title: Assessment of the InSiGHT Interpretation Criteria for the Clinical Classification of 24 MLH1 and MSH2 Gene Variants.
abstract: Pathogenicity assessment of DNA variants in disease genes to explain their clinical consequences is an integral component of diagnostic molecular testing. The International Society for Gastrointestinal Hereditary Tumors (InSiGHT) has developed specific criteria for the interpretation of mismatch repair (MMR) gene variants. Here, we performed a systematic investigation of 24 MLH1 and MSH2 variants. The assessments were done by analyzing population frequency, segregation, tumor molecular characteristics, RNA effects, protein expression levels, and in vitro MMR activity. Classifications were confirmed for 15 variants and changed for three, and for the first time determined for six novel variants. Overall, based on our results, we propose the introduction of some refinements to the InSiGHT classification rules. The proposed changes have the advantage of homogenizing the InSIGHT interpretation criteria with those set out by the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium for the BRCA1/BRCA2 genes. We also observed that the addition of only few clinical data was sufficient to obtain a more stable classification for variants considered as "likely pathogenic" or "likely nonpathogenic." This shows the importance of obtaining as many as possible points of evidence for variant interpretation, especially from the clinical setting.
authors.affiliation: Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.|Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
authors.forename: Rossella
authors.initials: R
authors.lastname: Tricarico
authors.affiliation: Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland.
authors.forename: Mariann
authors.initials: M
authors.lastname: Kasela
authors.affiliation: Tuscan Tumor Institute, Florence, Italy.
authors.forename: Cristina
authors.initials: C
authors.lastname: Mareni
authors.affiliation: Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.|Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Victoria, Australia.
authors.forename: Bryony A
authors.initials: BA
authors.lastname: Thompson
authors.affiliation: Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Drouet
authors.affiliation: Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.|Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
authors.forename: Lucia
authors.initials: L
authors.lastname: Staderini
authors.affiliation: Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.
authors.forename: Greta
authors.initials: G
authors.lastname: Gorelli
authors.affiliation: Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Crucianelli
authors.affiliation: Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Ingrosso
authors.affiliation: Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland.
authors.forename: Jukka
authors.initials: J
authors.lastname: Kantelinen
authors.affiliation: Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Papi
authors.affiliation: Cancer Genetics and Gene Transfer - Core Research Laboratory, Istituto Toscano Tumori, Florence, Italy.|ICCOM-CNR, Sesto Fiorentino, Italy.
authors.forename: Maria
authors.initials: M
authors.lastname: De Angioletti
authors.affiliation: Cancer Genetics and Gene Transfer - Core Research Laboratory, Istituto Toscano Tumori, Florence, Italy.
authors.forename: Margherita
authors.initials: M
authors.lastname: Berardi
authors.affiliation: Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France.
authors.forename: Pascaline
authors.initials: P
authors.lastname: Gaildrat
authors.affiliation: Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France.
authors.forename: Omar
authors.initials: O
authors.lastname: Soukarieh
authors.affiliation: Medical Genetics, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
authors.forename: Daniela
authors.initials: D
authors.lastname: Turchetti
authors.affiliation: Inserm-U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Martins
authors.affiliation: Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
authors.forename: Amanda B
authors.initials: AB
authors.lastname: Spurdle
authors.affiliation: Department of Biosciences, Division of Genetics, University of Helsinki, Helsinki, Finland.
authors.forename: Minna
authors.initials: M
authors.lastname: Nyström
authors.affiliation: Department of Biomedical, Experimental and Clinical Sciences, Medical Genetics Unit, University of Florence, Florence, Italy.|Institute of Genomic Medicine, A. Gemelli School of Medicine, Medical Genetics Unit, Catholic University of the Sacred Heart, Rome, Italy.
authors.forename: Maurizio
authors.initials: M
authors.lastname: Genuardi
mesh_terms: D000483:Alleles; D017398:Alternative Splicing; D014408:Biomarkers, Tumor; D002874:Chromosome Mapping; D030541:Databases, Genetic; D005787:Gene Frequency; D056726:Genetic Association Studies; D008040:Genetic Linkage; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D007150:Immunohistochemistry; D053842:Microsatellite Instability; D018895:Microsatellite Repeats; D000070957:MutL Protein Homolog 1 / Q000235:genetics* / Q000378:metabolism; D051718:MutS Homolog 2 Protein / Q000235:genetics* / Q000378:metabolism; D009154:Mutation; D010641:Phenotype; D011401:Promoter Regions, Genetic
chemical_list: D014408:Biomarkers, Tumor; C497172:MSH2 protein, human; D000070957:MutL Protein Homolog 1; D051718:MutS Homolog 2 Protein
keywords: Lynch syndrome; Variants of Uncertain Significance (VUS); functional assays; microsatellite instability; multifactorial analysis; splicing