Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment

PeerJ

article

Valentina S. Vysotskaia¹  Gregory J. Hogan¹  Genevieve M. Gould¹  Xin Wang¹  Alex D. Robertson¹  Kevin R. Haas¹  Mark R. Theilmann¹  Lindsay Spurka¹  Peter V. Grauman¹  Henry H. Lai¹  Diana Jeon¹  Genevieve Haliburton¹  Matt Leggett³  Clement S. Chu¹  Kevin Iori¹  Jared R. Maguire¹  Kaylene Ready⁴  Eric A. Evans¹  Hyunseok P. Kang⁵  Imran S. Haque¹ 

[1] Research and Development Department, Counsyl, Inc;Color Genomics, Inc.;Project Management Department, Counsyl, Inc;Medical Affairs Department, Counsyl, Inc;Clinical Laboratory, Counsyl, Inc;Current affiliation:  Freenome, Inc.

关键词: Hereditary cancer;    Multigene panel testing;    Next generation sequencing;    Analytical validation;   

DOI  :  10.7717/peerj.3046

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

The past two decades have brought many important advances in our understanding of the hereditary susceptibility to cancer. Numerous studies have provided convincing evidence that identification of germline mutations associated with hereditary cancer syndromes can lead to reductions in morbidity and mortality through targeted risk management options. Additionally, advances in gene sequencing technology now permit the development of multigene hereditary cancer testing panels. Here, we describe the 2016 revision of the Counsyl Inherited Cancer Screen for detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy number variants (CNVs) in 36 genes associated with an elevated risk for breast, ovarian, colorectal, gastric, endometrial, pancreatic, thyroid, prostate, melanoma, and neuroendocrine cancers. To determine test accuracy and reproducibility, we performed a rigorous analytical validation across 341 samples, including 118 cell lines and 223 patient samples. The screen achieved 100% test sensitivity across different mutation types, with high specificity and 100% concordance with conventional Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). We also demonstrated the screen’s high intra-run and inter-run reproducibility and robust performance on blood and saliva specimens. Furthermore, we showed that pathogenic Alu element insertions can be accurately detected by our test. Overall, the validation in our clinical laboratory demonstrated the analytical performance required for collecting and reporting genetic information related to risk of developing hereditary cancers.

【 授权许可】

CC BY