The Genomics Unit at IJC aims to provide scientific services to the IJC community as well as to external researchers. Several technologies have been implemented in the Unit to assess relevant genomic and epigenomic features in order to unravel basic molecular mechanisms of disease, and contribute to discover therapeutic targets and biomarkers.
The Genomics Unit is equipped with cutting-edge technology to offer solutions on both basic and translational epigenomic and genomic studies in many type of samples (primary cells, cell lines, frozen and paraffin-embeded tissues, etc). We have long standing experience in arrays-based genome-wide DNA methylation analysis, and we also perform pyrosequencing for DNA analysis. We use next-generation sequencing (NGS) technology to investigate subsets of genes or specific genome regions with MiSeqDx System from Illumina.
1. Infinium MethylationEPICTM BeadChip technology (Illumina)
Infinium MethylationEPIC BeadChip Kit, allows interrogation of over 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution. It provides a Comprehensive Genome-Wide Coverage as interrogated sites include CpG sites outside of CpG islands, Non-CpG methylated sites identified in human stem cells (CHH sites), differentially methylated sites identified in tumor versus normal, FANTOM5 enhancers, ENCODE open chromatin and enhancers, DNase hypersensitive sites and miRNA promoter regions. High-throughput is supported by chip analysis performed using Illumina HiScanTM SQ fluorescent scanner and the Freedom EVO® platform.
2. Infinium Mouse Methylation BeadChip (Illumina)
The mouse methylation kit is ideal for genome-wide DNA methylation studies with a large number of samples, as it allows the interrogation with sample high throughput of > 285k methylation sites per sample at single-nucleotide resolution. It provides balanced coverage of CpG islands, translation start sites, enhancers, imprinted loci, and other regions.
3. MySeqTMDx NGS sequencer (Illumina)
The MiSeqDx technology is used for targeted sequencing of DNA libraries from human genomic DNA extracted from peripheral whole blood or formalin-fixed, paraffin-embedded (FFPE) tissue. It can be used for basic research purposes or for in vitro diagnostic (IVD) assays. It reachs a throughput of 1–96 samples/run depending on the assay, and gives a read length of up to 2 × 300 bp.
3. PyroMarkTMQ48 (Qiagen)
Pyrosequencing is a sequence-based platform, that integrates detection and quantitative real-time data for the analysis of targeted short DNA sequences. It is used to characterize single nucleotide polymorphisms (SNPs), insertion-deletions (indels), and unknown sequence variants, and DNA methylation levels at both CpG and non-CpG (CpN) sites.
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Genomics Unit Services
-Global methylation studies of mouse and human methylomes using Illumina DNA methylation beadchip platforms (Infinium MethylationEPIC Kit and Infinium Mouse Methylation kit, respectively).
-Global methylation studies using EPIC DNA methylation beadchip platform from Illumina, and custom array-based genomic analysis (SNPs, genotyping) with Illumina technology. Fluorimetric quality control of DNA samples is performed.
- Validation of NGS or array results using and analysis of sequence variation (SNPs, mutations, DNA methylation) by pyrosequencing using PyroMark Pyromark Q48TM.
- Next-generation sequencing (NGS) for detection of genetic variants, targeted genes sequencing with MiSeqDx System from Illumina, which is the first FDA-regulated, CE-IVD-marked, NGS platform for in vitro diagnostic (IVD).