Population stratification and spurious allelic association

@article{Cardon2003PopulationSA,
  title={Population stratification and spurious allelic association},
  author={Lon R. Cardon and Lyle J. Palmer},
  journal={The Lancet},
  year={2003},
  volume={361},
  pages={598-604}
}
How to interpret a genome-wide association study.
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The design, interpretation, application, and limitations of GWA studies for clinicians and scientists for whom this evolving science may have great relevance are described.
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A computationally efficient approach to testing association between SNPs and quantitative phenotypes, which can be applied to whole-genome association scans and allows estimation of missing genotypes, resulting in substantial increases in power when genotyping resources are limited.
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A novel statistical method to control spurious LD in GWAS from population structure by incorporating a control marker into testing for significance of genetic association of a polymorphic marker with phenotypic variation of a complex trait is proposed.
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Population Stratification Analysis in Genome-Wide Association Studies
TLDR
This chapter discusses the state-of-the-art of strategies used for correcting the statistics for genome-wide association analysis by taking into account the ancestral structure of the population.
Evidence of Admixture from Haplotyping in an Epidemiological Study of UK Caucasian Males: Implications for Association Analyses
TLDR
Combinations of Y haplotyping, autosomal haplotypes, and genome-wide SNP typing, taken together with phenotypic2 associations, should improve epidemiological recognition and interpretation of possible confounding by genetic subdivision.
Linkage disequilibrium based eQTL analysis and comparative evolutionary epigenetic regulation of gene transcription
TLDR
Both intensive computer simulation study and eQTL analysis in genetically divergent human populations show that the new method confers an improved statistical power for detecting genuine genetic association in subpopulations and an effective control of spurious associations stemmed from population structure.
Accounting for Population Stratification in Practice: A Comparison of the Main Strategies Dedicated to Genome-Wide Association Studies
TLDR
A comparison of the most commonly used methods to deal with stratification that are the Genomic Control, Principal Component based methods such as implemented in Eigenstrat, adjusted Regressions and Meta-Analyses strategies, and more details about these methods are provided.
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