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Prostate cancer heterogeneity assessment with multi-regional sampling and alignment-free methods
- Source :
- Nar Genomics and Bioinformatics, Murphy, R, McArt, D, O'Sullivan, J, Waugh, D, Srivastava, S K, Roddy, A, Baena, E, Jain, S & LaBonte Wilson, M 2020, ' Prostate cancer heterogeneity assessment with multi-regional sampling and alignment-free methods ', NAR Genomics and Bioinformatics, vol. 2, no. 3, lqaa062 . https://doi.org/10.1093/nargab/lqaa062
- Publication Year :
- 2020
- Publisher :
- Oxford University Press, 2020.
-
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.
- Subjects :
- 0301 basic medicine
AcademicSubjects/SCI01140
Tumour heterogeneity
AcademicSubjects/SCI01060
Application Notes
AcademicSubjects/SCI00030
Single sample
Computational biology
Biology
AcademicSubjects/SCI01180
03 medical and health sciences
Prostate cancer
0302 clinical medicine
SDG 3 - Good Health and Well-being
medicine
therapeutic strategies
business.industry
prostate cancer
medicine.disease
030104 developmental biology
030220 oncology & carcinogenesis
DECIPHER
alignment-free methods
Personalized medicine
AcademicSubjects/SCI00980
business
Subjects
Details
- Language :
- English
- ISSN :
- 26319268
- Volume :
- 2
- Issue :
- 3
- Database :
- OpenAIRE
- Journal :
- Nar Genomics and Bioinformatics
- Accession number :
- edsair.doi.dedup.....9f18218a2e260284f886fb58d8386c0c