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

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.