Effective selection of informative SNPs and classification on the HapMap genotype data

Abstract

Background: Since the single nucleotide polymorphisms (SNPs) are genetic variations which

determine the difference between any two unrelated individuals, the SNPs can be used to identify

the correct source population of an individual. For efficient population identification with the

HapMap genotype data, as few informative SNPs as possible are required from the original 4 million

SNPs. Recently, Park et al. (2006) adopted the nearest shrunken centroid method to classify the

three populations, i.e., Utah residents with ancestry from Northern and Western Europe (CEU),

Yoruba in Ibadan, Nigeria in West Africa (YRI), and Han Chinese in Beijing together with Japanese

in Tokyo (CHB+JPT), from which 100,736 SNPs were obtained and the top 82 SNPs could

completely classify the three populations.