2023
DOI: 10.1111/tan.15020
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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, incr… Show more

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Cited by 17 publications
(14 citation statements)
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“…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.…”
Section: Resultsmentioning
confidence: 99%
See 2 more Smart Citations
“…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.…”
Section: Resultsmentioning
confidence: 99%
“…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.…”
Section: Resultsmentioning
confidence: 99%
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“…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)).…”
Section: Methodsmentioning
confidence: 99%
“…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)).…”
Section: Localization Of the Recombination Sitementioning
confidence: 99%