ArticleGenome research2017
Assembly and analysis of 100 full MHC haplotypes from the Danish population.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 23 citations in OpenAlex.
- Haplotypic resolution of the challenging genomic regions of MHC and KIR using a combination of targeted sequencing and a novel assembly pipeline.Nucleic acids research · 2025Article
- Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples.Genome research · 2024Article
- MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge.Genome biology · 2024Article
- Article
- MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge.bioRxiv : the preprint server for biology · 2024Article
- HLA Genetics for the Human Diseases.Advances in experimental medicine and biology · 2024Review
- JTK: targeted diploid genome assembler.Bioinformatics (Oxford, England) · 2023Article
- Human leukocyte antigen super-locus: nexus of genomic supergenes, SNPs, indels, transcripts, and haplotypes.Human genome variation · 2022Review
- Transethnic analysis of psoriasis susceptibility in South Asians and Europeans enhances fine-mapping in the MHC and genomewide.HGG advances · 2022Article
- Article
- SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction.Frontiers in genetics · 2020Article
- Article
- Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes.Nucleic acids research · 2019Article
- Article
- Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios.BMC bioinformatics · 2018Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genes in the major histocompatibility complex (MHC, also known as HLA) play a critical role in the immune response and variation within the extended 4-Mb region shows association with major risks of many diseases. Yet, deciphering the underlying causes of these associations is difficult because the MHC is the most polymorphic region of the genome with a complex linkage disequilibrium structure. Here, we reconstruct full MHC haplotypes from de novo assembled trios without relying on a reference genome and perform evolutionary analyses. We report 100 full MHC haplotypes and call a large set of structural variants in the regions for future use in imputation with GWAS data. We also present the first complete analysis of the recombination landscape in the entire region and show how balancing selection at classical genes have linked effects on the frequency of variants throughout the region.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.