Next generation sequencing for HLA loci in full heritage Pima Indians of Arizona, Part II: HLA-A, -B, and -C with selected non-classical loci at 4-field resolution from whole genome sequences.
Allele frequencies
HLA non-classical loci
Haplotype frequencies
Population genetics
Journal
Human immunology
ISSN: 1879-1166
Titre abrégé: Hum Immunol
Pays: United States
ID NLM: 8010936
Informations de publication
Date de publication:
Jun 2021
Jun 2021
Historique:
received:
16
04
2019
revised:
26
03
2021
accepted:
29
03
2021
pubmed:
21
4
2021
medline:
26
11
2021
entrez:
20
4
2021
Statut:
ppublish
Résumé
While the samples and data from the Pima Indians of the Gila River Indian Community have been included in many international HLA workshops and conferences and have been the focus of numerous population reports and the source of novel alleles at the classical HLA loci, they have not been studied for the non-classical loci. In order to expand our HLA-disease association studies, we typed over 300 whole genome sequences from full Pima heritage members, controlled for first degree relationship, and employed recently developed computer algorithms to resolve HLA alleles. Both classical-HLA-A, -B, and -C- and non-classical- HLA-E, -F, -G, -J, -L, -W, -Y, -DPA2, -DPB2, -DMA, -DMB, -DOA, -DRB2, -DRB9, TAP1- loci were typed at the 4-field level of resolution. We present allele and selected haplotype frequencies, test the genotype distributions for population structure, discuss the issues that are created for tests of Hardy-Weinberg equilibrium over the four sample spaces of high resolution HLA typing, and address the implications for the evolution of non-classical pseudogenes that are no longer expressed in a phenotype subject to natural selection.
Identifiants
pubmed: 33875299
pii: S0198-8859(21)00085-9
doi: 10.1016/j.humimm.2021.03.013
pmc: PMC8119369
mid: NIHMS1695079
pii:
doi:
Substances chimiques
HLA Antigens
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
385-403Subventions
Organisme : Intramural NIH HHS
ID : Z99 DK999999
Pays : United States
Informations de copyright
Published by Elsevier Inc.
Déclaration de conflit d'intérêts
Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
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