A functional assay-based procedure to classify mismatch repair gene variants in Lynch syndrome.

Drost M1, Tiersma Y1, Thompson BA2,3, Frederiksen JH4, Keijzers G4, Glubb D5, Kathe S6, Osinga J7, Westers H7, Pappas L8, Boucher KM8, Molenkamp S9, Zonneveld JB9, van Asperen CJ9, Goldgar DE10, Wallace SS6, Sijmons RH7, Spurdle AB5, Rasmussen LJ11, Greenblatt MS12, de Wind N13, Tavtigian SV14.

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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.