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.

The MURAL collection of prostate cancer patient-derived xenografts enables discovery through preclinical models of uro-oncology

“…Two gene panels were used for targeting DNA sequencing of distinct PDX samples. The first platform, denoted as the Garvan panel (Supplementary Data 4 ), is a cancer gene sequencing panel (PV2) designed through Roche/Nimblegen spanning 633 cancer-associated genes (2.01 Mb target region) 60 . The second platform, denoted as the Twist panel (Supplementary Data 4 ), is a custom gene capture panel from Twist Biosciences targeting a total of 2.13 Mb of exonic sequence from 16,875 regions in 662 genes.…”

HGNChelper: identification and correction of invalid gene symbols for human and mouse

“…Such correction should be routinely done when gene symbols are part of high-throughput analysis, such as re-analysis of targeted gene panels for precision medicine, which tend to be annotated with gene symbols (e.g. 10 ), in Gene Set Enrichment Analysis using the gene symbol versions of popular databases such as MSigDB 9 or GeneSigDB 11 , or when performing systematic review or meta-analysis of published multi-gene signatures (e.g. 12 ).…”

Shifting Gears in Precision Oncology—Challenges and Opportunities of Integrative Data Analysis

“…Targeted gene panels, which captures key genes or areas of interest, is another attractive option to a significant reduction in time and cost compared to WGS and WES. As a result, several targeted gene panels have already been adopted and used regularly in clinical settings [ 27 , 28 , 29 ]. Diagnostically, WGS, WES as well as targeted gene panels are also being used for detection of copy number variations, tumor mutational burden, homologous repair deficiency and genomic scarring patterns, as well as mutational signatures.…”