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

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

Wing Chan  1 , Mianne Lee  1 , Zhen Xuan Yeo  1 , Dingge Ying  1 , Keith A Grimaldi  2 , Craig Pickering  2 , Michael M S Yang  3 , Senthil K Sundaram  1 , Lawrence C H Tzang  1
Affiliations

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

Wing Chan et al. Hered Cancer Clin Pract. .

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.

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Conflict of interest statement

Competing interestsSome authors are current or former employees of Prenetics Limited or DNAfit.

Figures

Fig. 1
Fig. 1
Exonic coverage of 35 hereditary cancer genes based on a benchmark sequencing run with 43 samples
See this image and copyright information in PMC

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