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

TY - JOUR

T1 - A functional assay–based procedure to classify mismatch repair gene variants in Lynch syndrome

AU - Drost, Mark

AU - Tiersma, Yvonne

AU - Thompson, Bryony A.

AU - Frederiksen, Jane H.

AU - Keijzers, Guido

AU - Glubb, Dylan

AU - Kathe, Scott

AU - Osinga, Jan

AU - Westers, Helga

AU - Pappas, Lisa

AU - Boucher, Kenneth M.

AU - Molenkamp, Siska

AU - Zonneveld, José B.

AU - van Asperen, Christi J.

AU - Goldgar, David E.

AU - Wallace, Susan S.

AU - Sijmons, Rolf H.

AU - Spurdle, Amanda B.

AU - Rasmussen, Lene J.

AU - Greenblatt, Marc S.

AU - de Wind, Niels

AU - Tavtigian, Sean V.

PY - 2019/7/1

Y1 - 2019/7/1

N2 - 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.

AB - 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.

KW - assay calibration

KW - functional assay

KW - Lynch syndrome

KW - variant classification

KW - variants of uncertain significance

U2 - 10.1038/s41436-018-0372-2

DO - 10.1038/s41436-018-0372-2

M3 - Journal article

C2 - 30504929

AN - SCOPUS:85058010232

SN - 1098-3600

JO - Genetics in Medicine

JF - Genetics in Medicine

ER -