High Resolution Haplotype Analyses of Classical HLA Genes in Families With Multiple Sclerosis Highlights the Role of HLA-DP Alleles in Disease Susceptibility

Abstract

Multiple sclerosis (MS) susceptibility shows strong genetic associations with HLA alleles and haplotypes. We genotyped 11 HLA genes in 477 non-Hispanic European MS patients and their 954 unaffected parents using a validated next-generation sequencing (NGS) methodology. HLA haplotypes were assigned unequivocally by tracing HLA allele transmissions. We explored HLA haplotype/allele associations with MS using the genotypic transmission disequilibrium test (gTDT) and multiallelic TDT (mTDT). We also conducted a case-control (CC) study with all patients and 2029 healthy unrelated ethnically matched controls. We performed separate analyses of 54 extended multi-case families by reviewing transmission of haplotype blocks. The haplotype fragment including DRB5*01:01:01~DRB1*15:01:01:01 was significantly associated with predisposition (gTDT: p < 2.20e-16; mTDT: p =1.61e-07; CC: p < 2.22e-16) as reported previously. A second risk allele, DPB1*104:01 (gTDT: p = 3.69e-03; mTDT: p = 2.99e-03; CC: p = 1.00e-02), independent from the haplotype bearing DRB1*15:01 was newly identified. The allele DRB1*01:01:01 showed significant protection (gTDT: p = 8.68e-06; mTDT: p = 4.50e-03; CC: p = 1.96e-06). Two DQB1 alleles, DQB1*03:01 (gTDT: p = 2.86e-03; mTDT: p = 5.56e-02; CC: p = 4.08e-05) and DQB1*03:03 (gTDT: p = 1.17e-02; mTDT: p = 1.16e-02; CC: p = 1.21e-02), defined at two-field level also showed protective effects. The HLA class I block, A*02:01:01:01~C*03:04:01:01~B*40:01:02 (gTDT: p = 5.86e-03; mTDT: p = 3.65e-02; CC: p = 9.69e-03) and the alleles B*27:05 (gTDT: p = 6.28e-04; mTDT: p = 2.15e-03; CC: p = 1.47e-02) and B*38:01 (gTDT: p = 3.20e-03; mTDT: p = 6.14e-03; CC: p = 1.70e-02) showed moderately protective effects independently from each other and from the class II associated factors. By comparing statistical significance of 11 HLA loci and 19 haplotype segments with both untruncated and two-field allele names, we precisely mapped MS candidate alleles/haplotypes while eliminating false signals resulting from ‘hitchhiking’ alleles. We assessed genetic burden for the HLA allele/haplotype identified in this study. This family-based study including the highest-resolution of HLA alleles proved to be powerful and efficient for precise identification of HLA genotypes associated with both, susceptibility and protection to development of MS.

High‐resolution HLA class II sequencing of Swedish multiple sclerosis patients

“…Here, we could not confirm recent allelic MS associations using high‐resolution sequencing to HLA‐DPB1*104:01 (predisposing), HLA‐DQB1*03:01 and HLA‐ DQB1*03:03 (protective), and HLA‐DRB1*14:04:01 (protective) (Osoegawa et al., 2021; Vinoy et al., 2021). These alleles were not found to be commonly present in the Swedish population, with exception of HLA‐DQB1*03:01 .…”

“…A recent family‐study used high‐resolution sequencing to report a novel predisposing association to MS for HLA‐DPB1*104:01 , independent of HLA‐DRB1*15:01 haplotype. High‐resolution sequencing also conferred negative MS association to HLA‐DRB1*01:01:01 , HLA‐DQB1*03:01 and HLA‐DQB1*03:03 (Osoegawa et al., 2021) and HLA‐DRB1*14:04:01 (Vinoy et al., 2021).…”

Improved detection of evolutionary selection highlights potential bias from different sequencing strategies in complex genomic-regions

“…There is a known recombination event in the DP region [40][41][42] and the -DPA1 and -DPB1 genes overlap with opposite orientations. Additionally, there are multiple functional elements within this overlap region, including multiple eQTLs, 43,44 two promoters (one for each gene), and a processed pseudogene of the ribosomal protein L32 45 , further constraining this portion of sequence. It is noteworthy that correspondingly, we saw a distinct dip in the LD-ABF (Supplemental Figure 17) over this region.…”

A registry‐based population study of the HLA in Québec, Canada

“…According to Immuno Polymorphism Database‐ImMunoGeneTics/HLA (IPD‐IMGT/HLA) Database version 3.51 update, 36,625 HLA alleles have been identified worldwide so far, with novel alleles constantly being discovered 7 . In addition, some HLA alleles confer protection or susceptibility to certain diseases, including infections, cancer, and autoimmune diseases 8–12 …”