Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology
Jobanputra, Vaidehi; Wrzeszczynski, Kazimierz O.; Buttner, Reinhard; Caldas, Carlos; Cuppen, Edwin; Grimmond, Sean; Haferlach, Torsten; Mullighan, Charles; Schuh, Anna; Elemento, Olivier
(2022) Seminars in Cancer Biology, volume 84, pp. 23 - 31
(Article)
Abstract
Whole-genome sequencing either alone or in combination with whole-transcriptome sequencing has started to be used to analyze clinical tumor samples to improve diagnosis, provide risk stratification, and select patient-specific therapies. Compared with current genomic testing strategies, largely focused on small number of genes tested individually or targeted panels, whole-genome and
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transcriptome sequencing (WGTS) provides novel opportunities to identify and report a potentially much larger number of actionable alterations with diagnostic, prognostic, and/or predictive impact. Such alterations include point mutations, indels, copy- number aberrations and structural variants, but also germline variants, fusion genes, noncoding alterations and mutational signatures. Nevertheless, these comprehensive tests are accompanied by many challenges ranging from the extent and diversity of sequence alterations detected by these methods to the complexity and limited existing standardization in interpreting them. We describe the challenges of WGTS interpretation and the opportunities with comprehensive genomic testing.
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Keywords: Clinical genomics, Data integration, Electronic medical records, Molecular tumor boards, Targeted therapy, Whole-genome sequencing, Whole-transcriptome sequencing
ISSN: 1044-579X
Publisher: Academic Press Inc.
Note: Funding Information: AS: The research was funded/supported by the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. OE is supported by NIH grants UL1TR002384, R01CA194547 and LLS SCOR grants 180078-02, 7021-20.RB: Honoraria from Abbvie, Amgen, Astra Zeneca, BMS, Illumina, MSD, Merck-Serono, Lilly, Roche. CC is a member of the External Science Panel of AstraZeneca iMED, honoraria from Illumina and research grants (administered by the University of Cambridge) from AstraZeneca, Sevier, Genentech and Roche. TH is part owner of MLL Munich Leukemia Laboratory. CGM: honoraria from Amgen, Illumina; research funding from Pfizer, Abbvie. AS: honoraria from Gilead, Roche, Janssen, Abbvie, Astra Zeneca, Adaptive Biotechnology, Jazz, Base Genomics, Illumina, Oxford Nanopore Technology. Unrestricted educational grants from Astra Zeneca and Janssen. In-kind contributions from Illumina and Oxford Nanopore Technology. OE is equity holder and scientific advisor for Volastra Therapeutics, One Three Biotech, Owkin and Freenome and receives research funding from Eli Lilly, Janssen and Sanofi. Funding Information: AS: The research was funded/supported by the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC) . The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. OE is supported by NIH grants UL1TR002384 , R01CA194547 and LLS SCOR grants 180078-02 , 7021-20 . Publisher Copyright: © 2021 Elsevier Ltd
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