Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research

The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducte...

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Autores principales:	Venceslas Douillard, Erick C. Castelli, Steven J. Mack, Jill A. Hollenbach, Pierre-Antoine Gourraud, Nicolas Vince, Sophie Limou
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	Major Histocompatibility Complex (MHC) HLA association analysis imputation immunogenetics Genetics QH426-470
Acceso en línea:	https://doaj.org/article/832f3f2615a04582b9fbab5288352b51
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spelling	oai:doaj.org-article:832f3f2615a04582b9fbab5288352b512021-12-02T11:37:21ZApproaching Genetics Through the MHC Lens: Tools and Methods for HLA Research1664-802110.3389/fgene.2021.774916https://doaj.org/article/832f3f2615a04582b9fbab5288352b512021-12-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.774916/fullhttps://doaj.org/toc/1664-8021The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducted with variable scale and success; convincing results were mostly obtained with broader whole-genome association studies. Here, we propose a technical review of HLA analysis, including basic HLA knowledge as well as available tools and advice. We notably describe recent algorithms to infer and call HLA genotypes from GWAS SNPs and NGS data, respectively, which opens the possibility to investigate HLA from large datasets without a specific initial focus on this region. We thus hope this overview will empower geneticists who were unfamiliar with HLA to run MHC-focused analyses following the footsteps of the Covid-19\|HLA & Immunogenetics Consortium.Venceslas DouillardErick C. CastelliSteven J. MackJill A. HollenbachJill A. HollenbachPierre-Antoine GourraudNicolas VinceSophie LimouSophie LimouFrontiers Media S.A.articleMajor Histocompatibility Complex (MHC)HLAassociation analysisimputationimmunogeneticsGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Major Histocompatibility Complex (MHC) HLA association analysis imputation immunogenetics Genetics QH426-470
spellingShingle	Major Histocompatibility Complex (MHC) HLA association analysis imputation immunogenetics Genetics QH426-470 Venceslas Douillard Erick C. Castelli Steven J. Mack Jill A. Hollenbach Jill A. Hollenbach Pierre-Antoine Gourraud Nicolas Vince Sophie Limou Sophie Limou Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research
description	The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducted with variable scale and success; convincing results were mostly obtained with broader whole-genome association studies. Here, we propose a technical review of HLA analysis, including basic HLA knowledge as well as available tools and advice. We notably describe recent algorithms to infer and call HLA genotypes from GWAS SNPs and NGS data, respectively, which opens the possibility to investigate HLA from large datasets without a specific initial focus on this region. We thus hope this overview will empower geneticists who were unfamiliar with HLA to run MHC-focused analyses following the footsteps of the Covid-19\|HLA & Immunogenetics Consortium.
format	article
author	Venceslas Douillard Erick C. Castelli Steven J. Mack Jill A. Hollenbach Jill A. Hollenbach Pierre-Antoine Gourraud Nicolas Vince Sophie Limou Sophie Limou
author_facet	Venceslas Douillard Erick C. Castelli Steven J. Mack Jill A. Hollenbach Jill A. Hollenbach Pierre-Antoine Gourraud Nicolas Vince Sophie Limou Sophie Limou
author_sort	Venceslas Douillard
title	Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research
title_short	Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research
title_full	Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research
title_fullStr	Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research
title_full_unstemmed	Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research
title_sort	approaching genetics through the mhc lens: tools and methods for hla research
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/832f3f2615a04582b9fbab5288352b51
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Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research

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