Dataset associated with paper "Comprehensive genetic and epigenetic characterization of Lynch-Like Syndrome patients."

Dataset associated with paper "Comprehensive genetic and epigenetic characterization of Lynch-Like Syndrome patients."

This set of raw data cannot be made publicy available, but might be made available to interested researcher upon reasonable request. Please forward your request to [e-mail] or/and [e-mail].

Description

This dataset contains the B-values obtained from the Infinium MethylationEPIC (v1.0) BeadChip analysis for Lynch, Lynch-like, sporadic cases, and controls.

DNA from whole blood was extracted from peripheral blood lymphocytes of individuals (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by using NanoPhotometer Pearl (Implen GmbH). Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocols. Fluorescence intensities were captured by using the fluorescent scanner Illumina HiScan SQ (Illumina). Quality control, pre-processing and generation of β-values matrix were performed by using the ChAMP package (release 2.32.0) package, implemented R environment (version 4.3.1): after the quality control/pre-processing step, 740840 probes and 123 samples were retained (Lynch, n=32; Lynch-Like, n=32; Sporadic. N=30; Controls, n= 29). After BMIQ normalization, data were adjusted for batch effect by using ComBat library.