Chapter 10: Mining Genome-Wide Genetic Markers

PLoS Computational Biology

Volumn 8, Issue 12, 2012, Pages

  Zhang, Xiang ^a   Huang, Shunping ^b   Zhang, Zhaojun ^b   Wang, Wei ^c  

^a Case Western Reserve University   (United States)

^b University of North Carolina   (United States)

^c University of California   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; GENES;

'CURRENT; COMPUTATIONAL APPROACH; GENETIC FACTORS; GENETIC MARKERS; GENOME-WIDE ASSOCIATION STUDIES; LARGE-SCALES; MACHINE LEARNING METHODS; PHENOTYPIC TRAITS; SCIENCE COMMUNITY;

LEARNING SYSTEMS;

ANALYSIS OF VARIANCE; ARTICLE; DATA MINING; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENETIC EPISTASIS; GENETIC MARKER; GENETIC VARIABILITY; GENOTYPING TECHNIQUE; HEREDITY; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MEDICAL DECISION MAKING; MORPHOLOGICAL TRAIT; PHENOTYPIC VARIATION; PROCESS DEVELOPMENT; QUANTITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84872036304     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002828     Document Type: Article

References (25)

1. Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, et al. (2004) The collaborative cross, a community resource for the genetic analysis of complex traits. Nat Genet 36: 1133-1137.
2. The International HapMap Consortium (2003) The international hapmap project. Nature 426 (6968):: 789-796.
3. Saxena R, Voight B, Lyssenko V, Burtt N, de Bakker P, et al. (2007) Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 316: 1331-1336.
4. Scuteri A, Sanna S, Chen W, Uda M, Albai G, et al. (2007) Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits. PLoS Genet 3 (7):: e115 doi:10.1371/journal.pgen.0030115.
5. 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.
6. Weedon M, Lettre G, Freathy R, Lindgren C, Voight B, et al. (2007) A common variant of HMGA2 is associated with adult and childhood height in the general population. Nat Genet 39: 1245-1250.
7. Hirschhorn J, Daly M, (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6: 95-108.
8. McCarthy M, Abecasis G, Cardon L, Goldstein D, Little J, et al. (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9 (5):: 356-369.
9. Thorisson GA, Smith AV, Krishnan L, Stein LD, (2005) The international hapmap project web site. Genome Res 15: 1592.
10. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
11. Balding DJ, (2006) A tutorial on statistical methods for population association studies. Nat Rev Genet 7 (10):: 781-791.
12. Samani NJ, Erdmann J, Hall AS, Hengstenberg C, Mangino M, et al. (2007) Genomewide association analysis of coronary artery disease. N Engl J Med 357: 443-453.
13. Westfall PH, Young SS (1993) Resampling-based multiple testing. Wiley: New York.
14. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol 57 (1):: 289-300.
15. Zhang X, Zou F, Wang W, (2008) FastANOVA: an efficient algorithm for genome-wide association study. KDD 2008: 821-829.
16. Zhang X, Zou F, Wang W, (2009) FastChi: an effcient algorithm for analyzing gene-gene interactions. PSB 2009: 528-539.
17. Zhang X, Pan F, Xie Y, Zou F, Wang W, (2010) COE: a general approach for efficient genome-wide two-locus epistatic test in disease association study. J Comput Biol 17 (3):: 401-415.
18. Zhang X, Huang S, Zou F, Wang W, (2010) TEAM: Efficient two-locus epistasis tests in human genome-wide association study. Bioinformatics 26 (12):: 217-227.
19. Cormen TH, Leiserson CE, Rivest RL, Stein C (2001) Introduction to algorithms. MIT Press and McGraw-Hill.
20. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, et al. (2001) Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 69: 138-147.
21. Cordell HJ, (2002) Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. Hum Mol Genet 11: 2463-2468.
22. Wason J, Dudbridge F, (2010) Comparison of multimarker logistic regression models, with application to a genomewide scan of schizophrenia. BMC Genet 11: 80.
23. Yang C, Wan X, Yang Q, Xue H, Tang N, et al. (2011) A hidden two- locus disease association pattern in genome-wide association studies. BMC Bioinformatics 12: 156.
24. Hoh J, Ott J, (2003) Mathematical multi-locus approaches to localizing complex human trait genes. Nat Rev Genet 4: 701-709.
25. Musani S, Shriner D, Liu N, Feng R, Coffey C, et al. (2007) Detection of gene×gene interactions in genome-wide association studies of human population data. Hum Hered 63 (2):: 67-84.