Haplotype Analysis Reveals Pleiotropic Disease Associations in the HLA Region

Abstract

The human leukocyte antigen (HLA) region plays an important role in human health through involvement in immune cell recognition and maturation. While genetic variation in the HLA region is associated with many diseases, the pleiotropic patterns of these associations have not been systematically investigated. Here, we developed a haplotype approach to investigate disease associations phenome-wide for 412,181 Finnish individuals and 2,459 traits. Across the 1,035 diseases with a GWAS association, we found a 17-fold average per-SNP enrichment of hits in the HLA region. Altogether, we identified 7,649 HLA associations across 647 traits, including 1,750 associations uncovered by haplotype analysis. We find some haplotypes show trade-offs between diseases, while others consistently increase risk across traits, indicating a complex pleiotropic landscape involving a range of diseases. This study highlights the extensive impact of HLA variation on disease risk, and underscores the importance of classical and non-classical genes, as well as non-coding variation.

Figure 1:. Study Overview.

A. An overview of the HLA region showing the nearest genes to traitassociated SNPs, colored by HLA class, spanning approximately 5 megabases. B. An overview of the study data and design.

Figure 2:. Distribution of GWAS hits across the genome and trait group enrichment.

A. Distribution of fine-mapped GWAS hits throughout the genome across 1,035 FinnGen disease traits, binned into 100 kb bins. B. Enrichment of association signal in the HLA region by disease group. The 1,035 diseases were categorized into 45 disease groups based on ICD codes and the average per SNP enrichment in the HLA region was calculated by comparing the number of independent associations in the HLA region relative to that in the rest of the genome. C. Classification of traits with at least one significant association in the HLA region by shared pathophysiology.

Figure 3:. Pleiotropic structure of the HLA region.

A. Distribution of significant SNP associations across the HLA region, binned by nearest gene. Each bar represents a different gene and the width corresponds to the length of the gene boundaries. B. Heatmap of normalized Z-scores for the 428 variants in the HLA region significantly associated with at least one trait. The x-axis corresponds to the genome position of the variant, the y-axis corresponds to the HLA-associated traits. Associations with all HLA-associated traits are shown for all variants that had an independent significant association with at least one trait. The three blocks used in subsequent analysis are circled, underlined, and labeled by well-known genes within each block. C. Linkage disequilibrium as measured by r² and D′ of the approximately 40,000 SNPs covering the HLA region (MAF > 1%).

Figure 4:. Haplotype group regression analysis pipeline.

Overview of the pipeline for identifying the haplotype groups for each of the three blocks in the HLA region and performing trait associations. For each block, all unique phased combinations of nucleotides at 1,000 randomly selected SNPs were considered as haplotypes. We then clustered related haplotypes into groups by recursively splitting the dendrogram at each branch point (see Methods). Finally, for each of the three blocks, we performed association analyses between the haplotype groups and the 269 HLA-associated diseases, including all haplotype groups for a given block except the most frequent in each regression, as well as sex, age, and the first ten principal components of the genome-wide genotype matrix as covariates.

Figure 5:. Haplotype group regression results.

A dendrogram showing the clustering of the 40 most frequent haplotypes per haplotype group, with white representing the reference allele and black representing the effect allele. Genes are labeled below the corresponding SNPs overlapping their genome position, indicating which are within gene boundaries and which are intergenic. Heatmap showing the Z-scores from the haplotype group regression analysis across associated traits for A. Block 1, B. Block 2, and C. Block 3, including all traits with at least one association |Z| > 4 in that block, and all haplotype groups with at least one trait association or total copies greater than the minimum cutoff of 20,000 copies. For visualization purposes, traits are clustered and Z-scores were set to a maximum of |Z| of 5.

Figure 6:. Correlation of haplotype associated traits.

A. Overview and comparison of the pairwise relationships between traits that were significantly associated with the haplotype group regression analysis, comparing genome-wide LDSC genetic correlations, Pearson’s correlation across haplotype groups in each block, and phenotypic correlations. B. Comparison of correlation measures between Graves Disease and Rheumatoid Arthritis.