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

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 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.

Type Journal
ISBN 2045-2322
Authors McCabe, Mark J.; Gauthier, Marie-Emilie A.; Chan, Chia-Ling; Thompson, Tanya J.; De Sousa, Sunita M. C.; Puttick, Clare; Grady, John P.; Gayevskiy, Velimir; Tao, Jiang; Ying, Kevin; Cipponi, Arcadi; Deng, Niantao; Swarbrick, Alex; Thomas, Melissa L.; Lord, Reginald V.; Johns, Amber L.; Kohonen-Corish, Maija; OaToole, Sandra A.; Clark, Jonathan; Mueller, Simon A.; Gupta, Ruta; McCormack, Ann I.; Dinger, Marcel E.; Cowley, Mark J.; Aghmesheh, Morteza; Amor, David; Andrews, Lesley; Antill, Yoland; Armitage, Shane; Arnold, Leanne; Balleine, Rosemary; Bastick, Patti; Beesley, Jonathan; Beilby, John; Bennett, Ian; Blackburn, Anneke; Bogwitz, Michael; Botes, Leon; Brennan, Meagan; Brown, Melissa; Buckley, Michael; Burgess, Matthew; Burke, Jo; Butow, Phyllis; Caldon, Liz; Callen, David; Campbell, Ian; Chauhan, Deepa; Chauhan, Manisha; Chenevix-Trench, Georgia; Christian, Alice; Clarke, Christine; Cohen, Paul; Colley, Alison; Crook, Ashley; Cui, James; Culling, Bronwyn; Cummings, Margaret; Dawson, Sarah-Jane; deFazio, Anna; Delatycki, Martin; Dickson, Rebecca; Dixon, Joanne; Dobrovic, Alexander; Dudding, Tracy; Edkins, Ted; Edwards, Stacey; Eisenbruch, Maurice; Farshid, Gelareh; Fellows, Andrew; Fenton, Georgina; Field, Michael; Flanagan, James; Fong, Peter; Forrest, Laura; Fox, Stephen; French, Juliet; Friedlander, Michael; Gaff, Clara; Ortega, Davi Gallego; Gattas, Mike; George, Peter; Giles, Graham; Gill, Grantley; Greening, Sian; Haan, Eric; Harris, Marion; Hart, Stewart; Hayward, Nick; Heiniger, Louise; Hopper, John; Hunt, Clare; James, Paul; Jenkins, Mark; Kefford, Rick; Kidd, Alexa; Kirk, Judy; Koehler, Jessica; Kollias, James; Lakhani, Sunil; Lindeman, Geoff; Lipton, Lara; Lobb, Liz; Mann, Graham; Marsh, Deborah; McLachaln, Sue Ann; Meiser, Bettina; Milne, Roger; Nightingale, Sophie; OaConnell, Shona; OaSullivan, Sarah; Pachter, Nick; Patterson, Briony; Phillips, Kelly; Pieper, Ellen; Rickard, Edwina; Robinson, Bridget; Saleh, Mona; Salisbury, Elizabeth; Sambrook, Joe; Saunders, Christobel; Saunus, Jodi; Scott, Elizabeth; Scott, Clare; Scott, Rodney; Sexton, Adrienne; Shelling, Andrew; Simpson, Peter; Southey, Melissa; Spurdle, Amanda; Taylor, Jessica; Thorne, Heather; Trainer, Alison; Tucker, Kathy; Visvader, Jane; Walker, Logan; Williams, Rachael; Winship, Ingrid; Young, Mary-Anne; kConFab
Responsible Garvan Author (missing name)
Publisher Name Scientific Reports
Published Date 2019-11-19
Published Volume 9
Published Issue 1
Published Pages 17052
Status Published in-print
DOI 10.1038/s41598-019-52000-3
URL link to publisher's version https://www.ncbi.nlm.nih.gov/pubmed/31745186