Efficient estimation for large-scale linkage disequilibrium patterns of the human genome.

ABSTRACT: In this study, we proposed an efficient algorithm (X-LD) for estimating linkage disequilibrium (LD) patterns for a genomic grid, which can be of inter-chromosomal scale or of small segments. Compared with conventional methods, the proposed method was significantly faster, dropped from O(nm²) to O(n²m)-n the sample size and m the number of SNPs, and consequently we were permitted to explore in depth unknown or reveal long-anticipated LD features of the human genome. Having applied the algorithm for 1000 Genome Project (1KG), we found (1) the extended LD, driven by population structure, universally existed, and the strength of inter-chromosomal LD was about 10% of their respective intra-chromosomal LD in relatively

SUBMITTER: Huang X 

PROVIDER: S-EPMC10752592 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature