A panel of seven microsatellite markers (5 mononucleotide and 2 pentanucleotide repeats) was used (MSI Analysis system Version 1.2– Promega). Samples were run on an Applied Biosystems 3130 Genetic Analyzer (Life Technologies). Output data were analyzed FG-4592 supplier with GeneMapper® Analysis Software (Life Technologies). MSI status was assigned as MSI high (MSI-H, ≥ 30% markers unstable), MSI low (MSI-L, < 30% markers unstable), or

microsatellite stable (MSS, no unstable markers). Methylation analysis MMR genes promoter methylation was investigated by Methylation-Specific MLPA (MS-MLPA) following the manufacturer’s instructions (SALSA MLPA kit ME011-B1) [36, 37]. Methylation analysis was performed by comparing MMR gene promoter methylation profiles of tumour samples and that of normal adjacent tissue. PCR products were analyzed on an 8 capillary 3500 DX Genetic Analyser (Life Technologies) using GeneMapper v4.1 software (Life Technologies). A dosage ratio of 0.15 or higher, corresponding to 15% of methylated DNA, was interpreted to indicate promoter methylation. Mutation analysis Four MMR genes were extensively analysed in our study: MLH1, MSH2, MHS6

and PMS2. The coding exons and exon-intron boundaries of each gene were amplified under optimized PCR conditions and directly sequenced. Primer sequences and PCR conditions are available upon request. MLPA reactions were performed following the manufacturer’s instructions (MRC-Holland, Netherlands), and the test kits used were SALSA MLPA P003, P008, P072 and P248. Since deletions of buy Elafibranor the most 3’ exon

of EPCAM can result in silencing the MSH2 gene, this region was also analyzed (SALSA MLPA P003-B1 kit includes two probes for the most 3’ exon of EPCAM). If Atorvastatin an aberrant MLPA result was observed, relative quantification with Real-Time PCR was performed as a confirmatory test (LightCycler480II – Roche). Genomic DNA and total RNA extractions were performed using respectively the QIAamp DNA blood Mini Kit (QIAGEN) and the RNeasy Plus mini Kit (QIAGEN). RT-PCR was performed using the SuperScript® One-Step RT-PCR System with Platinum®Taq DNA Polymerase (Life Technologies). Full-length sequencing was held on an 8 capillary 3500 DX Genetic Analyser (Life Technologies) and data was analysed with Mac Vector 9.0 ClustalW (v1.4) multiple sequence alignment software (Accelrys). MLPA data were analysed with Coffalyser Software. Classification of genomic variants was performed pooling the information reported in the publicly accessible InSiGHT database (International Society for Gastrointestinal Hereditary Tumours) and findings gathered from peer-reviewed journals and literature and other public genomic data sources. As to variants of unknown clinical significance and new variants, four sets of data were integrated.