HLA diversity in the Russian population assessed by next generation sequencing

Next generation sequencing is used to determine full-length sequences of HLA genes at the 4-field (allelic) resolution. The study was aimed at determining frequency and diversity of HLA alleles in a cohort of blood donors from the Registry of the National Research Center for Hematology who design at...

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Autores principales:	E. G. Khamaganova, E. A. Leonov, A. R. Abdrakhimova, S. P. Khizhinskiy, T. V. Gaponova, V. G. Savchenko
Formato:	article
Lenguaje:	RU
Publicado:	SPb RAACI 2021
Materias:	hla alleles diversity next generation sequencing Immunologic diseases. Allergy RC581-607
Acceso en línea:	https://doaj.org/article/efdf35ab83c64eb496a0db0292513a0d
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spelling	oai:doaj.org-article:efdf35ab83c64eb496a0db0292513a0d2021-11-18T08:03:51ZHLA diversity in the Russian population assessed by next generation sequencing1563-06252313-741X10.15789/1563-0625-HDI-2182https://doaj.org/article/efdf35ab83c64eb496a0db0292513a0d2021-06-01T00:00:00Zhttps://www.mimmun.ru/mimmun/article/view/2182https://doaj.org/toc/1563-0625https://doaj.org/toc/2313-741XNext generation sequencing is used to determine full-length sequences of HLA genes at the 4-field (allelic) resolution. The study was aimed at determining frequency and diversity of HLA alleles in a cohort of blood donors from the Registry of the National Research Center for Hematology who design ated themselves as Russians (including some not routinely typed variations in HLA gene regions). The studied population consisted of 1510 donors. HLA typing was performed by next generation sequencing. Libraries were performed with AllType NGS Amplification Kits (One Lambda, USA) and sequenced using MiSeq (Illumina, USA). Data analysis used the TypeStream Visual Software V2.0.0.68 (One Lambda, USA) and IPD-IMGT/HLA database 3.40.0.1. Arlequin 3.5 software was used for estimation of allele and haplotype frequencies, deviation from Hardy-Weinberg equilibrium. 82 HLA-A, 156 HLA-В and 85 HLA-С alleles were identified with four-field resolution. 45 HLA-DRB1 and 18 HLA-DQB1 alleles were identified with 2-3-field resolution. Considerable HLA diversity was found among the donors self-designated as Russians: the population had large numbers of distinct alleles at each HLA gene, high percentage of alleles (25-32% of HLA class I) were revealed only once. Sufficient numbers of new alleles were registered which are absent in the IPD-IMGT/HLA database. Considerable allelic diversity in Russian population is due to low-incidence alleles. Despite this diversity, the majority of HLA alleles detected at each locus were common. Significant HLA diversity of the donors was connected with a large number of alleles with rare occurrence. The novel alleles identified in our study differed from the known alleles by single nucleotide substitutions. The most common alleles at the four-field level were as follows: A02:01:01:01 (27.1%), C07:02:01:03 (13.1%), A03:01:01:01 (13.0%), B07:02:01:01 (13.0%), A01:01:01:01 (11.6%) and C07:01:01:01/16 (10.4%). The HLA alleles, which are common for Russian populations, are not always common or well-documented alleles in present catalogues. The data obtained in this study may be used as a reference sample for estimation of HLA allele frequencies in Russian population, for proper frequency evaluation of specific alleles when searching donors for allogeneic hematopoietic stem cell transplantation, as well as for association studies between HLA alleles and different diseases, and for research in population genetics.E. G. KhamaganovaE. A. LeonovA. R. AbdrakhimovaS. P. KhizhinskiyT. V. GaponovaV. G. SavchenkoSPb RAACIarticlehlaallelesdiversitynext generation sequencingImmunologic diseases. AllergyRC581-607RUMedicinskaâ Immunologiâ, Vol 23, Iss 3, Pp 509-522 (2021)
institution	DOAJ
collection	DOAJ
language	RU
topic	hla alleles diversity next generation sequencing Immunologic diseases. Allergy RC581-607
spellingShingle	hla alleles diversity next generation sequencing Immunologic diseases. Allergy RC581-607 E. G. Khamaganova E. A. Leonov A. R. Abdrakhimova S. P. Khizhinskiy T. V. Gaponova V. G. Savchenko HLA diversity in the Russian population assessed by next generation sequencing
description	Next generation sequencing is used to determine full-length sequences of HLA genes at the 4-field (allelic) resolution. The study was aimed at determining frequency and diversity of HLA alleles in a cohort of blood donors from the Registry of the National Research Center for Hematology who design ated themselves as Russians (including some not routinely typed variations in HLA gene regions). The studied population consisted of 1510 donors. HLA typing was performed by next generation sequencing. Libraries were performed with AllType NGS Amplification Kits (One Lambda, USA) and sequenced using MiSeq (Illumina, USA). Data analysis used the TypeStream Visual Software V2.0.0.68 (One Lambda, USA) and IPD-IMGT/HLA database 3.40.0.1. Arlequin 3.5 software was used for estimation of allele and haplotype frequencies, deviation from Hardy-Weinberg equilibrium. 82 HLA-A, 156 HLA-В and 85 HLA-С alleles were identified with four-field resolution. 45 HLA-DRB1 and 18 HLA-DQB1 alleles were identified with 2-3-field resolution. Considerable HLA diversity was found among the donors self-designated as Russians: the population had large numbers of distinct alleles at each HLA gene, high percentage of alleles (25-32% of HLA class I) were revealed only once. Sufficient numbers of new alleles were registered which are absent in the IPD-IMGT/HLA database. Considerable allelic diversity in Russian population is due to low-incidence alleles. Despite this diversity, the majority of HLA alleles detected at each locus were common. Significant HLA diversity of the donors was connected with a large number of alleles with rare occurrence. The novel alleles identified in our study differed from the known alleles by single nucleotide substitutions. The most common alleles at the four-field level were as follows: A02:01:01:01 (27.1%), C07:02:01:03 (13.1%), A03:01:01:01 (13.0%), B07:02:01:01 (13.0%), A01:01:01:01 (11.6%) and C07:01:01:01/16 (10.4%). The HLA alleles, which are common for Russian populations, are not always common or well-documented alleles in present catalogues. The data obtained in this study may be used as a reference sample for estimation of HLA allele frequencies in Russian population, for proper frequency evaluation of specific alleles when searching donors for allogeneic hematopoietic stem cell transplantation, as well as for association studies between HLA alleles and different diseases, and for research in population genetics.
format	article
author	E. G. Khamaganova E. A. Leonov A. R. Abdrakhimova S. P. Khizhinskiy T. V. Gaponova V. G. Savchenko
author_facet	E. G. Khamaganova E. A. Leonov A. R. Abdrakhimova S. P. Khizhinskiy T. V. Gaponova V. G. Savchenko
author_sort	E. G. Khamaganova
title	HLA diversity in the Russian population assessed by next generation sequencing
title_short	HLA diversity in the Russian population assessed by next generation sequencing
title_full	HLA diversity in the Russian population assessed by next generation sequencing
title_fullStr	HLA diversity in the Russian population assessed by next generation sequencing
title_full_unstemmed	HLA diversity in the Russian population assessed by next generation sequencing
title_sort	hla diversity in the russian population assessed by next generation sequencing
publisher	SPb RAACI
publishDate	2021
url	https://doaj.org/article/efdf35ab83c64eb496a0db0292513a0d
work_keys_str_mv	AT egkhamaganova hladiversityintherussianpopulationassessedbynextgenerationsequencing AT ealeonov hladiversityintherussianpopulationassessedbynextgenerationsequencing AT arabdrakhimova hladiversityintherussianpopulationassessedbynextgenerationsequencing AT spkhizhinskiy hladiversityintherussianpopulationassessedbynextgenerationsequencing AT tvgaponova hladiversityintherussianpopulationassessedbynextgenerationsequencing AT vgsavchenko hladiversityintherussianpopulationassessedbynextgenerationsequencing
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HLA diversity in the Russian population assessed by next generation sequencing

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