Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database

Bryony A. Thompson, Amanda B. Spurdle, John Paul Plazzer, Marc S. Greenblatt, Kiwamu Akagi, Fahd Al-Mulla, Bharati Bapat, Inge Bernstein, Gabriel Capellá, Johan T. Den Dunnen, Desiree Du Sart, Aurelie Fabre, Michael P. Farrell, Susan M. Farrington, Ian M. Frayling, Thierry Frebourg, David E. Goldgar, Christopher D. Heinen, Elke Holinski-Feder, Maija Kohonen-CorishKristina Lagerstedt Robinson, Suet Yi Leung, Alexandra Martins, Pal Moller, Monika Morak, Minna Nystrom, Paivi Peltomaki, Marta Pineda, Ming Qi, Rajkumar Ramesar, Lene Juel Rasmussen, Brigitte Royer-Pokora, Rodney J. Scott, Rolf Sijmons, Sean V. Tavtigian, Carli M. Tops, Thomas Weber, Juul Wijnen, Michael O. Woods, Finlay Macrae, Maurizio Genuardi, Adela Castillejo, Adrienne Sexton, Anthony K.W. Chan, Alessandra Viel, Amie Blanco, Amy French, Andreas Laner, Anja Wagner, Ans Van Den Ouweland, Arjen Mensenkamp, Artemio Payá, Beate Betz, Bert Redeker, Betsy Smith, Carin Espenschied, Carole Cummings, Christoph Engel, Claudia Fornes, Cristian Valenzuela, Cristina Alenda, Daniel Buchanan, Daniela Barana, Darina Konstantinova, Dianne Cairns, Elizabeth Glaser, Felipe Silva, Fiona Lalloo, Francesca Crucianelli, Frans Hogervorst, Graham Casey, Ian Tomlinson, Ignacio Blanco, Isabel López Villar, Javier Garcia-Planells, Jeanette Bigler, Jinru Shia, Joaquin Martinez-Lopez, Johan J.P. Gille, John Hopper, John Potter, José Luis Soto, Jukka Kantelinen, Kate Ellis, Kirsty Mann, Liliana Varesco, Liying Zhang, Loic Le Marchand, Makia J. Marafie, Margareta Nordling, Maria Grazia Tibiletti, Mariano Ariel Kahan, Marjolijn Ligtenberg, Mark Clendenning, Mark Jenkins, Marsha Speevak, Martin Digweed, Matthias Kloor, Megan Hitchins, Megan Myers, Melyssa Aronson, Mev Dominguez Valentin, Michael Kutsche, Michael Parsons, Michael Walsh, Minttu Kansikas, Mohd Nizam Zahary, Monica Pedroni, Nao Heider, Nicola Poplawski, Nils Rahner, Noralane M. Lindor, Paola Sala, Peng Nan, Peter Propping, Polly Newcomb, Rajiv Sarin, Robert Haile, Robert Hofstra, Robyn Ward, Rossella Tricarico, Ruben Bacares, Sean Young, Sergio Chialina, Serguei Kovalenko, Shanaka R. Gunawardena, Sira Moreno, Siu Lun Ho, Siu Tsan Yuen, Stephen N. Thibodeau, Steve Gallinger, Terrilea Burnett, Therese Teitsch, Tsun Leung Chan, Tom Smyrk, Treena Cranston, Vasiliki Psofaki, Verena Steinke-Lange, Victor Manuel Barbera

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Abstract

The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases.

Original languageEnglish
Pages (from-to)107-115
Number of pages9
JournalNature Genetics
Volume46
Issue number2
DOIs
StatePublished - Feb 2014

Bibliographical note

Funding Information:
We thank all submitters of data to the InSiGHT database (retrospective and prospective), the Colon Cancer Family Registry and the German Hereditary Non-polyposis Colorectal Cancer Consortium for their contributions of unpublished data, acknowledged formally through microattribution. We would also like to acknowledge L. Marquart for providing statistical advice and T. O’Mara for providing advice and assistance with the statistical package R. We are extremely grateful to the Hicks Foundation (Australia) for inaugural support of InSiGHT database curator J.-P.P. Funding for VIC teleconferences was provided by the Cancer Council of Victoria. B.A.T. is supported by a Cancer Council of Queensland PhD scholarship and by a Queensland Institute of Medical Research PhD Top-Up award. A.B.S. is a National Health and Medical Research Council Senior Research Fellow. The work performed by A.B.S. and B.A.T. was additionally supported by Cancer Australia (1010859). M.G. is supported by a grant from the Tuscan Tumor Institute (ITT). J.-P.P. is currently supported by the Royal Melbourne Hospital Foundation. S.V.T., M.S.G., A.B.S., L.J.R. and R.S. are supported by grant 1R01CA164944 from the National Cancer Institute/US National Institutes of Health (NCI/US NIH). G.C. and M.P. were supported by the Ministerio de Ciencia e Innovación (SAF 12-33636) and by the Fundación Científica de la Asociación Española Contra el Cáncer. A.F. is supported by the French National Cancer Institute and by the Institut National du Cancer (INCa) French MMR Committee. S.M.F. is supported by grants from the Association of International Cancer Research (12-1087) and by the Medical Research Council UK (MR/K018647/1). NHS Wales National Institute for Health and Social Care (NIHSCR) funding was provided to I.M.F. via the Cardiff & Vale University Health Board. D.E.G. is supported by funding from Mayo Specialized Programs of Research Excellence (SPORE) grant P50CA11620106 (principal investigator J. Ingle). C.D.H. is funded by US NIH grant R01 CA115783-02/CA/NCI. E.H.-F. and M.M. are supported by German Cancer Aid (Deutsche Krebshilfe) and by the Wilhelm Sander Foundation. M.K.-C. is funded by Cancer Institute NSW. S.Y.L. is supported by the Hong Kong Cancer Fund. A.M. is supported by the French National Cancer Institute and by the Direction Générale de l’Offre des Soins (INCa/DGOS). The Sigrid Juselius Foundation funds M.N. Funding for P.P. is provided by the European Research Council (FP7-ERC-232635). L.J.R. is funded by Nordea-Fonden. B.R.-P. is supported by German Cancer Aid. M.O.W. was supported by the Canadian Cancer Society Research Institute (grant 18223).

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