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

Wing Chan; Mianne Lee; Zhen Xuan Yeo; Dingge Ying; Keith A Grimaldi; Craig Pickering; Michael M S Yang; Senthil K Sundaram; Lawrence C H Tzang

doi:10.1186/s13053-020-00141-2

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

Hered Cancer Clin Pract. 2020 Apr 28:18:9. doi: 10.1186/s13053-020-00141-2. eCollection 2020.

Authors

Wing Chan¹, Mianne Lee¹, Zhen Xuan Yeo¹, Dingge Ying¹, Keith A Grimaldi², Craig Pickering², Michael M S Yang³, Senthil K Sundaram¹, Lawrence C H Tzang¹

Affiliations

¹ 1Prenetics Limited, 7/F, Prosperity Millennia Plaza, 663 King's Road, Quarry Bay, Hong Kong SAR, China.
² Exercise and Nutritional Genomics Research Centre, DNAfit Ltd, FORA, 71 Central Street, London, EC1V 8AB UK.
³ 3Department of Biomedical Science, City University of Hong Kong, 1A-107, 1/F, Block 1, To Yuen Building, Kowloon Tong, Hong Kong SAR, China.

Abstract

Background: 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.

Methods: 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.

Results: 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.

Conclusions: 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.

Keywords: Analytical validation; Genetic testing; Hereditary cancer; Multigene panel testing; Next generation sequencing.