Development and validation of next generation sequencing based 35-gene hereditary cancer panel

• Published in: Hereditary cancer in clinical practice 2020-04, Vol.18 (1), p.9-9, Article 9
• Main Authors: Chan, Wing, Lee, Mianne, Yeo, Zhen Xuan, Ying, Dingge, Grimaldi, Keith A, Pickering, Craig, Yang, Michael M S, Sundaram, Senthil K, Tzang, Lawrence C H
• Format: Article
• Language: English
• Subjects: Accuracy; Analysis; Analytical validation; Bioinformatics; Breast; Breast cancer; Cancer; Cancer genetics; Cancer research; Deoxyribonucleic acid; Disease susceptibility; DNA; Genes; Genetic aspects; Genetic diversity; Genetic research; Genetic testing; Genomes; Genomics; Health aspects; Hereditary cancer; Laboratories; Melanoma; Multigene panel testing; Mutation; Next generation sequencing; Ovarian cancer; Pancreas; Prostate; Quality standards; Reference materials; Risk assessment; Uterine cancer; Uterus
• ISSN: 1731-2302; 1897-4287; 1897-4287
• DOI: 10.1186/s13053-020-00141-2

Understanding the genetic basis of cancer risk is a major international endeavor. The emergence of next-generation sequencing (NGS) in late 2000's has further accelerated the discovery of many cancer susceptibility genes. The use of targeted NGS-based multigene testing panels to provide comprehensive analysis of cancer susceptible genes has proven to be a viable option, with the accurate and robust detection of a wide range of clinically relevant variants in the targeted genes being crucial. We have developed and validated a targeted NGS-based test for hereditary cancer risk assessment using Illumina's NGS platform by analyzing the protein-coding regions of 35 hereditary cancer genes with a bioinformatics pipeline that utilizes standard practices in the field. This 35-gene hereditary cancer panel is designed to identify germline cancer-causing mutations for 8 different cancers: breast, ovarian, prostate, uterine, colorectal, pancreatic, stomach cancers and melanoma. The panel was validated using well-characterized DNA specimens [NIGMS Human Genetic Cell Repository], where DNA had been extracted using blood of individuals whose genetic variants had been previously characterized by the 1000 Genome Project and the Coriell Catalog. The 35-gene hereditary cancer panel shows high sensitivity (99.9%) and specificity (100%) across 4820 variants including single nucleotide variants (SNVs) and small insertions and deletions (indel; up to 25 bp). The reproducibility and repeatability are 99.8 and 100%, respectively. The use of targeted NGS-based multigene testing panels to provide comprehensive analysis of cancer susceptible genes has been considered a viable option. In the present study, we developed and validated a 35-gene panel for testing 8 common cancers using next-generation sequencing (NGS). The performance of our hereditary cancer panel is assessed across a board range of variants in the 35 genes to support clinical use.