Refined HLA Linkage Disequilibrium Architectures of World Populations by a Novel Allelic Correlation Measure

Fei Zhang; Weixiong Zhang

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arXiv · 2512.05573

Refined HLA Linkage Disequilibrium Architectures of World Populations by a Novel Allelic Correlation Measure

Fei Zhang·Weixiong Zhang

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Abstract

Numerous diseases, particularly autoimmune disorders, are associated with the human leukocyte antigen (HLA), a small genomic region located on human chromosome 6. Adequate characterization of linkage disequilibrium (LD) in the HLA across populations is crucial for identifying genetic markers associated with specific traits and phenotypes. However, current LD measures often fail to capture HLA's structural complexity due to methodological limitations and sensitivity to low-frequency variants, marginal allele frequencies, and haplotype composition. To address these challenges, we introduced the Conditional Informatics Correlation Coefficient (CICC), which integrates conditional probability, information content, and haplotype-aware XOR logic to quantify LD robustly. When applied to high-resolution haploid genomes from the Human Pangenome Reference Consortium (HPRC), CICC revealed 10 novel high-LD regions in HLA. Further analyses using the 1000 Genomes Project and Genome Asia datasets identified nine strongly linked regions shared across five global populations-five in Class I and four in Class II. These results demonstrate CICC's ability to capture complex HLA LD structures across populations, highlighting its broad potential for disease gene mapping, population genomics, and guiding precision medicine.

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Fei Zhang, Weixiong Zhang. 2025-12-05. Refined HLA Linkage Disequilibrium Architectures of World Populations by a Novel Allelic Correlation Measure. https://arxiv.org/abs/2512.05573

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