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Jobanputra V, Wrzeszczynski KO, Buttner R, et al. Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology. Semin Cancer Biol. 2021;doi: 10.1016/j.semcancer.2021.07.003.
Jobanputra, V., Wrzeszczynski, K. O., Buttner, R., Caldas, C., Cuppen, E., Grimmond, S., Haferlach, T., Mullighan, C., Schuh, A., & Elemento, O. (2021). Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology. Seminars in cancer biology, . https://doi.org/10.1016/j.semcancer.2021.07.003
Jobanputra, Vaidehi, et al. "Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology." Seminars in cancer biology vol. (2021). doi: https://doi.org/10.1016/j.semcancer.2021.07.003
Jobanputra V, Wrzeszczynski KO, Buttner R, Caldas C, Cuppen E, Grimmond S, Haferlach T, Mullighan C, Schuh A, Elemento O. Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology. Semin Cancer Biol. 2021 Jul 10; doi: 10.1016/j.semcancer.2021.07.003. Epub 2021 Jul 10. PMID: 34256129.
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Semin Cancer Biol. 2021 Jul 10; doi: 10.1016/j.semcancer.2021.07.003. Epub 2021 Jul 10.

Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology.

Seminars in cancer biology

Vaidehi Jobanputra, Kazimierz O Wrzeszczynski, Reinhard Buttner, Carlos Caldas, Edwin Cuppen, Sean Grimmond, Torsten Haferlach, Charles Mullighan, Anna Schuh, Olivier Elemento

Affiliations

  1. New York Genome Center, 101 Avenue of the Americas, New York, NY 100132, United States; Columbia University Medical Center, 650 W 168th St, New York, NY 10032, United States. Electronic address: [email protected].
  2. New York Genome Center, 101 Avenue of the Americas, New York, NY 100132, United States.
  3. Institute of Pathology, University Hospital Cologne, Germany.
  4. Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, United Kingdom.
  5. Hartwig Medical Foundation, Amsterdam, Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, Netherlands.
  6. Centre for Cancer Research, University of Melbourne, Melbourne, Australia.
  7. MLL Munich Leukemia Laboratory, Munich, Germany.
  8. Department of Pathology, St. Jude Children's Research Hospital, United States.
  9. NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom.
  10. Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, United States. Electronic address: [email protected].

PMID: 34256129 DOI: 10.1016/j.semcancer.2021.07.003

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 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.

Copyright © 2021 Elsevier Ltd. All rights reserved.

Keywords: Clinical genomics; Data integration; Electronic medical records; Molecular tumor boards; Targeted therapy; Whole-genome sequencing; Whole-transcriptome sequencing

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