N34: A Functional Assay-Based Procedure To Classify Mismatch Repair Gene Variants In Lynch Syndrome

M. Drost1, Y. Tiersma1, B. A. Thompson2, J. H. Frederiksen3, G. Keijzers3, D. Glubb4, S. Kathe5, J. Osinga6, L. Pappas7, K. M. Boucher8, S. Molenkamp9, J. B. Zonneveld9, C. J. van Asperen9, D. E. Goldgar10, S. S. Wallace5, R. H. Sijmons6, A. B. Spurdle4, L. J. Rasmussen3, M. S. Greenblatt11, N. de Wind1, S. V. Tavtigian2

1 – Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. 2 – Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA. 3 – Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark. 4 – Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia. 5 – Department of Microbiology and Molecular Genetics, University of Vermont Robert Larner, M.D. College of Medicine, Burlington, Vermont, USA. 6 – Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands. 7 – Department of Medicine, Division of Epidemiology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA. 8 – Department of Medicine, Division of Epidemiology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA. 9 – Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands. 10 – Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA. 11 – Department of Medicine and University of Vermont Cancer Center, University of Vermont Robert Larner, M.D. College of Medicine, Burlington, Vermont, USA.

 

Aim: Determining pathogenicity of the increasingly prevalent Variants of Uncertain Significance (VUS) in cancer-predisposing genes provides a major challenge to clinical geneticists. Lynch syndrome is a prevalent cancer predisposition syndrome caused by a germ line defect in one of four DNA mismatch repair (MMR) genes. Thus far, the large majority of missense variants identified in MMR genes cannot be classified. As clinical multi-gene testing increases, many more VUS are being identified, emphasizing the need of a calibrated and validated classification method.

Method: Here we calibrate and validate an assay that rapidly quantifies the biochemical activity of variants in MMR proteins MLH1 and MSH2.

Results: We show that Bayesian integration of functional assay results with in silico analysis correctly classifies ~85% of missense variants, and we demonstrate inter-laboratory assay reproducibility.

Conclusion: This integrated diagnostic procedure provides a paradigm for the assessment of pathogenicity of VUS in disease-predisposing genes.

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