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Murphy RG, Roddy AC, Srivastava S, Baena E, Waugh D, M. O’Sullivan J, McArt DG, Jain S, LaBonte M. Prostate cancer heterogeneity assessment with multi-regional sampling and alignment-free methods. NAR Genom Bioinform 2020; 2:lqaa062. [PMID: 32856020 PMCID: PMC7440682 DOI: 10.1093/nargab/lqaa062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 07/16/2020] [Accepted: 08/05/2020] [Indexed: 11/14/2022] Open
Abstract
Combining alignment-free methods for phylogenetic analysis with multi-regional sampling using next-generation sequencing can provide an assessment of intra-patient tumour heterogeneity. From multi-regional sampling divergent branching, we validated two different lesions within a patient's prostate. Where multi-regional sampling has not been used, a single sample from one of these areas could misguide as to which drugs or therapies would best benefit this patient, due to the fact these tumours appear to be genetically different. This application has the power to render, in a fraction of the time used by other approaches, intra-patient heterogeneity and decipher aberrant biomarkers. Another alignment-free method for calling single-nucleotide variants from raw next-generation sequencing samples has determined possible variants and genomic locations that may be able to characterize the differences between the two main branching patterns. Alignment-free approaches have been applied to relevant clinical multi-regional samples and may be considered as a valuable option for comparing and determining heterogeneity to help deliver personalized medicine through more robust efforts in identifying targetable pathways and therapeutic strategies. Our study highlights the application these tools could have on patient-aligned treatment indications.
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Affiliation(s)
- Ross G Murphy
- Movember FASTMAN Centre of Excellence, Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7AE, UK
| | - Aideen C Roddy
- Movember FASTMAN Centre of Excellence, Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7AE, UK
| | - Shambhavi Srivastava
- Movember FASTMAN Centre of Excellence, Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7AE, UK
- Molecular Oncology, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park SK10 4TG, UK
- Belfast–Manchester Movember Centre of Excellence, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park SK10 4TG, UK
| | - Esther Baena
- Belfast–Manchester Movember Centre of Excellence, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park SK10 4TG, UK
- Prostate Oncobiology, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park SK10 4TG, UK
| | - David J Waugh
- Movember FASTMAN Centre of Excellence, Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7AE, UK
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, QLD 4000, Australia
| | - Joe M. O’Sullivan
- Movember FASTMAN Centre of Excellence, Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7AE, UK
- Northern Ireland Cancer Centre, Belfast Health & Social Care Trust, Belfast BT9 7JL, UK
| | - Darragh G McArt
- Movember FASTMAN Centre of Excellence, Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7AE, UK
| | - Suneil Jain
- Movember FASTMAN Centre of Excellence, Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7AE, UK
- Northern Ireland Cancer Centre, Belfast Health & Social Care Trust, Belfast BT9 7JL, UK
| | - Melissa J LaBonte
- Movember FASTMAN Centre of Excellence, Patrick G Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7AE, UK
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