An evaluation of HapMap sample size and tagging SNP performance in large-scale empirical and simulated data sets.
A substantial investment has been made in the generation of large public resources designed to enable the identification of tag SNP sets, but data establishing the adequacy of the sample sizes used are limited. Using large-scale empirical and simulated data sets, we found that the sample sizes used in the HapMap project are sufficient to capture common variation, but that performance declines substantially for variants with minor allele frequencies of <5%.
Zeggini
Eleftheria
E
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. elez@well.ox.ac.uk
Rayner
William
W
Morris
Andrew P
AP
Hattersley
Andrew T
AT
Walker
Mark
M
Hitman
Graham A
GA
Deloukas
Panos
P
Cardon
Lon R
LR
McCarthy
Mark I
MI
D002874:Chromosome Mapping; D030561:Databases, Nucleic Acid; D003924:Diabetes Mellitus, Type 2 / Q000235:genetics*; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D018401:Sample Size