DNA sequence patterns in human major histocompatibility complex region in southern Chinese

Abstract

1. We developed a programme, quantLD, for genome-wide comparisons of linkage disequilibrium difference between two populations and applied the methods to the major histocompatibility complex region in 1000 Genomes Project phase 3 data. Results suggested that linkage disequilibrium difference exists across populations. 2. We also developed a programme PyHLA for HLA alleles association analysis and applied to a set of 246 APOE ε4 allele negative Alzheimer disease cases and 172 normal controls. HLA-DRB1*07:01 and HLA-C*03 were inversely associated with Alzheimer disease, whereas HLA-DQB1*03:01 and DRB1*09:21 were associated with Alzheimer disease.