Global similarity with local differences in linkage disequilibrium between the Dutch and HapMap-CEU populations.

European Journal of Human Genetics : EJHG
Luba PardoPeter Heutink

Abstract

The HapMap project has facilitated the selection of tagging single nucleotide polymorphisms (tagSNPs) for genome-wide association studies (GWAS) under the assumption that linkage disequilibrium (LD) in the HapMap populations is similar to the populations under investigation. Earlier reports support this assumption, although in most of these studies only a few loci were evaluated. We compared pair-wise LD and LD block structure across autosomes between the Dutch population and the CEU-HapMap reference panel. The impact of sampling distribution on the estimation of LD blocks was studied by bootstrapping. A high Pearson correlation (genome-wide; 0.93) between pair-wise r(2) for the Dutch and the CEU populations was found, indicating that tagSNPs from the CEU-HapMap panel capture common variation in the Dutch population. However, some genomic regions exhibited, significantly lower correlation than the genome-wide estimate. This might decrease the validity of HapMap tagSNPs in these regions and the power of GWAS. The LD block structure differed considerably between the Dutch and CEU-HapMap populations. This was not explained by demographic differences between the CEU and Dutch samples, as testing for population stratification was no...Continue Reading

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Citations

Mar 2, 2012·European Journal of Human Genetics : EJHG·Luba M PardoPeter Heutink
Feb 18, 2010·Twin Research and Human Genetics : the Official Journal of the International Society for Twin Studies·Jenny H D A van BeekDorret I Boomsma
May 19, 2010·Twin Research and Human Genetics : the Official Journal of the International Society for Twin Studies·Gonneke WillemsenDorret I Boomsma
Aug 22, 2009·Genetic Epidemiology·Emma E ThompsonCarole Ober
Sep 26, 2019·PloS One·Andréa Carla Bastos AndradeFabyano Fonseca E Silva
Jul 10, 2010·Current Opinion in Lipidology

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