Journal article

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Mark J McCabe, Marie-Emilie A Gauthier, Chia-Ling Chan, Tanya J Thompson, Sunita MC De Sousa, Clare Puttick, John P Grady, Velimir Gayevskiy, Jiang Tao, Kevin Ying, Arcadi Cipponi, Niantao Deng, Alex Swarbrick, Melissa L Thomas, undefined kConFab, Reginald V Lord, Amber L Johns, Maija Kohonen-Corish, Sandra A O'Toole, Jonathan Clark Show all

Scientific Reports | Nature Publishing Group | Published : 2019

Abstract

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 A..

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Grants

Awarded by Cancer Institute NSW (Cancer Institute New South Wales)


Awarded by Cancer Council NSW (Cancer Council New South Wales)


Funding Acknowledgements

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.