A functional assay–based procedure to classify mismatch repair gene variants in Lynch syndrome
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A functional assay–based procedure to classify mismatch repair gene variants in Lynch syndrome. / Drost, Mark; Tiersma, Yvonne; Thompson, Bryony A.; Frederiksen, Jane H.; Keijzers, Guido; Glubb, Dylan; Kathe, Scott; Osinga, Jan; Westers, Helga; Pappas, Lisa; Boucher, Kenneth M.; Molenkamp, Siska; Zonneveld, José B.; van Asperen, Christi J.; Goldgar, David E.; Wallace, Susan S.; Sijmons, Rolf H.; Spurdle, Amanda B.; Rasmussen, Lene J.; Greenblatt, Marc S.; de Wind, Niels; Tavtigian, Sean V.
In: Genetics in Medicine, Vol. 21, 2019, p. 1486–1496.Research output: Contribution to journal › Journal article › Research › peer-review
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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
Y1 - 2019
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
VL - 21
SP - 1486
EP - 1496
JO - Genetics in Medicine
JF - Genetics in Medicine
SN - 1098-3600
ER -
ID: 212124417