PT  - JOURNAL ARTICLE
AU  - Valentina S. Vysotskaia
AU  - Gregory J. Hogan
AU  - Genevieve M. Gould
AU  - Xin Wang
AU  - Alex D. Robertson
AU  - Kevin R. Haas
AU  - Mark R. Theilmann
AU  - Lindsay Spurka
AU  - Peter V. Grauman
AU  - Henry H. Lai
AU  - Diana Jeon
AU  - Genevieve Haliburton
AU  - Matt Leggett
AU  - Clement S. Chu
AU  - Kevin Lori
AU  - Jared R. Maguire
AU  - Kaylene Ready
AU  - Eric A. Evans
AU  - H. Peter Kang
AU  - Imran S. Haque
TI  - Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment
AID  - 10.1101/088252
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 088252
4099  - http://biorxiv.org/content/early/2016/11/17/088252.short
4100  - http://biorxiv.org/content/early/2016/11/17/088252.full
AB  - 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.