Complete sequences of six major histocompatibility complex haplotypes, including all the major MHC class II structures

Abstract

Accurate and comprehensive immunogenetic reference panels are key to the successful implementation of population-scale immunogenomics. The 5Mbp Major Histocompatibility Complex (MHC) is the most polymorphic region of the human genome and associated with multiple immune-mediated diseases, transplant matching and therapy responses. Analysis of MHC genetic variation is severely complicated by complex patterns of sequence variation, linkage disequilibrium and a lack of fully resolved MHC reference haplotypes, increasing the risk of spurious findings on analyzing this medically important region. Integrating Illumina, ultra-long Nanopore, and PacBio HiFi sequencing as well as bespoke bioinformatics, we completed five of the alternative MHC reference haplotypes of the current (GRCh38/hg38) build of the human reference genome and added one other. The six assembled MHC haplotypes encompass the DR1 and DR4 haplotype structures in addition to the previously completed DR2 and DR3, as well as six distinct classes of the structurally variable C4 region. Analysis of the assembled haplotypes showed that MHC class II sequence structures, including repeat element positions, are generally Torsten Houwaart and Stephan Scholz contributed equally. Paul J. Norman and Alexander T. Dilthey jointly supervised this work.

Full resolution HLA and KIR genes annotation for human genome assemblies

“…To evaluate our pipeline, we first applied Immuannot to eight well-annotated MHC assemblies that were published in 2023 (Houwaart et al 2023). We compared our allele calls to theirs on HLA genes and C4 genes.…”

“…We applied Immuannot to 212 full genome haploid assemblies, including HPRC (n=94) (Liao et al 2023), CPC (n=114) (Gao et al 2023), CHM13.0 (Nurk et al 2022), GRCh38.p14 (Schneider et al 2017), and CN-T2T (n=2) (He et al 2023), 50 KIR reference contigs and 6 HLA reference assemblies (Houwaart et al 2023). This resulted in 7,519 HLA genes, represented by 2,673 unique alleles as some unique alleles were present in multiple samples.…”

“…The HLA class II region is highly structured (Klitz et al 2003; Norman et al 2017; Chin et al 2023), which is commonly characterized by DR haplotype. Following earlier work (Houwaart et al 2023), HLA DR haplotype is defined by the combination of HLA-DRB1 allele groups and the presence or absence of DRB3/4/5 genes. All 217 HLA haplotypes in our analysis are in agreement with DR haplotype definition: DRB1*03 , 11 , 12 , 13 , and 14 are always linked to DRB3 (DR3), DRB1*04 , 07 and 09 linked to DRB4 (DR4), DRB1*15 and 16 are linked to DRB5 (DR5), and DRB1*01 , 10 , or 08 never carry DRB3/4/5 alleles (DR1+DR8) (Figure 4B).…”

High population frequencies of MICA copy number variations originate from independent recombination events

“…All sequences with larger assembly gaps or obvious assembly errors were excluded. Finally, 37 and 34 sequences for MICA - and MICB regions of diverse haplotypes were included, respectively ( Supplementary Data 4 ) ( 48 , 49 ). These sequences were aligned with the generated breakpoint consensus sequences of the MICA duplication- and MICA deletion samples (CLC Genomics Workbench 21 (Qiagen, Hilden, Germany)).…”

High population frequencies of MICA copy number variations originate from independent recombination events

“…All sequences with larger assembly gaps or obvious assembly errors were excluded. Finally, 37 and 34 sequences for MICA-and MICB regions of diverse haplotypes were included, respectively (Supplementary Data 7) (64,65). These sequences were aligned with the generated breakpoint consensus sequences of the MICA duplication-and MICA deletion samples (CLC Genomics Workbench 21 (Qiagen, Hilden, Germany)).…”