ArticlePloS one2014
HLA diversity in the 1000 genomes dataset.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers, 1 of them a synthesis that pooled it.
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Who cites it
120 citing papers in PubMed, 1 synthesis or guideline pooled it, 207 citations in OpenAlex.
- A Meta-analysis of Multiple Myeloma Risk Regions in African and European Ancestry Populations Identifies Putatively Functional Loci.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2016Pooled it
- Targeting Amastigote and Trypomastigote Phases: Multi-Epitope Vaccine Strategy Against Trypanosoma cruzi.Biotechnology and applied biochemistry · 2026Article
- Classical HLA allele and haplotype frequency estimates in US populations.Human immunology · 2026Article
- Defining the molecular interaction between influenza hemagglutinin and MHC-II.bioRxiv : the preprint server for biology · 2026Article
- Shared trans-ancestry architecture of HLA-mediated disease risk in theResearch square · 2026Article
- Shared trans-ancestry architecture of HLA-mediated disease risk in themedRxiv : the preprint server for health sciences · 2026Article
- Allele frequency patterns of 78,122,254 SNPs illuminate diverse possible evolutionary trajectories of human populations.Scientific reports · 2026Article
- Classical HLA Allele and Haplotype Frequency Estimates in US Populations.bioRxiv : the preprint server for biology · 2026Article
- Lower Dose-Normalized Tacrolimus Exposure in CYP3A5*6 vs. *3 Loss-of-Function Allele Carriers: A Longitudinal Retrospective Real-World Study in Kidney Transplant Recipients.Clinical pharmacology and therapeutics · 2026Article
- HLA class I signal peptide variation predicts strength of NKG2ANature immunology · 2026Article
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- Patient-specific HLA-I subtypes predict response to immune checkpoint blockade.Oncoimmunology · 2025Article
- Cut or bind? Antigen-specific processing mechanisms define CD4Genome medicine · 2025Article
- NovumRNA: Accurate prediction of non-canonical tumor antigens from RNA sequencing data.iScience · 2025Article
- Characterizing the HLA region's genetic architecture through local heritability and correlation analyses across complex traits in diverse ancestries.Human genetics · 2025Article
- HLA variation associated with peanut allergy and anaphylaxis among non-Hispanic Black individuals.The journal of allergy and clinical immunology. Global · 2025Article
- High resolution class I HLA-A, -B, and -C diversity in Eastern and Southern African populations.Scientific reports · 2025Article
- Pathogen Adaptation of HLA Alleles and Its Correlation with Autoimmune Diseases in the Han Chinese.Genomics, proteomics & bioinformatics · 2025Article
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- Genomic landscape of cancer in racially and ethnically diverse populations.Nature reviews. Genetics · 2025Review
60 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors at 6 institutions in 2 countries.
Funding
Abstract
The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation by sequencing at a level that should allow the genome-wide detection of most variants with frequencies as low as 1%. However, in the major histocompatibility complex (MHC), only the top 10 most frequent haplotypes are in the 1% frequency range whereas thousands of haplotypes are present at lower frequencies. Given the limitation of both the coverage and the read length of the sequences generated by the 1000 Genomes Project, the highly variable positions that define HLA alleles may be difficult to identify. We used classical Sanger sequencing techniques to type the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 genes in the available 1000 Genomes samples and combined the results with the 103,310 variants in the MHC region genotyped by the 1000 Genomes Project. Using pairwise identity-by-descent distances between individuals and principal component analysis, we established the relationship between ancestry and genetic diversity in the MHC region. As expected, both the MHC variants and the HLA phenotype can identify the major ancestry lineage, informed mainly by the most frequent HLA haplotypes. To some extent, regions of the genome with similar genetic or similar recombination rate have similar properties. An MHC-centric analysis underlines departures between the ancestral background of the MHC and the genome-wide picture. Our analysis of linkage disequilibrium (LD) decay in these samples suggests that overestimation of pairwise LD occurs due to a limited sampling of the MHC diversity. This collection of HLA-specific MHC variants, available on the dbMHC portal, is a valuable resource for future analyses of the role of MHC in population and disease studies.
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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.