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
| Autor: | Robert L. Hanson, Clifton Bogardus, Nehal Gosalia, Leslie J. Baier, Robert C. Williams, Alan R. Shuldiner, Cristopher V. Van Hout, Çiğdem Köroğlu, William C. Knowler |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Genotype Immunology Population Population genetics Human leukocyte antigen Biology Article Evolution Molecular 03 medical and health sciences 0302 clinical medicine Gene Frequency HLA Antigens Humans Immunology and Allergy education Allele frequency American Indian or Alaska Native Genetic association Genetics education.field_of_study Whole Genome Sequencing Histocompatibility Testing Haplotype Arizona High-Throughput Nucleotide Sequencing General Medicine HLA-A Genetics Population 030104 developmental biology Genetic Loci Algorithms 030215 immunology |
| Zdroj: | Hum Immunol |
| ISSN: | 0198-8859 |
| DOI: | 10.1016/j.humimm.2021.03.013 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full Text from ScienceDirect