ArticleNAR genomics and bioinformatics2020
Increasing accuracy of HLA imputation by a population-specific reference panel in a FinnGen biobank cohort.
Article in NAR genomics and bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 2 of them syntheses that pooled it.
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Who cites it
40 citing papers in PubMed, 2 syntheses or guidelines pooled it, 72 citations in OpenAlex.
- The genetic basis of dermatophytosis skin infection susceptibility.Nature communications · 2026Pooled it
- Genome-wide meta-analysis identifies genetic risk loci for mono- and polyneuropathies in 983 477 individuals.Human molecular genetics · 2026Pooled it
- GWAS of Second-Generation Antihistamine Use: Locus Specificity and Highlighted Signalling Pathways.Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology · 2026Article
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- Shared Genetics of Kidney Function Traits and Bladder Cancer: A Genome-Wide Cross-Trait Analysis.Cancer medicine · 2026Article
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- EBV genome analysis in multiple sclerosis shows extensive viral diversity and links to autoimmunity.NAR molecular medicine · 2026Article
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- Blood donor biobank pipeline to collect genome-based samples for research.Scientific reports · 2026Article
- A Genome-Wide Association Study of Hidradenitis Suppurativa from the VA's Million Veteran Program.Dermatology (Basel, Switzerland) · 2026Article
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- Genetic Loci Associated With Periodontitis: The FinnGen Study Based on National Health Registers.Journal of clinical periodontology · 2025Article
- Genome-wide association study of pulpal and apical diseases.Nature communications · 2025Article
- Effects of parental autoimmune diseases on type 1 diabetes in offspring can be partially explained by HLA and non-HLA polymorphisms.Cell genomics · 2025Article
- Female-mediated selective sperm activation may remodel major histocompatibility complex-based mate choice decisions in humans.Heredity · 2025Article
- Genetic analysis implicates ERAP1 and HLA as risk factors for severe Puumala virus infection.Human molecular genetics · 2025Article
- Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data.PLoS computational biology · 2024Article
- Article
- Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy.bioRxiv : the preprint server for biology · 2024Article
- Oral and non-oral lichen planus show genetic heterogeneity and differential risk for autoimmune disease and oral cancer.American journal of human genetics · 2024Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The HLA genes, the most polymorphic genes in the human genome, constitute the strongest single genetic susceptibility factor for autoimmune diseases, transplantation alloimmunity and infections. HLA imputation via statistical inference of alleles based on single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with alleles is a powerful first-step screening tool. Due to different LD structures between populations, the accuracy of HLA imputation may benefit from matching the imputation reference with the study population. To evaluate the potential advantage of using population-specific reference in HLA imputation, we constructed an HLA reference panel consisting of 1150 Finns with 5365 major histocompatibility complex region SNPs consistent between genome builds. We evaluated the accuracy of the panel against a European panel in an independent test set of 213 Finnish subjects. We show that the Finnish panel yields a lower imputation error rate (1.24% versus 1.79%). More than 30% of imputation errors occurred in haplotypes enriched in Finland. The frequencies of imputed HLA alleles were highly correlated with clinical-grade HLA allele frequencies and allowed accurate replication of established HLA-disease associations in ∼102 000 biobank participants. The results show that a population-specific reference increases imputation accuracy in a relatively isolated population within Europe and can be successfully applied to biobank-scale genome data collections.
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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.