Practical issues in imputation-based association mapping

PLoS Genetics

Volumn 4, Issue 12, 2008, Pages

  Guan, Yongtao ^a   Stephens, Matthew ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYSIS; ARTICLE; AVERAGE; BAYES THEOREM; COMPUTER PROGRAM; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; GENE MAPPING; GENETIC ASSOCIATION; GENOME; GENOTYPE; IMPUTATION; INFORMATION; PHENOTYPE; PROFESSIONAL PRACTICE; SAMPLING; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARD; BIOLOGICAL MODEL; GENETIC DATABASE; GENETIC PROCEDURES; HUMAN; MATHEMATICAL COMPUTING; STATISTICAL MODEL;

DATABASES, GENETIC; GENETIC TECHNIQUES; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MATHEMATICAL COMPUTING; MODELS, GENETIC; MODELS, STATISTICAL; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 58149175796     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000279     Document Type: Article

References (22)

1. The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million snps. Nature 449:7164: 851-861.
2. Servin B, Stephens M (2007) Efficient multipoint analysis of association studies: candidate regions and quantitative traits. PLoS Genetics 3.
3. Marchini J, Howie B, Myers S, McVean G, Donnelly P (2007) A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 39: 906-913.
4. Lin DY, Hu Y, Huang BE (2008) Simple and efficient analysis of disease association with missing genotype data. Am J Hum Genet 82: 444-452.
5. Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, Duren WL, Erdos MR, Stringham HM, et al. (2007) A genome-wide association study of type 2 diabetes in finns detects multiple susceptibility variants. Science 316: 1341-1345.
6. Reiner AP, Barber MJ, Guan Y, Ridker PM, Lange LA, Chasman DI, Walston JD, Cooper GM, Jenny NS, Rieder MJ, Durda JP, Smith JD, Novembre J, Tracy RP, Rotter JI, Stephens M, Nickerson DA, Krauss RM (May 2008) Polymorphisms of the hnf1a gene encoding hepatocyte nuclear factor-1 alpha are associated with c-reactive protein. Am J Hum Genet 82(5): 1193-1201.
7. Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78: 629-644.
8. Wakefield J (2007) A bayesian measure of the probability of false discovery in genetic epidemiology studies. Am J Hum Genet 81: 208-227.
9. 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.
10. Nicolae DL (2006) Quantifying the amount of missing information in genetic association studies. Genetic Epidemiology 30: 703-717.
11. Dai JY, Ruczinski I, LeBlanc M, Kooperberg C (2006) Imputation methods to improve inference in snp association studies. Genet Epidemiol 30: 690-702.
12. Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81(5): 1084-1097.
13. Li N, Stephens M (2003) Modelling linkage disequilibrium, and identifying recombination hotspots using snp data. Genetics 165: 2213-2233.
14. Albert MA, Danielson E, Rifai N, Ridker PM (2001) Effect of statin therapy on c-reactive protein levels. Journal of American Medical Aassociation 286: 64-70.
15. Ripley BD (1987) Stochastic Simulation. New York: Wiley.
16. Sellke T, Bayarri MJ, Berger JO (2001) Calibration of p-values for testing precise null hypotheses. American Statistician 55(1): 62-71.
17. Wakefield J (2008) Bayes factors for genome-wide association studies: Comparison with p-values. Genetic Epidemiology, to appear, 2008.
18. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100(16): 9440-9445.
19. Cox DR, Snell EJ (1989) Analysis of Binary Data. London: Chapman and Hall/CRC, 2nd edition.
20. Plagnol V, Cooper JD, Todd JA, Clayton DG (2007) A method to address differential bias in genotyping in large-scale association studies. PLoS Genetics 3.
21. Seaman SR, Richardson S (2004) Equivalence of prospective and retrospective models in the bayesian analysis of case-control studies. Biometrika 91: 15-25.
22. Cohen J, Pertsemlidis A, Kotowski IK, Graham R, Garcia CK, Hobbs HH (2005) Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9. Nature Genetics 37: 161-165.