Functional characterization of all CDKN2A missense variants and comparison to in silico models of pathogenicity
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Curated by eLife
eLife assessment
This is a saturation mutagenesis screening of the CDKN2A gene, successfully assessing the functionality of the missense variants. The results seem robust, but currently, the manuscript is incomplete with a number of weaknesses. The work has the potential to serve as a valuable resource for diagnostic labs as well as cancer geneticists.
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Abstract
Interpretation of variants identified during genetic testing is a significant clinical challenge. In this study, we developed a high-throughput CDKN2A functional assay and characterized all possible CDKN2A missense variants. We found that 40% of all missense variants were functionally deleterious. We also used our functional classification to assess the performance of in silico models that predict the effect of variants, including recently reported models based on machine learning. Notably, we found that all in silico models similarly when compared to our functional classifications with accuracies of 54.6 – 70.9%. Furthermore, while we found that functionally deleterious variants were enriched within ankyrin repeats, rarely were all missense variants at a single residue functionally deleterious. Our functional classifications are a resource to aid the interpretation of CDKN2A variants and have important implications for the application of variant interpretation guidelines, particularly the use of in silico models for clinical variant interpretation.
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eLife assessment
This is a saturation mutagenesis screening of the CDKN2A gene, successfully assessing the functionality of the missense variants. The results seem robust, but currently, the manuscript is incomplete with a number of weaknesses. The work has the potential to serve as a valuable resource for diagnostic labs as well as cancer geneticists.
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Reviewer #1 (Public Review):
Summary:
Kimura et al performed a saturation mutagenesis study of CDKN2A to assess the functionality of all possible missense variants and compare them to previously identified pathogenic variants. They also compared their assay result with those from in silico predictors.Strengths:
CDKN2A is an important gene that modulates cell cycle and apoptosis, therefore it is critical to accurately assess the functionality of missense variants. Overall, the paper reads well and touches upon major discoveries in a logical manner.Weaknesses:
The paper lacks proper details for experiments and basic data, leaving the results less convincing. Analyses are superficial and do not provide variant-level resolution. -
Reviewer #2 (Public Review):
This study describes a deep mutational scan across CDKN2A using suppression of cell proliferation in pancreatic adenocarcinoma cells as a readout for CDKN2A function. The results are also compared to in silico variant predictors currently utilized by the current diagnostic frameworks to gauge these predictors' performance. The authors also functionally classify CDKN2A somatic mutations in cancers across different tissues.
This study is a potentially important contribution to the field of cancer variant interpretation for CDKN2A, but is almost impossible to review because of the severe lack of details regarding the methods and incompleteness of the data provided with the paper. We do believe that the cell proliferation suppression assay is robust and works, but when it comes to the screening of the library of …
Reviewer #2 (Public Review):
This study describes a deep mutational scan across CDKN2A using suppression of cell proliferation in pancreatic adenocarcinoma cells as a readout for CDKN2A function. The results are also compared to in silico variant predictors currently utilized by the current diagnostic frameworks to gauge these predictors' performance. The authors also functionally classify CDKN2A somatic mutations in cancers across different tissues.
This study is a potentially important contribution to the field of cancer variant interpretation for CDKN2A, but is almost impossible to review because of the severe lack of details regarding the methods and incompleteness of the data provided with the paper. We do believe that the cell proliferation suppression assay is robust and works, but when it comes to the screening of the library of CDKN2A variants the lack of primary data and experimental detail prevents assessment of the scientific merit and experimental rigor.
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