Using de novo assembly to identify structural variation of eight complex immune system gene regions.

Driven by the necessity to survive environmental pathogens, the human immune system has evolved exceptional diversity and plasticity, to which several factors contribute including inheritable structural polymorphism of the underlying genes. Characterizing this variation is challenging due to the com...

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Autores principales:	Jia-Yuan Zhang, Hannah Roberts, David S C Flores, Antony J Cutler, Andrew C Brown, Justin P Whalley, Olga Mielczarek, David Buck, Helen Lockstone, Barbara Xella, Karen Oliver, Craig Corton, Emma Betteridge, Rachael Bashford-Rogers, Julian C Knight, John A Todd, Gavin Band
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/bea2427071be4bdeb11fe0c7dccabc1c
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spelling	oai:doaj.org-article:bea2427071be4bdeb11fe0c7dccabc1c2021-12-02T19:58:09ZUsing de novo assembly to identify structural variation of eight complex immune system gene regions.1553-734X1553-735810.1371/journal.pcbi.1009254https://doaj.org/article/bea2427071be4bdeb11fe0c7dccabc1c2021-08-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009254https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Driven by the necessity to survive environmental pathogens, the human immune system has evolved exceptional diversity and plasticity, to which several factors contribute including inheritable structural polymorphism of the underlying genes. Characterizing this variation is challenging due to the complexity of these loci, which contain extensive regions of paralogy, segmental duplication and high copy-number repeats, but recent progress in long-read sequencing and optical mapping techniques suggests this problem may now be tractable. Here we assess this by using long-read sequencing platforms from PacBio and Oxford Nanopore, supplemented with short-read sequencing and Bionano optical mapping, to sequence DNA extracted from CD14+ monocytes and peripheral blood mononuclear cells from a single European individual identified as HV31. We use this data to build a de novo assembly of eight genomic regions encoding four key components of the immune system, namely the human leukocyte antigen, immunoglobulins, T cell receptors, and killer-cell immunoglobulin-like receptors. Validation of our assembly using k-mer based and alignment approaches suggests that it has high accuracy, with estimated base-level error rates below 1 in 10 kb, although we identify a small number of remaining structural errors. We use the assembly to identify heterozygous and homozygous structural variation in comparison to GRCh38. Despite analyzing only a single individual, we find multiple large structural variants affecting core genes at all three immunoglobulin regions and at two of the three T cell receptor regions. Several of these variants are not accurately callable using current algorithms, implying that further methodological improvements are needed. Our results demonstrate that assessing haplotype variation in these regions is possible given sufficiently accurate long-read and associated data. Continued reductions in the cost of these technologies will enable application of these methods to larger samples and provide a broader catalogue of germline structural variation at these loci, an important step toward making these regions accessible to large-scale genetic association studies.Jia-Yuan ZhangHannah RobertsDavid S C FloresAntony J CutlerAndrew C BrownJustin P WhalleyOlga MielczarekDavid BuckHelen LockstoneBarbara XellaKaren OliverCraig CortonEmma BetteridgeRachael Bashford-RogersJulian C KnightJohn A ToddGavin BandPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 8, p e1009254 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Jia-Yuan Zhang Hannah Roberts David S C Flores Antony J Cutler Andrew C Brown Justin P Whalley Olga Mielczarek David Buck Helen Lockstone Barbara Xella Karen Oliver Craig Corton Emma Betteridge Rachael Bashford-Rogers Julian C Knight John A Todd Gavin Band Using de novo assembly to identify structural variation of eight complex immune system gene regions.
description	Driven by the necessity to survive environmental pathogens, the human immune system has evolved exceptional diversity and plasticity, to which several factors contribute including inheritable structural polymorphism of the underlying genes. Characterizing this variation is challenging due to the complexity of these loci, which contain extensive regions of paralogy, segmental duplication and high copy-number repeats, but recent progress in long-read sequencing and optical mapping techniques suggests this problem may now be tractable. Here we assess this by using long-read sequencing platforms from PacBio and Oxford Nanopore, supplemented with short-read sequencing and Bionano optical mapping, to sequence DNA extracted from CD14+ monocytes and peripheral blood mononuclear cells from a single European individual identified as HV31. We use this data to build a de novo assembly of eight genomic regions encoding four key components of the immune system, namely the human leukocyte antigen, immunoglobulins, T cell receptors, and killer-cell immunoglobulin-like receptors. Validation of our assembly using k-mer based and alignment approaches suggests that it has high accuracy, with estimated base-level error rates below 1 in 10 kb, although we identify a small number of remaining structural errors. We use the assembly to identify heterozygous and homozygous structural variation in comparison to GRCh38. Despite analyzing only a single individual, we find multiple large structural variants affecting core genes at all three immunoglobulin regions and at two of the three T cell receptor regions. Several of these variants are not accurately callable using current algorithms, implying that further methodological improvements are needed. Our results demonstrate that assessing haplotype variation in these regions is possible given sufficiently accurate long-read and associated data. Continued reductions in the cost of these technologies will enable application of these methods to larger samples and provide a broader catalogue of germline structural variation at these loci, an important step toward making these regions accessible to large-scale genetic association studies.
format	article
author	Jia-Yuan Zhang Hannah Roberts David S C Flores Antony J Cutler Andrew C Brown Justin P Whalley Olga Mielczarek David Buck Helen Lockstone Barbara Xella Karen Oliver Craig Corton Emma Betteridge Rachael Bashford-Rogers Julian C Knight John A Todd Gavin Band
author_facet	Jia-Yuan Zhang Hannah Roberts David S C Flores Antony J Cutler Andrew C Brown Justin P Whalley Olga Mielczarek David Buck Helen Lockstone Barbara Xella Karen Oliver Craig Corton Emma Betteridge Rachael Bashford-Rogers Julian C Knight John A Todd Gavin Band
author_sort	Jia-Yuan Zhang
title	Using de novo assembly to identify structural variation of eight complex immune system gene regions.
title_short	Using de novo assembly to identify structural variation of eight complex immune system gene regions.
title_full	Using de novo assembly to identify structural variation of eight complex immune system gene regions.
title_fullStr	Using de novo assembly to identify structural variation of eight complex immune system gene regions.
title_full_unstemmed	Using de novo assembly to identify structural variation of eight complex immune system gene regions.
title_sort	using de novo assembly to identify structural variation of eight complex immune system gene regions.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/bea2427071be4bdeb11fe0c7dccabc1c
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Using de novo assembly to identify structural variation of eight complex immune system gene regions.

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