Whole genome sequencing facilitates intragenic variant interpretation following modifier screening in C. elegans

Abstract Background Intragenic modifiers (in-phase, second-site variants) are known to have dramatic effects on clinical outcomes, affecting disease attributes such as severity or age of onset. However, despite their clinical importance, the focus of many genetic screens in model systems is on the d...

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Autores principales:	Francesca Jean, Susan Stasiuk, Tatiana Maroilley, Catherine Diao, Andrew Galbraith, Maja Tarailo-Graovac
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Mutagenesis screen Intragenic modifier Whole genome sequencing C. elegans CRISPR/Cas9 Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/89e331a0c6c34531acfc0e878d10e41d
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spelling	oai:doaj.org-article:89e331a0c6c34531acfc0e878d10e41d2021-11-14T12:26:49ZWhole genome sequencing facilitates intragenic variant interpretation following modifier screening in C. elegans10.1186/s12864-021-08142-81471-2164https://doaj.org/article/89e331a0c6c34531acfc0e878d10e41d2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08142-8https://doaj.org/toc/1471-2164Abstract Background Intragenic modifiers (in-phase, second-site variants) are known to have dramatic effects on clinical outcomes, affecting disease attributes such as severity or age of onset. However, despite their clinical importance, the focus of many genetic screens in model systems is on the discovery of extragenic variants, with many labs still relying upon more traditional methods to identify modifiers. However, traditional methods such as PCR and Sanger sequencing can be time-intensive and do not permit a thorough understanding of the intragenic modifier effects in the context of non-isogenic genomic backgrounds. Results Here, we apply high throughput approaches to identify and understand intragenic modifiers using Caenorhabditis elegans. Specifically, we applied whole genome sequencing (WGS) to a mutagen-induced forward genetic screen to identify intragenic suppressors of a temperature-sensitive zyg-1(it25) allele in C. elegans. ZYG-1 is a polo kinase that is important for centriole function and cell divisions, and mutations that truncate its human orthologue, PLK4, have been associated with microcephaly. Combining WGS and CRISPR/Cas9, we rapidly identify intragenic modifiers, show that these variants are distributed non-randomly throughout zyg-1 and that genomic context plays an important role on phenotypic outcomes. Conclusions Ultimately, our work shows that WGS facilitates high-throughput identification of intragenic modifiers in clinically relevant genes by reducing hands-on research time and overall costs and by allowing thorough understanding of the intragenic phenotypic effects in the context of different genetic backgrounds.Francesca JeanSusan StasiukTatiana MaroilleyCatherine DiaoAndrew GalbraithMaja Tarailo-GraovacBMCarticleMutagenesis screenIntragenic modifierWhole genome sequencingC. elegansCRISPR/Cas9BiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Mutagenesis screen Intragenic modifier Whole genome sequencing C. elegans CRISPR/Cas9 Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Mutagenesis screen Intragenic modifier Whole genome sequencing C. elegans CRISPR/Cas9 Biotechnology TP248.13-248.65 Genetics QH426-470 Francesca Jean Susan Stasiuk Tatiana Maroilley Catherine Diao Andrew Galbraith Maja Tarailo-Graovac Whole genome sequencing facilitates intragenic variant interpretation following modifier screening in C. elegans
description	Abstract Background Intragenic modifiers (in-phase, second-site variants) are known to have dramatic effects on clinical outcomes, affecting disease attributes such as severity or age of onset. However, despite their clinical importance, the focus of many genetic screens in model systems is on the discovery of extragenic variants, with many labs still relying upon more traditional methods to identify modifiers. However, traditional methods such as PCR and Sanger sequencing can be time-intensive and do not permit a thorough understanding of the intragenic modifier effects in the context of non-isogenic genomic backgrounds. Results Here, we apply high throughput approaches to identify and understand intragenic modifiers using Caenorhabditis elegans. Specifically, we applied whole genome sequencing (WGS) to a mutagen-induced forward genetic screen to identify intragenic suppressors of a temperature-sensitive zyg-1(it25) allele in C. elegans. ZYG-1 is a polo kinase that is important for centriole function and cell divisions, and mutations that truncate its human orthologue, PLK4, have been associated with microcephaly. Combining WGS and CRISPR/Cas9, we rapidly identify intragenic modifiers, show that these variants are distributed non-randomly throughout zyg-1 and that genomic context plays an important role on phenotypic outcomes. Conclusions Ultimately, our work shows that WGS facilitates high-throughput identification of intragenic modifiers in clinically relevant genes by reducing hands-on research time and overall costs and by allowing thorough understanding of the intragenic phenotypic effects in the context of different genetic backgrounds.
format	article
author	Francesca Jean Susan Stasiuk Tatiana Maroilley Catherine Diao Andrew Galbraith Maja Tarailo-Graovac
author_facet	Francesca Jean Susan Stasiuk Tatiana Maroilley Catherine Diao Andrew Galbraith Maja Tarailo-Graovac
author_sort	Francesca Jean
title	Whole genome sequencing facilitates intragenic variant interpretation following modifier screening in C. elegans
title_short	Whole genome sequencing facilitates intragenic variant interpretation following modifier screening in C. elegans
title_full	Whole genome sequencing facilitates intragenic variant interpretation following modifier screening in C. elegans
title_fullStr	Whole genome sequencing facilitates intragenic variant interpretation following modifier screening in C. elegans
title_full_unstemmed	Whole genome sequencing facilitates intragenic variant interpretation following modifier screening in C. elegans
title_sort	whole genome sequencing facilitates intragenic variant interpretation following modifier screening in c. elegans
publisher	BMC
publishDate	2021
url	https://doaj.org/article/89e331a0c6c34531acfc0e878d10e41d
work_keys_str_mv	AT francescajean wholegenomesequencingfacilitatesintragenicvariantinterpretationfollowingmodifierscreeningincelegans AT susanstasiuk wholegenomesequencingfacilitatesintragenicvariantinterpretationfollowingmodifierscreeningincelegans AT tatianamaroilley wholegenomesequencingfacilitatesintragenicvariantinterpretationfollowingmodifierscreeningincelegans AT catherinediao wholegenomesequencingfacilitatesintragenicvariantinterpretationfollowingmodifierscreeningincelegans AT andrewgalbraith wholegenomesequencingfacilitatesintragenicvariantinterpretationfollowingmodifierscreeningincelegans AT majatarailograovac wholegenomesequencingfacilitatesintragenicvariantinterpretationfollowingmodifierscreeningincelegans
_version_	1718429242147995648

Whole genome sequencing facilitates intragenic variant interpretation following modifier screening in C. elegans

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