Journal article

Low-coverage whole-genome sequencing of extracellular vesicle-associated DNA in patients with metastatic cancer

Bella Nguyen, Nicholas C Wong, Tim Semple, Michael Clark, Stephen Q Wong, Connull Leslie, Bob Mirzai, Michael Millward, Katie Meehan, Annette M Lim

SCIENTIFIC REPORTS | NATURE RESEARCH | Published : 2021

Abstract

Low-coverage whole-genome sequencing (LC-WGS) can provide insight into oncogenic molecular changes. Serum extracellular vesicles (EV) represent a novel liquid biopsy source of tumoral DNA. This study compared copy number alteration (CNA) profiles generated from LC-WGS of formalin-fixed paraffin-embedded (FFPE) tumoral DNA and EV-DNA obtained from cancer patients. Patients with squamous cell carcinoma of the base of tongue (n = 3) and cutaneous squamous cell carcinoma (n = 2) were included. LC-WGS (0.5-1X coverage) was performed on FFPE-DNA and serum EV-DNA. Similarity between CNA profiles was analysed using QDNAseq. FFPE samples had a mean CNA of 31 (range 17-50) over 1.9 × 109 (range 1.0-2...

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Grants

Funding Acknowledgements

This research was supported by a Garnett Passe and Rodney Williams Memorial Foundation Conjoint Grant, CCWA Suzanne Cavanagh Award, RACP-GSK Research Establishment Fellowship and Western Australian Department of Health Merit Award. Dr B Nguyen is supported by the WA Cancer and Palliative Care Network Research Fellowship, and the Garnett Passe and Rodney Williams Memorial Foundation Research Scholarship. Dr AM Lim was supported by the WA Health/Raine Foundation Clinician Research Fellowship.