Development and validation of next generation sequencing based 35-gene hereditary cancer panel
Posted on 2020-04-29 - 04:36
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.
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Chan, Wing; Lee, Mianne; Yeo, Zhen Xuan; Ying, Dingge; Grimaldi, Keith A.; Pickering, Craig; et al. (2020). Development and validation of next generation sequencing based 35-gene hereditary cancer panel. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.4957040.v1
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AUTHORS (9)
WC
Wing Chan
ML
Mianne Lee
ZY
Zhen Xuan Yeo
DY
Dingge Ying
KG
Keith A. Grimaldi
CP
Craig Pickering
MY
Michael M. S. Yang
SS
Senthil K. Sundaram
LT
Lawrence C. H. Tzang