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Human Molecular Genetics Advance Access published online on October 7, 2003
Human Molecular Genetics, doi:10.1093/hmg/ddg337
© 2003 by Oxford University Press
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©2003 Oxford University Press

Article

The usefulness of different density SNP maps for disease association studies of common variants

William Y.S. Wang 1 and John A. Todd 1*

1 JDRF/WT Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 2XY, UK

* To whom correspondence should be addressed. E-mail: john.todd{at}cimr.cam.ac.uk.


  Abstract

Large-scale discovery and validation of single nucleotide polymorphisms (SNPs) facilitates indirect association mapping. It has recently been estimated that, in Europeans, 77% of all SNPs with frequency of 10% or more, could be ascertained through linkage disequilibrium (LD) by genotyping variants in the database dbSNP. Using a sampling approach from 73 genes with near complete SNP maps, we show here the usefulness of SNP maps at different densities and the large variability of SNP coverage in different genomic regions. While even sparse SNP maps are of some value to genetic mapping, in order to undertake disease association studies providing at least 80% of SNPs in 90% of genes, much denser maps need to be constructed, perhaps more than one SNP per kb in some regions.


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