Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools

Abstract

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.

Figure 1.

Overview of the main features in AFND. (A) Data sets are sourced from short population reports or direct AFND user submissions, both using the upload tool, from International HLA and Immunogenetics Workshops and from other peer reviewed publications, with allele and gene nomenclature synchronized with IMGT/HLA; (B) data undergo curation, including classification into gold–silver–bronze quality, and are stored under the different sections of the database; (C) a variety of query and custom-built visualization tools allow users to explore the different data sets.

Figure 2.

Map showing the distribution of countries with data available for at least one classical HLA locus. Countries with no frequency/genotype data are shown in white; countries with only silver and/or bronze standard populations are shown in grey; gold standard populations are shown in light yellow (1–4 populations with gold standards), yellow (6–9), dark yellow (10–19), brown (≥20).