Development and validation of a targeted gene sequencing panel for application to disparate cancers
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 , O’Toole Sandra A. , Clark Jonathan , Mueller Simon A. , Gupta Ruta , McCormack Ann I. , Dinger Marcel E. , Cowley Mark J. ,   kConFab, 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 , O’Connell Shona , O’Sullivan 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 
Published: November 2019

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.