, M., King, E., Masters, J., Hulme, J., Maier, L. M., Smyth, D., Bailey, R., Cooper, J. D., Ribas, G., Campbell, R. D., Clayton, D. G., Todd, J. A. and The Wellcome Trust Case Control Consortium (2007). Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A. Nature 450 887-892.
16. Nielsen, D. M., Ehm, M. G., Zaykin, D. V. and Weir, B. S. (2004). Effect of two-and three-locus linkage disequilibrium on the power to detect marker/phenotype associations. Genetics 168 1029-1040.
17. Phillips, M. S., Lawrence, R., Sachidanandam, R., Morris, A. P., Balding, D. J., Donaldson, M. A., Studebaker, J. F., Ankener, W. M., Alfisi, S. V., Kuo, F.-S., Camisa, A. L., Pazorov, V., Scott, K. E., Carey, B. J., Faith, J., Katari, G., Bhatti, H. A., Cyr, J. M., Derohannessian, V., Elosua, C., Forman, A. M., Grecco, N. M., Hock, C. R., Kuebler, J. M., Lathrop, J. A., Mockler, M. A., Nachtman, E. P., Restine, S. L., Varde, S. A., Hozza, M. J., Gelfand, C. A., Broxholme, J., Abecasis, G. R., Boyce-Jacino, M. T. and Cardon, L. R. (2003). Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat. Genet. 33 382-387.
18. Przeworski, M. and Wall, J. D. (2001). Why is there so little intragenic linkage disequilibrium in humans? Genet. Res. 77 143-151.
19. Reich, D. E., Cargill, M., Bolk, S., Ireland, J., Sabeti, P. C., Richter, D. J., Lavery, T., Kouyoumjian, R., Farhadian, S. F., Ward, R. and Lander, E. S. (2001). Linkage disequilibrium in the human genome. Nature 411 199-204.
20. Steenkiste, A., Valdes, A., Feolo, M., Hoffman, D., Concannon, P., Noble, J., Schoch, G., Hansen, J., Helmberg, W., Dorman, J. S., Thomson, G. and Pugliese, A. (2007). 13th IHWS 1 diabetes component participating investigators. 14th International HLA and Immunogenetics Workshop: Report on the HLA component of type 1 diabetes. Tissue Antigens 69 214-225.
21. Stumpf, M. P. H. and Goldstein, D. B. (2003). Demography, recombination hotspot intensity, and the block structure of linkage disequilibrium. Curr. Biol. 13 1-8.
22. Viken, M. K., Blomhoff, A., Olsson, M., Akselsen, H. E., Pociot, F., Nerup, J., Kockum, I., Cambon-Thomsen, A., Thorsby, E., Undlien, D. E. et al. (2009). Reproducible association with type 1 diabetes in the extended class I region of the major histocompatibility complex. Genes and Immune 10 303-333.
23. Wall, J. D. and Pritchard, J. K. (2003). Assessing the performance of the haplotype block model of linkage disequilibrium. Am. J. Hum. Genet. 73 502-515.
24. Wang, N., Akey, J. M., Zhang, K., Chakraborty, R. and Jin, L. (2002). Distribution of recombination crossovers and the origin of haplotype blocks: The interplay of population history, recombination, and mutation. Am. J. Hum. Genet. 71 1227-1234.
25. The Wellcome Trust Case Control Consortium (2007). Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447 661-678.
26. Yuan, M. and Lin, Y. (2006). Model selection and estimation in regression with grouped variables. J. R. Stat. Soc. Ser. B Stat. Methodol. 68 49-67.
27. Zhang, K., Calabrese, P., Nordborg, M. and Sun, F. (2002a). Haplotype structure and its applications to association studies: Power and study designs. Am. J. Hum. Genet. 71 1386-1394.
28. Zhang, K., Deng, M., Chen, T., Waterman, M. S. and Sun, F. (2002b). A dynamical programming algorithm for haplotype block partitioning. Proc. Natl. Acad. Sci. USA 99 7335-7339.
29. Zhang, K., Akey, J. M., Wang, N., Xiong, M., Chakraborty, R. and Jin, L. (2003). Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: An act of genetic drift. Hum. Genet. 113 51-59.
30. Zhang, Y. (2011). Bayesian epistasis association mapping via SNP imputation. Biostatistics 12 211-222.
31. Zhang, Y. and Liu, J. S. (2007). Bayesian inference of epistatic interactions in case-control studies. Nat. Genet. 39 1167-1173.
32. Zhang, Y., Niu, T. and Liu, J. S. (2006). A coalescence-guided hierarchical Bayesian method for haplotype inference. Am. J. Hum. Genet. 79 313-322.
33. Zhang, Y., Zhang, J. and Liu, J. S. (2011). Supplement to "Block-based Bayesian epistasis association mapping with application to WTCCC Type 1 diabetes data". DOI:10.1214/11-AOAS469SUPP.
34. Zöllner, S. and Pritchard, J. K. (2005). Coalescent-based association mapping and fine mapping of complex trait loci. Genetics 169 1071-1092.
35. Zou, H. and Hastie, T. (2005). Regularization and variable selection via the elastic net. J. R. Stat. Soc. Ser. B Stat. Methodol. 67 301-320.