Mark Drost1, Yvonne Tiersma1, Bryony A Thompson2,3, Jane H Frederiksen4, Guido Keijzers4, Dylan Glubb5, Scott Kathe6, Jan Osinga7, Helga Westers7, Lisa Pappas8, Kenneth M Boucher8, Siska Molenkamp9, José B Zonneveld9, Christi J van Asperen9, David E Goldgar10, Susan S Wallace6, Rolf H Sijmons7, Amanda B Spurdle5, Lene J Rasmussen11, Marc S Greenblatt12, Niels de Wind13, Sean V Tavtigian14. 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, UT, USA. 3. Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia. 4. Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark. 5. Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia. 6. Department of Microbiology and Molecular Genetics, University of Vermont Robert Larner, M.D. College of Medicine, Burlington, VT, USA. 7. Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands. 8. Department of Medicine, Division of Epidemiology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 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, UT, USA. 11. Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark. lenera@sund.ku.dk. 12. Department of Medicine and University of Vermont Cancer Center, University of Vermont Robert Larner, M.D. College of Medicine, Burlington, VT, USA. Marc.Greenblatt@uvmhealth.org. 13. Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. N.de_Wind@lumc.nl. 14. Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA. sean.tavtigian@hci.utah.edu.
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.
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.
Authors: Lene Juel Rasmussen; Christopher D Heinen; Brigitte Royer-Pokora; Mark Drost; Sean Tavtigian; Robert M W Hofstra; Niels de Wind Journal: Hum Mutat Date: 2012-08-13 Impact factor: 4.878
Authors: Mark Drost; José B M Zonneveld; Sandrine van Hees; Lene Juel Rasmussen; Robert M W Hofstra; Niels de Wind Journal: Hum Mutat Date: 2011-12-29 Impact factor: 4.878
Authors: Maxime P Vallée; Tiana C Francy; Megan K Judkins; Davit Babikyan; Fabienne Lesueur; Amanda Gammon; David E Goldgar; Fergus J Couch; Sean V Tavtigian Journal: Hum Mutat Date: 2011-11-03 Impact factor: 4.878
Authors: Anne Lützen; Niels de Wind; Dubravka Georgijevic; Finn Cilius Nielsen; Lene Juel Rasmussen Journal: Mutat Res Date: 2008-09-04 Impact factor: 2.433
Authors: Sue Richards; Nazneen Aziz; Sherri Bale; David Bick; Soma Das; Julie Gastier-Foster; Wayne W Grody; Madhuri Hegde; Elaine Lyon; Elaine Spector; Karl Voelkerding; Heidi L Rehm Journal: Genet Med Date: 2015-03-05 Impact factor: 8.822
Authors: Abhijit Rath; Akriti Mishra; Victoria Duque Ferreira; Chaoran Hu; Gregory Omerza; Kevin Kelly; Andrew Hesse; Honey V Reddi; James P Grady; Christopher D Heinen Journal: Hum Mutat Date: 2019-08-17 Impact factor: 4.878
Authors: Randall E Brand; Beth Dudley; Eve Karloski; Rohit Das; Kimberly Fuhrer; Rish K Pai; Reetesh K Pai Journal: Fam Cancer Date: 2020-04 Impact factor: 2.375
Authors: Anja R Ollodart; Chiann-Ling C Yeh; Aaron W Miller; Brian H Shirts; Adam S Gordon; Maitreya J Dunham Journal: Genetics Date: 2021-06-24 Impact factor: 4.562
Authors: Mev Dominguez-Valentin; John-Paul Plazzer; Julian R Sampson; Christoph Engel; Stefan Aretz; Mark A Jenkins; Lone Sunde; Inge Bernstein; Gabriel Capella; Francesc Balaguer; Finlay Macrae; Ingrid M Winship; Huw Thomas; Dafydd Gareth Evans; John Burn; Marc Greenblatt; Wouter H de Vos Tot Nederveen Cappel; Rolf H Sijmons; Maartje Nielsen; Lucio Bertario; Bernardo Bonanni; Maria Grazia Tibiletti; Giulia Martina Cavestro; Annika Lindblom; Adriana Della Valle; Francisco Lopez-Kostner; Karin Alvarez; Nathan Gluck; Lior Katz; Karl Heinimann; Carlos A Vaccaro; Sigve Nakken; Eivind Hovig; Kate Green; Fiona Lalloo; James Hill; Hans F A Vasen; Claudia Perne; Reinhard Büttner; Heike Görgens; Elke Holinski-Feder; Monika Morak; Stefanie Holzapfel; Robert Hüneburg; Magnus von Knebel Doeberitz; Markus Loeffler; Nils Rahner; Jürgen Weitz; Verena Steinke-Lange; Wolff Schmiegel; Deepak Vangala; Emma J Crosbie; Marta Pineda; Matilde Navarro; Joan Brunet; Leticia Moreira; Ariadna Sánchez; Miquel Serra-Burriel; Miriam Mints; Revital Kariv; Guy Rosner; Tamara Alejandra Piñero; Walter Hernán Pavicic; Pablo Kalfayan; Sanne W Ten Broeke; Jukka-Pekka Mecklin; Kirsi Pylvänäinen; Laura Renkonen-Sinisalo; Anna Lepistö; Päivi Peltomäki; John L Hopper; Aung Ko Win; Daniel D Buchanan; Noralane M Lindor; Steven Gallinger; Loïc Le Marchand; Polly A Newcomb; Jane C Figueiredo; Stephen N Thibodeau; Christina Therkildsen; Thomas V O Hansen; Lars Lindberg; Einar Andreas Rødland; Florencia Neffa; Patricia Esperon; Douglas Tjandra; Gabriela Möslein; Toni T Seppälä; Pål Møller Journal: J Clin Med Date: 2021-06-28 Impact factor: 4.241
Authors: Sarah E Brnich; Ahmad N Abou Tayoun; Fergus J Couch; Garry R Cutting; Marc S Greenblatt; Christopher D Heinen; Dona M Kanavy; Xi Luo; Shannon M McNulty; Lea M Starita; Sean V Tavtigian; Matt W Wright; Steven M Harrison; Leslie G Biesecker; Jonathan S Berg Journal: Genome Med Date: 2019-12-31 Impact factor: 11.117
Authors: Bryony A Thompson; Rhiannon Walters; Michael T Parsons; Troy Dumenil; Mark Drost; Yvonne Tiersma; Noralane M Lindor; Sean V Tavtigian; Niels de Wind; Amanda B Spurdle Journal: Front Genet Date: 2020-07-27 Impact factor: 4.599