Evaluation of whole genome sequencing utility in identifying driver alterations in cancer genome.

Humans Neoplasms / genetics Whole Genome Sequencing / methods Exome Sequencing / methods Genome, Human Oncogenes / genetics Female Male Gene Expression Profiling / methods Mutation Genomics / methods

Cancer genome analysis Driver alteration Gene expression profiling Whole genome sequencing

Journal

Scientific reports

ISSN: 2045-2322

Titre abrégé: Sci Rep

Pays: England

ID NLM: 101563288

Informations de publication

Date de publication:
12 Oct 2024

Historique:

received: 30 04 2024

accepted: 24 09 2024

medline: 13 10 2024

pubmed: 13 10 2024

entrez: 12 10 2024

Statut: epublish

Résumé

In cancer genome analysis, identifying pathogenic alterations and assessing their effects on oncogenic processes is important. Although whole exome sequencing (WES) can effectively detect such changes, driver alterations could not be identified in 27.8% of the cases, according to a previous study. The objectives of the present study were to evaluate the utility of whole genome sequencing (WGS) and clarify its differences with WES in terms of driver alteration detection. For this purpose, WGS analysis was conducted on 177 driverless WES samples, selected from 5,480 fresh frozen samples derived from 5,140 Japanese patients with cancer. These samples were selected as primary tumor, both WES and transcriptome profiling were performed, estimated tumor content of ≥ 30%, and no driver alterations were identified by WES. WGS identified driver and likely driver alterations in 68.4 and 22.6% of the samples, respectively. The most frequent alteration type was oncogene amplification, followed by tumor suppressor gene deletion and small variants located outside the coding region. In the remaining 9.0% of samples, no such signals were identified; therefore, further investigations are required. The current study clearly demonstrated the role and utility of WGS in identifying genomic alterations that contribute to tumorigenesis.

Identifiants

DOI: 10.1038/s41598-024-74272-0 PMID: 39396060

pubmed: 39396060

doi: 10.1038/s41598-024-74272-0

pii: 10.1038/s41598-024-74272-0

doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

Pagination

23898

Informations de copyright

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