A New Pedigree-Based SNP Haplotype Method for Genomic Polymorphism and Genetic Studies.

ABSTRACT: Single nucleotide polymorphisms (SNPs) are usually the most frequent genomic variants. Directly pedigree-phased multi-SNP haplotypes provide a more accurate view of polymorphic population genomic structure than individual SNPs. The former are, therefore, more useful in genetic correlation with subject phenotype. We describe a new pedigree-based methodology for generating non-ambiguous SNP haplotypes for genetic study. SNP data for haplotype analysis were extracted from a larger Type 1 Diabetes Genetics Consortium SNP dataset based on minor allele frequency variation and redundancy, coverage rate (the frequency of phased haplotypes in which each SNP is defined) and genomic location. Redundant SNPs were eliminated, overall haplotype polymorphism was optimized and the number of undefined hapl

SUBMITTER: Vadva Z 

PROVIDER: S-EPMC6721696 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature