title: Assessment of in silico protein sequence analysis in the clinical classification of variants in cancer risk genes.
abstract: Missense variants represent a significant proportion of variants identified in clinical genetic testing. In the absence of strong clinical or functional evidence, the American College of Medical Genetics recommends that these findings be classified as variants of uncertain significance (VUS). VUSs may be reclassified to better inform patient care when new evidence is available. It is critical that the methods used for reclassification are robust in order to prevent inappropriate medical management strategies and unnecessary, life-altering surgeries. In an effort to provide evidence for classification, several in silico algorithms have been developed that attempt to predict the functional impact of missense variants through amino acid sequence conservation analysis. We report an analysis comparing internally derived, evidence-based classifications with the results obtained from six commonly used algorithms. We compiled a dataset of 1118 variants in BRCA1, BRCA2, MLH1, and MSH2 previously classified by our laboratory's evidence-based variant classification program. We compared internally derived classifications with those obtained from the following in silico tools: Align-GVGD, CONDEL, Grantham Analysis, MAPP-MMR, PolyPhen-2, and SIFT. Despite being based on similar underlying principles, all algorithms displayed marked divergence in accuracy, specificity, and sensitivity. Overall, accuracy ranged from 58.7 to 90.8% while the Matthews Correlation Coefficient ranged from 0.26-0.65. CONDEL, a weighted average of multiple algorithms, did not perform significantly better than its individual components evaluated here. These results suggest that the in silico algorithms evaluated here do not provide reliable evidence regarding the clinical significance of missense variants in genes associated with hereditary cancer.
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA. ikerr@myriad.com.
authors.forename: Iain D
authors.initials: ID
authors.lastname: Kerr
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Hannah C
authors.initials: HC
authors.lastname: Cox
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Kelsey
authors.initials: K
authors.lastname: Moyes
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Brent
authors.initials: B
authors.lastname: Evans
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Brianna C
authors.initials: BC
authors.lastname: Burdett
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Aric
authors.initials: A
authors.lastname: van Kan
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Heather
authors.initials: H
authors.lastname: McElroy
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Paris J
authors.initials: PJ
authors.lastname: Vail
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Krystal L
authors.initials: KL
authors.lastname: Brown
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Dechie B
authors.initials: DB
authors.lastname: Sumampong
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Monteferrante
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Kennedy L
authors.initials: KL
authors.lastname: Hardman
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Aaron
authors.initials: A
authors.lastname: Theisen
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Erin
authors.initials: E
authors.lastname: Mundt
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Wenstrup
authors.affiliation: Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, 84108, USA.
authors.forename: Julie M
authors.initials: JM
authors.lastname: Eggington
keywords: HBOC; Lynch syndrome; Missense mutation; Sequence conservation; Variant classification; Variants of uncertain significance