Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches
| Autor: | Rachel Karchin, Vernon S. Pankratz, Namit Singh, Gary Bruce Lipton, Hermela Shimelis, David E. Goldgar, Fergus J. Couch, Edwin S. Iversen, Noralane M. Lindor, David L. Masica, Lucia Guidugli, Chunling Hu, Alvaro N.A. Monteiro |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Functional assay In silico Mutation Missense Gene Expression Breast Neoplasms Computational biology Biology Article 03 medical and health sciences 0302 clinical medicine Databases Genetic Genetics Clinical genetic Humans Bayesian hierarchical modeling Missense mutation Clinical significance Amino Acid Sequence Genetic Testing Functional studies Genetics (clinical) BRCA2 Protein Sequence Homology Amino Acid Computational Biology Bayes Theorem Pathogenicity Neoplasm Proteins 030104 developmental biology Amino Acid Substitution ROC Curve 030220 oncology & carcinogenesis Female Sequence Alignment Algorithms |
| Zdroj: | The American Journal of Human Genetics. 102:233-248 |
| ISSN: | 0002-9297 |
| DOI: | 10.1016/j.ajhg.2017.12.013 |
| Popis: | Many variants of uncertain significance (VUS) have been identified in BRCA2 through clinical genetic testing. VUS pose a significant clinical challenge because the contribution of these variants to cancer risk has not been determined. We conducted a comprehensive assessment of VUS in the BRCA2 C-terminal DNA binding domain (DBD) by using a validated functional assay of BRCA2 homologous recombination (HR) DNA-repair activity and defined a classifier of variant pathogenicity. Among 139 variants evaluated, 54 had ≥99% probability of pathogenicity, and 73 had ≥95% probability of neutrality. Functional assay results were compared with predictions of variant pathogenicity from the Align-GVGD protein-sequence-based prediction algorithm, which has been used for variant classification. Relative to the HR assay, Align-GVGD significantly (p < 0.05) over-predicted pathogenic variants. We subsequently combined functional and Align-GVGD prediction results in a Bayesian hierarchical model (VarCall) to estimate the overall probability of pathogenicity for each VUS. In addition, to predict the effects of all other BRCA2 DBD variants and to prioritize variants for functional studies, we used the endoPhenotype-Optimized Sequence Ensemble (ePOSE) algorithm to train classifiers for BRCA2 variants by using data from the HR functional assay. Together, the results show that systematic functional assays in combination with in silico predictors of pathogenicity provide robust tools for clinical annotation of BRCA2 VUS. |
| Databáze: | OpenAIRE |
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