Sequences of 95 humanMHChaplotypes reveal extreme coding variation in genes other than highly polymorphicHLA class IandII

Abstract

The most polymorphic part of the human genome, the encodes over 160 proteins of diverse function. Half of them, including the and genes, are directly involved in immune responses. Consequently, the region strongly associates with numerous diseases and clinical therapies. Notoriously, the region has been intractable to high-throughput analysis at complete sequence resolution, and current reference haplotypes are inadequate for large-scale studies. To address these challenges, we developed a method that specifically captures and sequences the 4.8-Mbp region from genomic DNA. For 95 homozygous cell lines we assembled, de novo, a set of high-fidelity contigs and a sequence scaffold, representing a mean 98% of the target region. Included are six alternative reference sequences of the human genome that we completed and refined. Characterization of the sequence and structural diversity of the region shows the approach accurately determines the sequences of the highly polymorphic and genes and the complex structural diversity of complement factor It has also uncovered extensive and unexpected diversity in other genes; an example is, which encodes a lung mucin and exhibits more coding sequence alleles than any or gene studied here. More than 60% of the coding sequence alleles analyzed were previously uncharacterized. We have created a substantial database of robust reference haplotype sequences that will enable future population scale studies of this complicated and clinically important region of the human genome.

In-depth genetic analysis of 6p21.3 reveals insights into associations between HLA types and complex traits and disease

“…SNPs/10kb across chromosome 6 ( Figure 1A); and 2) for the 377 HipSci genomes (146 fibroblast samples and 231 iPSCs) from 1 SNP/10kb to 995 SNPs/10kb (mean = 155.4 SNPs/10kb) compared with the average of 58.1 SNPs/10kb across chromosome 6. The region with the highest SNP density contained the HLA-DQA1 and HLA-DQB1 genes, which is consistent with previous studies (Norman et al, 2017). To determine whether the high SNP density interfered with read alignment, we analyzed the read depth across the region.…”

Assembly and analysis of 100 full MHC haplotypes from the Danish population

“…These haplotypes are likely to be better resolved than our haplotypes in some of the most polymorphic regions, but it is important to notice that they are built only from sequence captured by probes in the region, potentially missing novel sequence. It was also noted by Norman et al (2017) that the MHC haplotypes were not selected randomly and are therefore unsuitable for formal analysis of linkage disequilibrium. Our haplotypes are remarkable because they are built from de novo assemblies and phased essentially without the reference genome.…”

“…Similarly, the population reference graphs can greatly improve inference using mapping-based approaches but are constructed from known variation and depend largely on accurate alignment to known annotations. Recently, a novel method for capturing and sequencing the MHC based on homozygous cell lines was used to accurately determine the sequence of 95 MHC haplotypes, including the highly polymorphic class I and class II genes and the structurally variant C4 genes (Norman et al 2017). These haplotypes are likely to be better resolved than our haplotypes in some of the most polymorphic regions, but it is important to notice that they are built only from sequence captured by probes in the region, potentially missing novel sequence.…”

Allele Specific Expression in Human – Genomic Makeup and Phenotypic Implications

“…The system evolved to address conflicting objectives such as diversity, specificity, adaptability and self-tolerance. From a genomic perspective, the immune system is signified by high polymorphism (within MHC Class I and Class II and beyond (Norman et al 2017)), gene clusters, and polymorphic frozen blocks (Gaudieri et al 1997). The contribution of gene expression and specifically allele choice in cases of ASE in shaping the efficacy of the immune response, defining disease susceptibility and even in transplantation outcomes was only sporadically considered (see (Dawkins and Lloyd 2019;Petersdorf and O'HUigin 2019)).…”