Efficiency and power in genetic association studies

By P. D. Bakker, Roman Yelensky, Itsik Pe'er, Stacey Gabriel, Mark J. Daly, David Altshuler. Nature Genetics, 2005

1,821 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/00cd59ecbbfe6ee886d785b1ab0f6576ed1bca1e

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Citations in the corpus

IL28B is associated with response to chronic hepatitis C interferon-α and ribavirin therapy (2009, methodology): “To further refine this association and tag the common haplotypes in the IL28B , IL28A and IL29 gene cluster (chr 19: 44389814–44480955), we genotyped a total of 20 tag SNPs in this region (11 new tag SNPs selected using haplotype tagger, ref”
Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics (2011, background): “…genetic variation organized into a limited number of haplotypes spanning a causal variant would be associated with disease, and relatively few ‘‘tag’’ SNPs chosen to represent the haplotypes would need to be genotyped in each haplotype block (de Bakker et al. 2005) to capture the effect.”
A high resolution HLA and SNP haplotype map for disease association studies in the extended human MHC (2006, methodology): “To assess the extent to which allelic variation at HLA loci can be captured by nearby SNPs, we used the 'Tagger' algorith”
Two independent alleles at 6q23 associated with risk of rheumatoid arthritis (2007, methodology): “Specifically, we used these 17 SNPs to predict SNPs in CEU HapMap individuals that were not directly genotyped in our study but that could be well predicted using single SNPs or multi-marker haplotype”
Copy-number variation and association studies of human disease (2007, background): “But although this issue has been the subject of extensive discussion in the literature on SNP association studie”
A new multipoint method for genome-wide association studies by imputation of genotypes (2007, neutral): “This approach has advantages over other multipoint methods: the population genetics approach uses information from all markers in LD with an untyped SNP, but in a way that decreases with genetic distance from the SNP being imputed, thus avoiding the decisions faced in some other prediction methods, ”
Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1 (2008, methodology): “We evaluated the association of markers with lung cancer risk allowing for potential effects of population substructure by using a Cochran-Mantel-Haenszel tes”
Genotype Imputation (2009, background): “The intuition that short stretches of haplotype provide useful information about untyped genetic markers provides the justification for the power gains suggested for many haplotype analysis strategies (22, 60, 91, 115).”
Estimation of the multiple testing burden for genomewide association studies of nearly all common variants (2008, background): “The demonstrated ability of these regions to represent linkage disequilibrium among common variants across the genome [Pe’er et al., 2006a,b; The International HapMap Consortium, 2005] allows their use for simulating association studies with no true signal [de Bakker et al., 2005].”
Genotype imputation for genome-wide association studies (2010, methodology): “) carry out imputation using methods based on tag SNP approache”