Cargando…

Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing

The major histocompatibility complex (MHC) region contains many genes that are key regulators of both innate and adaptive immunity including the polymorphic MHCI and MHCII genes. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation that determi...

Descripción completa

Detalles Bibliográficos
Autores principales: Vasoya, Deepali, Law, Andy, Motta, Paolo, Yu, Mingyan, Muwonge, Adrian, Cook, Elizabeth, Li, Xiaoying, Bryson, Karen, MacCallam, Amanda, Sitt, Tatjana, Toye, Philip, Bronsvoort, Barend, Watson, Mick, Morrison, W. Ivan, Connelley, Timothy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5056950/
https://www.ncbi.nlm.nih.gov/pubmed/27516207
http://dx.doi.org/10.1007/s00251-016-0945-7
_version_ 1782458968592875520
author Vasoya, Deepali
Law, Andy
Motta, Paolo
Yu, Mingyan
Muwonge, Adrian
Cook, Elizabeth
Li, Xiaoying
Bryson, Karen
MacCallam, Amanda
Sitt, Tatjana
Toye, Philip
Bronsvoort, Barend
Watson, Mick
Morrison, W. Ivan
Connelley, Timothy
author_facet Vasoya, Deepali
Law, Andy
Motta, Paolo
Yu, Mingyan
Muwonge, Adrian
Cook, Elizabeth
Li, Xiaoying
Bryson, Karen
MacCallam, Amanda
Sitt, Tatjana
Toye, Philip
Bronsvoort, Barend
Watson, Mick
Morrison, W. Ivan
Connelley, Timothy
author_sort Vasoya, Deepali
collection PubMed
description The major histocompatibility complex (MHC) region contains many genes that are key regulators of both innate and adaptive immunity including the polymorphic MHCI and MHCII genes. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation that determines the nature of immune responses. Our current knowledge of the bovine MHCI repertoire is limited with only the Holstein-Friesian breed having been studied in any depth. Traditional methods of MHCI genotyping are of low resolution and laborious and this has been a major impediment to a more comprehensive analysis of the MHCI repertoire of other cattle breeds. Next-generation sequencing (NGS) technologies have been used to enable high throughput and much higher resolution MHCI typing in a number of species. In this study we have developed a MiSeq platform approach and requisite bioinformatics pipeline to facilitate typing of bovine MHCI repertoires. The method was validated initially on a cohort of Holstein-Friesian animals and then demonstrated to enable characterisation of MHCI repertoires in African cattle breeds, for which there was limited or no available data. During the course of these studies we identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00251-016-0945-7) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-5056950
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher Springer Berlin Heidelberg
record_format MEDLINE/PubMed
spelling pubmed-50569502016-10-26 Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing Vasoya, Deepali Law, Andy Motta, Paolo Yu, Mingyan Muwonge, Adrian Cook, Elizabeth Li, Xiaoying Bryson, Karen MacCallam, Amanda Sitt, Tatjana Toye, Philip Bronsvoort, Barend Watson, Mick Morrison, W. Ivan Connelley, Timothy Immunogenetics Original Article The major histocompatibility complex (MHC) region contains many genes that are key regulators of both innate and adaptive immunity including the polymorphic MHCI and MHCII genes. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation that determines the nature of immune responses. Our current knowledge of the bovine MHCI repertoire is limited with only the Holstein-Friesian breed having been studied in any depth. Traditional methods of MHCI genotyping are of low resolution and laborious and this has been a major impediment to a more comprehensive analysis of the MHCI repertoire of other cattle breeds. Next-generation sequencing (NGS) technologies have been used to enable high throughput and much higher resolution MHCI typing in a number of species. In this study we have developed a MiSeq platform approach and requisite bioinformatics pipeline to facilitate typing of bovine MHCI repertoires. The method was validated initially on a cohort of Holstein-Friesian animals and then demonstrated to enable characterisation of MHCI repertoires in African cattle breeds, for which there was limited or no available data. During the course of these studies we identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00251-016-0945-7) contains supplementary material, which is available to authorized users. Springer Berlin Heidelberg 2016-08-11 2016 /pmc/articles/PMC5056950/ /pubmed/27516207 http://dx.doi.org/10.1007/s00251-016-0945-7 Text en © The Author(s) 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Original Article
Vasoya, Deepali
Law, Andy
Motta, Paolo
Yu, Mingyan
Muwonge, Adrian
Cook, Elizabeth
Li, Xiaoying
Bryson, Karen
MacCallam, Amanda
Sitt, Tatjana
Toye, Philip
Bronsvoort, Barend
Watson, Mick
Morrison, W. Ivan
Connelley, Timothy
Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing
title Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing
title_full Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing
title_fullStr Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing
title_full_unstemmed Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing
title_short Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing
title_sort rapid identification of bovine mhci haplotypes in genetically divergent cattle populations using next-generation sequencing
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5056950/
https://www.ncbi.nlm.nih.gov/pubmed/27516207
http://dx.doi.org/10.1007/s00251-016-0945-7
work_keys_str_mv AT vasoyadeepali rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT lawandy rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT mottapaolo rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT yumingyan rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT muwongeadrian rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT cookelizabeth rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT lixiaoying rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT brysonkaren rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT maccallamamanda rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT sitttatjana rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT toyephilip rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT bronsvoortbarend rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT watsonmick rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT morrisonwivan rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing
AT connelleytimothy rapididentificationofbovinemhcihaplotypesingeneticallydivergentcattlepopulationsusingnextgenerationsequencing