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

2019; Nature Portfolio; Volume: 9; Issue: 1 Linguagem: Inglês

10.1038/s41598-019-52000-3

2045-2322

Mark J. McCabe, Marie Gauthier, Chia-Ling Chan, Tanya Thompson, Sunita M. C. De Sousa, Clare Puttick, John P. Grady, Velimir Gayevskiy, Tao Jiang, Kevin Ying, Arcadi Cipponi, Niantao Deng, Alexander Swarbrick, Mélissa Thomas, Reginald V. Lord, Amber L. Johns, Maija Kohonen‐Corish, Sandra O’Toole, Jonathan R. Clark, Simon A. Mueller, Ruta Gupta, Ann McCormack, Marcel E. Dinger, Mark J. Cowley, Morteza Aghmesheh, David J. Amor, Lesley Andrews, Yoland Antill, Shane Armitage, Leanne Arnold, Rosemary L. Balleine, Patti Bastick, Jonathan Beesley, John Beilby, Ian Bennett, Anneke C. Blackburn, Michael Bogwitz, Leon Botes, Meagan Brennan, Melissa A. Brown, Michael F. Buckley, Matthew Burgess, Jo Burke, Phyllis Butow, Liz Caldon, David F. Callen, Ian Campbell, Deepa Chauhan, Manisha Chauhan, Georgia Chenevix‐Trench, Alice Christian, Christine L. Clarke, Paul A. Cohen, Alison Colley, Ashley Crook, James Cui, Bronwyn Culling, Margaret C. Cummings, Sarah‐Jane Dawson, Anna deFazio, Martin Delatycki, Rebecca Dickson, Joanne Dixon, Alexander Dobrovic, Tracy Dudding, Ted Edkins, Stacey L. Edwards, Maurice Eisenbruch, Gelareh Farshid, Andrew Fellows, Georgina Fenton, Michael Field, James M. Flanagan, Peter C.C. Fong, Laura Forrest, Stephen B. Fox, Juliet D. French, Michael Friedlander, Clara Gaff, Davi Gallego Ortega, Mike Gattas, Peter George, Graham G. Giles, Grantley Gill, Sian Greening, Eric Haan, Marion Harris, Stewart Hart, Nicholas K. Hayward, Louise Heiniger, John L. Hopper, Clare Hunt, Paul A. James, Mark A. Jenkins, Richard Kefford, Alexa Kidd, Judy Kirk, Jessica Koehler, James Kollias, Sunil R. Lakhani, Geoffrey J. Lindeman, Lara Lipton, Liz Lobb, Graham J. Mann, Deborah J. Marsh, Sue Ann McLachaln, Bettina Meiser, Roger L. Milne, Sophie Nightingale, Shona O’Connell, Sarah O’Sullivan, Nick Pachter, Briony Patterson, Kelly‐Anne Phillips, Ellen Pieper, Edwina Rickard, Bridget A. Robinson, Mona Saleh, Elizabeth Salisbury, Joe Sambrook, Christobel Saunders, Jodi M. Saunus, Elizabeth Scott, Clare L. Scott, Rodney J. Scott, Adrienne Sexton, Andrew N. Shelling, Peter T. Simpson, Melissa C. Southey, Amanda B. Spurdle, Jessica Taylor, Heather Thorne, Alison Trainer, Kathy Tucker, Jane E. Visvader, Logan C. Walker, Rachael Williams, Ingrid Winship, Mary‐Anne Young,

Genetic factors in colorectal cancer

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.