Classifying variants of CDKN2A using computational and laboratory studies

Abstract

Variants in the CDKN2A tumor suppressor are associated with Familial Melanoma (FM), although for many variants the linkage is weak. The effects of missense variants on protein function and pathogenicity are often unclear. Multiple methods (e.g., laboratory, computational, epidemiological) have been developed to analyze whether a missense variant is pathogenic or not. It is not yet clear how to integrate these data types into a strategy for variant classification. We studied 51 CDKN2A missense variants using a cell cycle arrest assay. There was a continuum of results ranging from full wild-type effect through partial activity to complete loss of arrest. A reproducible decrease of 30% of cell cycle arrest activity correlated with FM association. We analyzed missense CDKN2A germline variants using a Bayesian method to combine multiple data types and derive a probability of pathogenicity. When equal to or more than two data types could be evaluated with this method, 22 of 25 FM-associated variants and 8 of 15 variants of uncertain significance were classified as likely pathogenic with 495% probability. The other 10 variants were classified as uncertain (probability 5-95%). For most variants, there were insufficient data to draw a conclusion. The Bayesian model appears to be a sound method of classifying missense variants in cancer susceptibility genes. Hum Mutat 32:900-911,

Clinical Evaluation of a Multiple-Gene Sequencing Panel for Hereditary Cancer Risk Assessment

“…69,78,79 One missense variant in CDKN2A (NM_000077.4: c.146TϾC) was classified as likely pathogenic based on functional evidence, [80][81][82][83] but with conflicting reports 69 ; it was therefore considered not actionable.…”

Interpreting the clinical significance of mismatch repair gene sequence variants

“…Quantifying data types and applying integrated Bayesian analysis appears to be a robust approach to classifying variants Miller et al, 2011]. An important principle of classification, using this method, is that at least two different sources of data should be used for variant classification .…”

“…They have unclear functional and medical consequences and cannot be easily classified as either pathogenic or neutral before they have been subjected to a detailed analysis. Accurately 23! placing them in a spectrum from neutral to clearly pathogenic through the development of classification systems will require a lot of work, but would allow resources for screening, prevention, and treatment to be focused on individuals truly at elevated genetic risk and provide reassurance to those who are not at risk [363][364][365] .…”

“…Strategies to integrate these methods have been a topic of significant activity for researchers and clinicians working with MMR and the melanoma susceptibility gene CDKNA2 136,314,365,[381][382][383] . The model integrates different lines of genetic evidence using Bayesian analysis 379,384 .…”

“…These variants of unknown clinical significance cannot be used to guide patient management, and are a source of anxiety for families [O'Neill et al, 2009]. Accurately placing them in a spectrum from neutral to clearly pathogenic through the development of robust classification systems would allow resources for screening, prevention, and treatment to be focused on individuals truly at elevated genetic risk and provide reassurance to those who are not at risk [Hicks et al, 2011;Miller et al, 2011;Tavtigian et al, 2008c].…”