FastANOVA: An efficient algorithm for genome-wide association study

Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining

Volumn , Issue , 2008, Pages 821-829

  Zhang, Xiang ^a   Zou, Fei ^b   Wang, Wei ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b IL   (United States)

Author keywords

ANOVA test; Association study

Indexed keywords

ANOVA TEST; ASSOCIATION STUDY; BATCH MODES; BONFERRONI CORRECTIONS; COMPLEX PHENOTYPES; COMPUTATIONAL COSTS; EFFICIENT ALGORITHMS; ERROR RATES; GENETIC EFFECTS; GENOME-WIDE ASSOCIATIONS; JOINT EFFECTS; ORDERS OF MAGNITUDES; PERMUTATION PROCEDURES; PERMUTATION TESTS; SINGLE NUCLEOTIDE POLYMORPHISMS; UNDERLYING MECHANISMS; UPPER BOUNDS;

ANALYSIS OF VARIANCE (ANOVA); ERROR CORRECTION; INFORMATION MANAGEMENT; MINING; REGRESSION ANALYSIS; RISK PERCEPTION;

TESTING;

EID: 65449155592     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1401890.1401988     Document Type: Conference Paper

References (27)

1. http://www.broad.mit.edu/.
2. http://www.gnf.org/.
3. http://www.jax.org/.
4. D. J. Balding. A tutorial on statistical methods for population association studies. Nature Reviews Genetics, 7(10):781-791, 2006.
5. O. Carlborg, L. Andersson, and B. Kinghom. The use of a genetic algorithm for simultaneous mapping of multiple interacting quantitative trait loci. Genetics, 155(4):2003-2010, 2000.
6. C. S. Carlson, M. A. Eberle, L. Kruglyak, and D. A. Nickerson. Mapping complex disease loci in whole-genome association studies. Nature, 429:446-452, 2004.
7. R. W. Doerge. Multifactorial genetics: Mapping and analysis of quantitative trait loci in experimental populations. Nature Reviews Genetics, 3:43-52, 2002.
8. D. M. Evans, J. Marchini, A. P. Morris, and L. R. Cardon. Two-stage two-locus models in genome-wide association. PLoS Genet., 2: e157, 2006.
9. E. Halperin, G. Kimmel, and R. Shamir. Tag snp selection in genotype data for maximizing snp prediction accuracy. In Proc. ISMB, 2005.
10. J. Hon and et al. Selecting snps in two-stage analysis of disease association data: a model-free approach. Ann. Hum. Genet., 64:413-417, 2000.
11. J. Hoh and J. Ott. Mathematical multi-locus approaches to localizing complex human trait genes. Nature Reviews Genetics, 4:701-709, 2003.
12. F. Y. Ideraabdullah and et al. Genetic and haplotype diversity among wild-derived mouse inbred strains. Genome Res., 14(10a):1880-1887, 2004.
13. H. Liu and H. Motoda. Feature selection for knowledge discovery and data mining. Boston: Kluwer Academic Publishers, 1998.
14. R. G. Miller. Simultaneous Statistical Inference. Springer Verlag New York, 1981.
15. R. Nakamichi and et al. Detection of closely linked multiple quantitative trait loci using a genetic algorithm. Genetics, 158(1):463-475, 2001.
16. M. R. Nelson, S. L. Kardia, R. E. Ferrell, and C. F. Sing. A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Research, 11:458-470, 2001.
17. Y. Ohno and et al. Selective genotyping with epistasis can be utilized for a major quantitative trait locus mapping in hypertension in rats. Genetics, 155:785-792, 2000.
18. M. Pagano and K. Gauvreau. Principles of Biostatistics. Pacific Grove, CA: Duxbury Press, 2000.
19. M. D. Ritchie, L. W. Hahn, N. Roodi, L. R. Bailey, W. D. Dupont, F. F. Parl, and J. H. Moore. Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. American Journal of Human Genetics, 69:138-147, 2001.
20. A. Roberts, L. McMillan, W. Wang, J. Parker, I. Rusyn, and D. Threadgill. Inferring missing genotypes in large snp panels using fast nearest-neighbor searches over sliding windows. In Proc. ISMB, 2007.
21. R. Saxena and et al. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science, 316:1331-1336, 2007.
22. A. Scuteri and et al. Genome-wide association scan shows genetic variants in the fto gene are associated with obesity-related traits. PLoS Genet., 3(7), 2007.
23. P. Sebastiani, R. Lazarus, S. T. Weiss, L. M. Kunkel, I. S. Kohane, and M. F. Ramoni. Minimal haplotype tagging. Proc. Natl. Acad. Sci. USA, 100(17):9900-9905, 2003.
24. D. Segrè, A. DeLuna, G. M. Church, and R. Kishony. Modular epistasis in yeast metabolism. Nat. Genet, 37:77-83, 2005.
25. K. Shimomura and et al. Genome-wide epistatic interaction analysis reveals complex genetic determinants of circadian behavior in mice. Genome Res., 11(6):959-980, 2001.
26. C. M. Wade and M. J. Daly. Genetic variation in laboratory mice. Nat. Genet., 37:1175-1180, 2005.
27. M. N. Weedon and et al. A common variant of hmga2 is associated with adult and childhood height in the general population. Nat. Genet., 39:1245-1250, 2007.