title: Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment.
abstract: 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.
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Valentina S
authors.initials: VS
authors.lastname: Vysotskaia
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Hogan
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Genevieve M
authors.initials: GM
authors.lastname: Gould
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.|Current affiliation:  Color Genomics, Inc., Burlingame, CA, United States.
authors.forename: Alex D
authors.initials: AD
authors.lastname: Robertson
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Kevin R
authors.initials: KR
authors.lastname: Haas
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Mark R
authors.initials: MR
authors.lastname: Theilmann
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Lindsay
authors.initials: L
authors.lastname: Spurka
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Peter V
authors.initials: PV
authors.lastname: Grauman
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Henry H
authors.initials: HH
authors.lastname: Lai
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Diana
authors.initials: D
authors.lastname: Jeon
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Genevieve
authors.initials: G
authors.lastname: Haliburton
authors.affiliation: Project Management Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Matt
authors.initials: M
authors.lastname: Leggett
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Clement S
authors.initials: CS
authors.lastname: Chu
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Kevin
authors.initials: K
authors.lastname: Iori
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Jared R
authors.initials: JR
authors.lastname: Maguire
authors.affiliation: Medical Affairs Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Kaylene
authors.initials: K
authors.lastname: Ready
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.
authors.forename: Eric A
authors.initials: EA
authors.lastname: Evans
authors.affiliation: Clinical Laboratory, Counsyl, Inc, South San Francisco, California, United States.
authors.forename: Hyunseok P
authors.initials: HP
authors.lastname: Kang
authors.affiliation: Research and Development Department, Counsyl, Inc, South San Francisco, CA, United States.|Current affiliation:  Freenome, Inc., South San Francisco, CA, United States.
authors.forename: Imran S
authors.initials: IS
authors.lastname: Haque
keywords: Analytical validation; Hereditary cancer; Multigene panel testing; Next generation sequencing