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

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 Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution.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.

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Figure 1: Overview of the five-tiered InSiGHT classification guidelines.
Figure 2: Outcome of standardized five-tiered InSiGHT classification of constitutional MMR gene variants.
Figure 3: Classifications of all documented unique variants by variant type.
Figure 4: Contribution of microattribution to the classification of variants that are not obviously truncating.
Figure 5: Probabilities of pathogenicity for 481 class 3 missense variants of uncertain effect derived by in silico analysis.

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Acknowledgements

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Cancer Family Registry and the German Hereditary Non-polyposis Colorectal Cancer Consortium for their contributions of unpublished data, acknowledged formally through microattribution.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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A.B.S. and B.A.T. drafted the manuscript. B.A.T. conducted InSiGHT database nomenclature standardization and data cleaning, systematic literature and data review, statistical analyses and final data analyses and assisted in the presentation of data in web-based format. B.A.T., A.B.S., S.V.T., M.S.G., D.E.G. and M.G. formulated the baseline guidelines for consideration by VIC members. B.A.T. and A.B.S. developed the functional flowchart and, with L.J.R., C.D.H., G.C., M.P., A.M., B.R.-P., E.H.-F., M.S.G., M.M., T.F. and M.N. formed the functional subcommittee contributing to the supporting documents for functional assay interpretation. D.E.G. provided statistical input. J.-P.P. provided data management, organized teleconferences, collated information after teleconferences, coordinated microattribution and was responsible for the presentation of data in web-based format. J.T.d.D. provided support for the LOVD database and created the LOVD nanopublications. F.M. is the responsible InSiGHT Councilor who initiated the concept of VIC in 2007 and has been responsible for advocating for funding and organizing the face-to-face meeting in Paris. M.G. coordinated VIC and chaired teleconferences and face-to-face meetings. B.A.T., A.B.S., S.V.T., M.S.G., D.E.G., M.G., F.M., L.J.R., C.D.H., G.C., M.P., A.M., B.R.-P., E.H.-F., M.S.G., M.M., T.F., M.N., K.A., F.A.-M., B.B., I.B., D.d.S., A.F., M.P.F., S.M.F., I.M.F., M.K.-C., K.L.R., S.Y.L., P.M., P.P., M.Q., R.R., R.J.S., R.S., C.M.T., T.W., J.W. and M.O.W. provided critique of the classification criteria and/or participated in review of variants at teleconferences or face-to-face meetings or by e-mail and provided critical review of the manuscript.

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Correspondence to Maurizio Genuardi.

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A full list of collaborators assigned microattributions for this study appears at the end of the paper with affiliations.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Figures 1 and 2, and Supplementary Tables 2–7 and 9 (PDF 4174 kb)

Supplementary Table 1

Details of non-constitutional variants on the InSiGHT database (XLSX 31 kb)

Supplementary Table 8

Summary justifications for class 4: likely pathogenic and class 5: pathogenic “not obviously truncating” nonsynonymous variants classified by the InSiGHT Variant Interpretation Committee (XLSX 67 kb)

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Thompson, B., Spurdle, A., Plazzer, JP. et al. Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. Nat Genet 46, 107–115 (2014). https://doi.org/10.1038/ng.2854

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