A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs.

ABSTRACT:

Motivation

Linkage disequilibrium (LD) block construction is required for research in population genetics and genetic epidemiology, including specification of sets of single nucleotide polymorphisms (SNPs) for analysis of multi-SNP based association and identification of haplotype blocks in high density sequencing data. Existing methods based on a narrow sense definition do not allow intermediate regions of low LD between strongly associated SNP pairs and tend to split high density SNP data into small blocks having high between-block correlation.

Results

We present Big-LD, a block partition method based on interval graph modeling of LD bins which are clusters of strong pairwise LD SNPs, not necessarily physically consecutive. Big-LD uses an agglomerative approach that starts

SUBMITTER: Kim SA 

PROVIDER: S-EPMC5860363 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature