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Description
Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy.
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15 citations in Scopus
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| ID Code: | 248628 | ||
|---|---|---|---|
| Item Type: | Contribution to Journal (Journal Article) | ||
| Refereed: | Yes | ||
| ORCID iD: |
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| Measurements or Duration: | 16 pages | ||
| DOI: | 10.1038/s41598-019-52000-3 | ||
| ISSN: | 2045-2322 | ||
| Pure ID: | 169067949 | ||
| Funding Information: | We would like to thank Mr. Ben Lundie at Garvan Institute of Medical Research for the provision of the four Coriell Institute samples. We would also like to thank the Kinghorn Centre for Clinical Genomics for technical assistance, and acknowledge the generous support of ICAP and the family and friends of Michael O’Sullivan, both donors to molecular cancer research at RPAH, Sydney. Finally, research was undertaken with assistance and services from the National Computational Infrastructure, which is supported by the Australian Government. This work was supported by a Cancer Institute NSW Early Career Fellowship (Grant Number 13/ECF/1-46), Cancer Institute NSW Career Development Fellowship (Grant Number 2019/CDF004), NSW Health Early-Mid Career Fellowship, Cancer Council NSW (Grant Number RG 15–19), Therapeutic Innovation Australia, and philanthropic donations from the Kinghorn Foundation. | ||
| Copyright Owner: | 2019 The Authors | ||
| Copyright Statement: | This work is covered by copyright. Unless the document is being made available under a Creative Commons Licence, you must assume that re-use is limited to personal use and that permission from the copyright owner must be obtained for all other uses. If the document is available under a Creative Commons License (or other specified license) then refer to the Licence for details of permitted re-use. It is a condition of access that users recognise and abide by the legal requirements associated with these rights. If you believe that this work infringes copyright please provide details by email to qut.copyright@qut.edu.au | ||
| Deposited On: | 21 May 2024 02:29 | ||
| Last Modified: | 21 May 2024 21:16 |
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