Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans.
More than 5 million single-nucleotide polymorphisms (SNPs) with minor-allele frequency greater than 10% are expected to exist in the human genome. Some of these SNPs may be associated with risk of developing common diseases. To assess the power of currently available SNPs to detect such associations, we resequenced 50 genes in two ethnic samples and measured patterns of linkage disequilibrium between the subset of SNPs reported in dbSNP and the complete set of common SNPs. Our results suggest that using all 2.7 million SNPs currently in the database would detect nearly 80% of all common SNPs in European populations but only 50% of those common in the African American population and that efficient selection of a minimal subset of SNPs for use in association studies requires measurement of allele frequency and linkage disequilibrium relationships for all SNPs in dbSNP.
Carlson
Christopher S
CS
Department of Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, Washington 98195-7730, USA.
Eberle
Michael A
MA
Rieder
Mark J
MJ
Smith
Joshua D
JD
Kruglyak
Leonid
L
Nickerson
Deborah A
DA
D000483:Alleles; D044383:Black People; D019295:Computational Biology; D019992:Databases as Topic; D015894:Genome, Human; D006801:Humans; D016014:Linear Models; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D001741:Black or African American