Allele Frequencies Net Database: Improvements for storage of individual genotypes and analysis of existing data

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• 作者：Eduardo Jose Melos dos Santos^a ; ^b ; ¹ ; Antony McCabe^b ; ¹ ; Faviel F. Gonzalez-Galarza^c ; Andrew R. Jones^b ; Derek Middleton^d ; ^e ; ^{derek.middleton@rlbuht.nhs.uk" class="auth_mail" title="E-mail the corresponding author}
• 关键词：AFND ; Allele Frequency Net Database ; BMDR ; Bone Marrow Donor Registries ; HLA ; human leukocyte antigen ; IMGT ; the international ImMunoGeneTics information system ; ID ; identification ; KIR ; killer-cell immunoglobulin-like receptors ; MICA ; MHC class I polypeptide-related sequence A ; MICB ; MHC class I polypeptide-related sequence B ; NMDP ; National Marrow Donor Program
• 刊名：Human Immunology
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：77
• 期：3
• 页码：238-248
• 全文大小：2676 K

文摘

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.