Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools
Open accessAbstract
The Allele Frequency Net Database (AFND, www.allelefrequencies.net) provides the scientific community with a freely available repository for the storage of frequency data (alleles, genes, haplotypes and genotypes) related to human leukocyte antigens (HLA), killer-cell immunoglobulin-like receptors (KIR), major histocompatibility complex Class I chain related genes (MIC) and a number of cytokine gene polymorphisms in worldwide populations. In the last five years, AFND has become more popular in terms of clinical and scientific usage, with a recent increase in genotyping data as a necessary component of Short Population Report article submissions to another scientific journal. In addition, we have developed a user-friendly desktop application for HLA and KIR genotype/population data submissions. We have also focused on classification of existing and new data into ‘gold–silver–bronze’ criteria, allowing users to filter and query depending on their needs. Moreover, we have also continued to expand other features, for example focussed on HLA associations with adverse drug reactions. At present, AFND contains >1600 populations from >10 million healthy individuals, making AFND a valuable resource for the analysis of some of the most polymorphic regions in the human genome.
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HLA-A*02:01 is the most frequent MHC class I allele in the Caucasian population, with up to 50% of individuals bearing this allele.
“To maximise the eligible patient population, the epitopes selected for CVGBM were either restricted to HLA-A*02:01 (BCAN, PTPRZ1, NLGNX4) as the most frequent MHC class I allele in the Caucasian population (up to 50% of individuals bearing this allele according to the allele frequency net database [39]), or to various HLA-DR alleles (BIRC5).”
From Preclinical development of an mRNA-based multiepitope immunotherapeutic for glioblastoma (2025) · cites this paper as [39]
The Database content section says AFND lets users browse HLA allele and genotype frequencies, but it gives no frequency or ranking for HLA-A*02:01. Searches for HLA-A*02:01, Caucasian or European populations, and 50% found no passage in our copy establishing that it is the most frequent MHC class I allele in that population or that up to 50% of individuals carry it. (LLM, conf=0.75)
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- Authors
- Gonzalez-Galarza, F. F., McCabe, A., Santos, E. J. M. D., Jones, J., Takeshita, L., Ortega-Rivera, N. D., Cid-Pavon, G. M. D., Ramsbottom, K., Ghattaoraya, G., Alfirevic, A., Middleton, D., & Jones, A. R.
- Affiliations
- Center for Biomedical Research, Faculty of Medicine, Autonomous University of Coahuila, Torreon, Mexico
- University of Liverpool (GB)
- Universidade Federal do Pará (BR)
- Universidad Autónoma de Coahuila (MX)
- Corresponding author
- Middleton, Derek
- Jones, Andrew R
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-11-13
- Volume
- 48
- Issue
- D1
- Pages
- D783-D788
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC7145554
- OpenAlex
- W2984055282
- Cited by
- 731
- References
- 24
- Citations by year
- 2026: 65 · 2025: 130 · 2024: 122 · 2023: 110 · 2022: 115 · 2021: 141 · 2020: 46 · 2019: 2
- FWCI
- 45.80
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Faculty of Medicine, UAdeC (P/PFCE-2018)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Immunology and Microbiology › Immunology › Immune Cell Function and Interaction
- Keywords
- HLA, killer cell immunoglobulin-like receptors, cytokine gene polymorphisms, genotype data, haplotype data, data classification, population genetics
- MeSH terms
- Gene Frequency, HLA Antigens, Humans, Polymorphism, Genetic, User-Computer Interface, Histocompatibility Antigens Class I, Genome, Human, Cytokines, Databases, Genetic, Receptors, KIR
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