Application of targeted nanopore sequencing for the screening and determination of structural variants in patients with Lynch syndrome.

Colorectal Neoplasms / complications Colorectal Neoplasms, Hereditary Nonpolyposis / complications DNA Mismatch Repair / genetics Female Genetic Predisposition to Disease Genetic Testing / standards Germ-Line Mutation / genetics Humans Male Mass Screening MutL Protein Homolog 1 / genetics MutS Homolog 2 Protein / genetics Nanopore Sequencing Polymorphism, Single Nucleotide / genetics Protein Conformation

Journal

Journal of human genetics

ISSN: 1435-232X

Titre abrégé: J Hum Genet

Pays: England

ID NLM: 9808008

Informations de publication

Date de publication:
Nov 2021

Historique:

received: 22 02 2021

accepted: 02 04 2021

revised: 23 03 2021

pubmed: 8 5 2021

medline: 8 2 2022

entrez: 7 5 2021

Statut: ppublish

Résumé

Lynch syndrome is a hereditary disease characterized by an increased risk of colorectal and other cancers. Germline variants in the mismatch repair (MMR) genes are responsible for this disease. Previously, we screened the MMR genes in colorectal cancer patients who fulfilled modified Amsterdam II criteria, and multiplex ligation-dependent probe amplification (MPLA) identified 11 structural variants (SVs) of MLH1 and MSH2 in 17 patients. In this study, we have tested the efficacy of long read-sequencing coupled with target enrichment for the determination of SVs and their breakpoints. DNA was captured by array probes designed to hybridize with target regions including four MMR genes and then sequenced using MinION, a nanopore sequencing platform. Approximately, 1000-fold coverage was obtained in the target regions compared with other regions. Application of this system to four test cases among the 17 patients correctly mapped the breakpoints. In addition, we newly found a deletion across an 84 kb region of MSH2 in a case without the pathogenic single nucleotide variants. These data suggest that long read-sequencing combined with hybridization-based enrichment is an efficient method to identify both SVs and their breakpoints. This strategy might replace MLPA for the screening of SVs in hereditary diseases.

Identifiants

DOI: 10.1038/s10038-021-00927-9 PMID: 33958709

pubmed: 33958709

doi: 10.1038/s10038-021-00927-9

pii: 10.1038/s10038-021-00927-9

doi:

Substances chimiques

MLH1 protein, human 0

MSH2 protein, human EC 3.6.1.3

MutL Protein Homolog 1 EC 3.6.1.3

MutS Homolog 2 Protein EC 3.6.1.3

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

Pagination

1053-1060

Subventions

Organisme : MEXT | Japan Society for the Promotion of Science (JSPS)

ID : #16H01569

Organisme : MEXT | Japan Science and Technology Agency (JST)

ID : Center of Innovation program

Informations de copyright

Références

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