140.668 Special Topics in Genomics - Association Studies

Some Basics

NCBI and Genetics Home Research

Pearson TA, Manolio TA. How to interpret a genome-wide association study. JAMA. 2008 Mar 19;299(11):1335-44. pdf

Devlin B, Risch N. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics. 1995 Sep 20;29(2):311-22. pdf



International HapMap Consortium. A haplotype map of the human genome. Nature. 2005 Oct 27;437(7063):1299-320. pdf

International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18;449(7164):851-61. pdf

Environmental Data

Platforms and Genotyping

Affymetrix and Illumina

Genotype Uncertainty

Affymetrix. BRLMM: an Improved Genotype Calling Method for the GeneChip Human Mapping 500K Array Set. 2006. pdf

Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics. 2007 Apr;8(2):485-99. pdf

Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, Lee C, Nizzari MM, Gabriel SB, Purcell S, Daly MJ, Altshuler D. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet. 2008 Oct;40(10):1253-60. pdf


Study Designs

Risch N, Merikangas K. The future of genetic studies of complex human diseases. Science. 1996 Sep 13;273(5281):1516-7. pdf

Laird NM, Lange C. Family-based designs in the age of large-scale gene-association studies. Nat Rev Genet. 2006 May;7(5):385-94. Review. pdf

Laird NM, Lange C. Family-based methods for linkage and association analysis. Adv Genet. 2008;60:219-52. pdf

EDA and Quality Control

Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000 Jun;155(2):945-59. pdf

Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. Genetic structure of human populations. Science. 2002 Dec 20;298(5602):2381-5. pdf

Devlin B, Roeder K. Genomic control for association studies. Biometrics. 1999 Dec;55(4):997-1004. pdf

Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006 Aug;38(8):904-9. pdf

Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD. Genes mirror geography within Europe. Nature. 2008 Nov 13;456(7219):274. pdf


Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 2006 Apr;78(4):629-44. pdf

Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet. 2007 Jul;39(7):906-13. pdf

Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007 Nov;81(5):1084-97. pdf


Analysis and Results


Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007 Jun 7;447(7145):661-78. pdf and supplementary material and commentary 1 and commentary 2.

Balding DJ. A tutorial on statistical methods for population association studies. Nat Rev Genet. 2006 Oct;7(10):781-91. pdf

Hunter DJ, Kraft P. Drinking from the fire hose - statistical issues in genomewide association studies. N Engl J Med. 2007 Aug 2;357(5):436-9. pdf

Manolio TA, Brooks LD, Collins FS. A HapMap harvest of insights into the genetics of common disease. J Clin Invest. 2008 May;118(5):1590-605. pdf


Homer N, Szelinger S, Redman M, Duggan D, Tembe W, Muehling J, Pearson JV, Stephan DA, Nelson SF, Craig DW. Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet. 2008 Aug 29;4(8):e1000167. pdf