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ABSTRACT: Purpose
To enhance classification of variants of uncertain significance (VUS) in the DNA mismatch repair (MMR) genes in the cancer predisposition Lynch syndrome, we developed the cell-free in vitro MMR activity (CIMRA) assay. Here, we calibrate and validate the assay, enabling its integration with in silico and clinical data.Methods
Two sets of previously classified MLH1 and MSH2 variants were selected from a curated MMR gene database, and their biochemical activity determined by the CIMRA assay. The assay was calibrated by regression analysis followed by symmetric cross-validation and Bayesian integration with in silico predictions of pathogenicity. CIMRA assay reproducibility was assessed in four laboratories.Results
Concordance between the training runs met our prespecified validation criterion. The CIMRA assay alone correctly classified 65% of variants, with only 3% discordant classification. Bayesian integration with in silico predictions of pathogenicity increased the proportion of correctly classified variants to 87%, without changing the discordance rate. Interlaboratory results were highly reproducible.Conclusion
The CIMRA assay accurately predicts pathogenic and benign MMR gene variants. Quantitative combination of assay results with in silico analysis correctly classified the majority of variants. Using this calibration, CIMRA assay results can be integrated into the diagnostic algorithm for MMR gene variants.
SUBMITTER: Drost M
PROVIDER: S-EPMC7901556 | biostudies-literature | 2019 Jul
REPOSITORIES: biostudies-literature
Drost Mark M Tiersma Yvonne Y Thompson Bryony A BA Frederiksen Jane H JH Keijzers Guido G Glubb Dylan D Kathe Scott S Osinga Jan J Westers Helga H Pappas Lisa L Boucher Kenneth M KM Molenkamp Siska S Zonneveld José B JB van Asperen Christi J CJ Goldgar David E DE Wallace Susan S SS Sijmons Rolf H RH Spurdle Amanda B AB Rasmussen Lene J LJ Greenblatt Marc S MS de Wind Niels N Tavtigian Sean V SV
Genetics in medicine : official journal of the American College of Medical Genetics 20181203 7
<h4>Purpose</h4>To enhance classification of variants of uncertain significance (VUS) in the DNA mismatch repair (MMR) genes in the cancer predisposition Lynch syndrome, we developed the cell-free in vitro MMR activity (CIMRA) assay. Here, we calibrate and validate the assay, enabling its integration with in silico and clinical data.<h4>Methods</h4>Two sets of previously classified MLH1 and MSH2 variants were selected from a curated MMR gene database, and their biochemical activity determined by ...[more]