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Stodolna A, He M, Vasipalli M, Kingsbury Z, Becq J, Stockton JD, Dilworth MP, James J, Sillo T, Blakeway D, Ward ST, Ismail T, Ross MT, Beggs AD. Clinical-grade whole-genome sequencing and 3' transcriptome analysis of colorectal cancer patients. Genome Med 2021; 13:33. [PMID: 33632293 PMCID: PMC7908713 DOI: 10.1186/s13073-021-00852-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 02/11/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Clinical-grade whole-genome sequencing (cWGS) has the potential to become the standard of care within the clinic because of its breadth of coverage and lack of bias towards certain regions of the genome. Colorectal cancer presents a difficult treatment paradigm, with over 40% of patients presenting at diagnosis with metastatic disease. We hypothesised that cWGS coupled with 3' transcriptome analysis would give new insights into colorectal cancer. METHODS Patients underwent PCR-free whole-genome sequencing and alignment and variant calling using a standardised pipeline to output SNVs, indels, SVs and CNAs. Additional insights into the mutational signatures and tumour biology were gained by the use of 3' RNA-seq. RESULTS Fifty-four patients were studied in total. Driver analysis identified the Wnt pathway gene APC as the only consistently mutated driver in colorectal cancer. Alterations in the PI3K/mTOR pathways were seen as previously observed in CRC. Multiple private CNAs, SVs and gene fusions were unique to individual tumours. Approximately 30% of patients had a tumour mutational burden of > 10 mutations/Mb of DNA, suggesting suitability for immunotherapy. CONCLUSIONS Clinical whole-genome sequencing offers a potential avenue for the identification of private genomic variation that may confer sensitivity to targeted agents and offer patients new options for targeted therapies.
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Affiliation(s)
- Agata Stodolna
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Miao He
- Illumina Cambridge, Granta Park, Cambridge, UK
| | | | | | | | - Joanne D Stockton
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Mark P Dilworth
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jonathan James
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Toju Sillo
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Daniel Blakeway
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Stephen T Ward
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Tariq Ismail
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Mark T Ross
- Illumina Cambridge, Granta Park, Cambridge, UK
| | - Andrew D Beggs
- Institute of Cancer and Genomic Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
- Surgical Research Laboratory, Institute of Cancer & Genomic Science, University of Birmingham, Vincent Drive, Birmingham, B15 2TT, UK.
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