Definition and analysis of SNP-free regions of current genome wide association study databases

Abstract

Single Nucleotide Polymorphism (SNP) is the important part in genome wide association study (GWAS). We investigated the SNPs that are not genotyped directly or indirectly by the current GWAS, and genomic regions associated with these unassayed SNPs. Through analysis of Hap Map CEU (European Caucasian), CHB (Han Chinese), JPT (Japanese) and YRI (Yoruba African) data, we identified the NGS SNP-free regions and the NGS common SNP-free regions (minor allele frequency (MAF) > = 0.05), We also calculated the number and the size of the NGS SNP-free regions and the NGS common SNP-free regions, where they have been reported so far, in different populations. In the analysis of NGS SNP-free regions and NGS common SNP-free regions, we found they have the character of independence. The distributions of the NGS SNP-free regions and NGS common SNP-free regions have the character of imbalance. The GW AS genotyping platforms could be further upgraded to include more SNPs to ensure true whole genome coverage.