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Pleasance E, Bohm A, Williamson LM, Nelson JMT, Shen Y, Bonakdar M, Titmuss E, Csizmok V, Wee K, Hosseinzadeh S, Grisdale CJ, Reisle C, Taylor GA, Lewis E, Jones MR, Bleile D, Sadeghi S, Zhang W, Davies A, Pellegrini B, Wong T, Bowlby R, Chan SK, Mungall KL, Chuah E, Mungall AJ, Moore RA, Zhao Y, Deol B, Fisic A, Fok A, Regier DA, Weymann D, Schaeffer DF, Young S, Yip S, Schrader K, Levasseur N, Taylor SK, Feng X, Tinker A, Savage KJ, Chia S, Gelmon K, Sun S, Lim H, Renouf DJ, Jones SJM, Marra MA, Laskin J. Whole genome and transcriptome analysis enhances precision cancer treatment options. Ann Oncol 2022; 33:939-949. [PMID: 35691590 DOI: 10.1016/j.annonc.2022.05.522] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/03/2022] [Accepted: 05/31/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Recent advances are enabling delivery of precision genomic medicine to cancer clinics. While the majority of approaches profile panels of selected genes or hotspot regions, comprehensive data provided by whole genome and transcriptome sequencing and analysis (WGTA) presents an opportunity to align a much larger proportion of patients to therapies. PATIENTS AND METHODS Samples from 570 patients with advanced or metastatic cancer of diverse types enrolled in the Personalized OncoGenomics (POG) program underwent WGTA. DNA-based data, including mutations, copy number, and mutation signatures, were combined with RNA-based data, including gene expression and fusions, to generate comprehensive WGTA profiles. A multidisciplinary molecular tumour board used WGTA profiles to identify and prioritize clinically actionable alterations and inform therapy. Patient responses to WGTA-informed therapies were collected. RESULTS Clinically actionable targets were identified for 83% of patients, 37% of whom received WGTA-informed treatments. RNA expression data were particularly informative, contributing to 67% of WGTA-informed treatments; 25% of treatments were informed by RNA expression alone. Of a total 248 WGTA-informed treatments, 46% resulted in clinical benefit. RNA expression data were comparable to DNA-based mutation and copy number data in aligning to clinically beneficial treatments. Genome signatures also guided therapeutics including platinum, PARP inhibitors, and immunotherapies. Patients accessed WGTA-informed treatments through clinical trials (19%), off-label use (35%), and as standard therapies (46%) including those which would not otherwise have been the next choice of therapy, demonstrating the utility of genomic information to direct use of chemotherapies as well as targeted therapies. CONCLUSIONS Integrating RNA expression and genome data illuminated treatment options that resulted in 46% of treated patients experiencing positive clinical benefit, supporting the use of comprehensive WGTA profiling in clinical cancer care. CLINICAL TRIAL NUMBER NCT02155621.
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Affiliation(s)
- E Pleasance
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - A Bohm
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver; Department of Medicine, University of British Columbia, Vancouver
| | - L M Williamson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - J M T Nelson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - Y Shen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - M Bonakdar
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - E Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - V Csizmok
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - K Wee
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - S Hosseinzadeh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver; Department of Medicine, University of British Columbia, Vancouver
| | - C J Grisdale
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - C Reisle
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - G A Taylor
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - E Lewis
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - M R Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - D Bleile
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - S Sadeghi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - W Zhang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - A Davies
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - B Pellegrini
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - T Wong
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - R Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - S K Chan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - K L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - E Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - A J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - R A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - Y Zhao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - B Deol
- Department of Medical Oncology, BC Cancer, Vancouver
| | - A Fisic
- Department of Medical Oncology, BC Cancer, Vancouver
| | - A Fok
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - D A Regier
- Canadian Centre for Applied Research in Cancer Control, Cancer Control Research, BC Cancer, Vancouver
| | - D Weymann
- Canadian Centre for Applied Research in Cancer Control, Cancer Control Research, BC Cancer, Vancouver
| | - D F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver; Pancreas Centre BC, Vancouver
| | - S Young
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver
| | - S Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver
| | - K Schrader
- Hereditary Cancer Program, BC Cancer, Vancouver; Department of Medical Genetics, University of British Columbia, Vancouver
| | - N Levasseur
- Department of Medical Oncology, BC Cancer, Vancouver
| | - S K Taylor
- Department of Medical Oncology, BC Cancer, Kelowna
| | - X Feng
- Department of Medical Oncology, BC Cancer, Victoria
| | - A Tinker
- Department of Medical Oncology, BC Cancer, Vancouver
| | - K J Savage
- Department of Medical Oncology, BC Cancer, Vancouver
| | - S Chia
- Department of Medical Oncology, BC Cancer, Vancouver
| | - K Gelmon
- Department of Medical Oncology, BC Cancer, Vancouver
| | - S Sun
- Department of Medical Oncology, BC Cancer, Vancouver
| | - H Lim
- Department of Medical Oncology, BC Cancer, Vancouver
| | - D J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver; Pancreas Centre BC, Vancouver
| | - S J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver; Department of Medical Genetics, University of British Columbia, Vancouver; Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, Canada
| | - M A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver; Department of Medical Genetics, University of British Columbia, Vancouver
| | - J Laskin
- Department of Medical Oncology, BC Cancer, Vancouver.
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