A Cell‐Based Functional Assay Calibrated for Analysis of <i>MSH6</i> and <i>MSH2</i> Mismatch Repair Gene Variants

Variants of uncertain significance (VUS) in the DNA mismatch repair (MMR) genes can confound the diagnosis and treatment of suspected Lynch syndrome (LS) patients. To aid the reclassification of VUS, we developed the in cellulo analysis of MMR variants (inCAMA) and used known control variants to calibrate this assay such that results can be readily applied as functional evidence by expert classification panels. We used CRISPR gene engineering to introduce known pathogenic and benign variants into the <i>MSH6</i> or <i>MSH2</i> loci in human embryonic stem cells and assessed their effects on cellular MMR repair and damage response functions. Our functional assay successfully discerned known pathogenic and benign variants. Using these results and performing a linear regression analysis with available odds of pathogenicity scores for the known calibration variants, we created equations that can generate a functional odds of pathogenicity score for any future <i>MSH6</i> or <i>MSH2</i> variant tested. In summary, inCAMA represents a new, calibrated assay for testing the function of virtually any <i>MSH6</i> or <i>MSH2</i> variant. The conversion of assay results directly into odds of pathogenicity scores makes it possible to use any PS3 or BS3 evidence strength level toward the reclassification of VUS.