Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers. Academic Article uri icon

Overview

abstract

  • The utility of cancer whole genome and transcriptome sequencing (cWGTS) in oncology is increasingly recognized. However, implementation of cWGTS is challenged by the need to deliver results within clinically relevant timeframes, concerns about assay sensitivity, reporting and prioritization of findings. In a prospective research study we develop a workflow that reports comprehensive cWGTS results in 9 days. Comparison of cWGTS to diagnostic panel assays demonstrates the potential of cWGTS to capture all clinically reported mutations with comparable sensitivity in a single workflow. Benchmarking identifies a minimum of 80× as optimal depth for clinical WGS sequencing. Integration of germline, somatic DNA and RNA-seq data enable data-driven variant prioritization and reporting, with oncogenic findings reported in 54% more patients than standard of care. These results establish key technical considerations for the implementation of cWGTS as an integrated test in clinical oncology.

publication date

  • May 18, 2022

Research

keywords

  • Gene Expression Profiling
  • Neoplasms

Identity

PubMed Central ID

  • PMC9117241

Scopus Document Identifier

  • 85130306976

Digital Object Identifier (DOI)

  • 10.1093/nar/gku181

PubMed ID

  • 35585047

Additional Document Info

volume

  • 13

issue

  • 1