title: Allele Frequencies Net Database: Improvements for storage of individual genotypes and analysis of existing data.
abstract: The Allele Frequencies Net Database (AFND) is a freely accessible database which stores population frequencies for alleles or genes of the immune system in worldwide populations. Herein we introduce two new tools. We have defined new classifications of data (gold, silver and bronze) to assist users in identifying the most suitable populations for their tasks. The gold standard datasets are defined by allele frequencies summing to 1, sample sizes >50 and high resolution genotyping, while silver standard datasets do not meet gold standard genotyping resolution and/or sample size criteria. The bronze standard datasets are those that could not be classified under the silver or gold standards. The gold standard includes >500 datasets covering over 3 million individuals from >100 countries at one or more of the following loci: HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1 and -DRB1 - with all loci except DPA1 present in more than 220 datasets. Three out of 12 geographic regions have low representation (the majority of their countries having less than five datasets) and the Central Asia region has no representation. There are 18 countries that are not represented by any gold standard datasets but are represented by at least one dataset that is either silver or bronze standard. We also briefly summarize the data held by AFND for KIR genes, alleles and their ligands. Our second new component is a data submission tool to assist users in the collection of the genotypes of the individuals (raw data), facilitating submission of short population reports to Human Immunology, as well as simplifying the submission of population demographics and frequency data.
authors.affiliation: Human and Medical Genetics, Institute of Biological Sciences, Federal University of Para, Brazil; Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
authors.forename: Eduardo Jose Melos Dos
authors.initials: EJMD
authors.lastname: Santos
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
authors.forename: Antony
authors.initials: A
authors.lastname: McCabe
authors.affiliation: Center for Biomedical Research, Faculty of Medicine, Autonomous University of Coahuila, Torreon, Mexico.
authors.forename: Faviel F
authors.initials: FF
authors.lastname: Gonzalez-Galarza
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jones
authors.affiliation: Transplant Immunology Laboratory, Royal Liverpool and Broadgreen University Hospital, UK; Institute of Infection and Global Health, University of Liverpool, UK. Electronic address: derek.middleton@rlbuht.nhs.uk.
authors.forename: Derek
authors.initials: D
authors.lastname: Middleton
mesh_terms: D000483:Alleles; D030541:Databases, Genetic; D005787:Gene Frequency; D056426:Genetic Loci; D005838:Genotype; D006680:HLA Antigens / Q000145:classification / Q000235:genetics / Q000276:immunology; D006801:Humans; D054340:Receptors, KIR / Q000235:genetics; D064878:Web Browser
chemical_list: D006680:HLA Antigens; D054340:Receptors, KIR
keywords: Allele Frequency Net Database; HLA; KIR