Genomics

Raquel Pluvinet

Introduction

The Genomics Unit focuses on the application of high throughput genomic and epigenomic technologies to support cutting-edge biomedical research. The facility houses specialized equipment to provide genomic services to the IJC community as well as to external customers.

We have a long-standing experience in genome-wide characterization of DNA methylation profiles using Illumina Infinium Technology (Human MethylationEPIC v2.0 and Mouse Methylation BeadChips).

The Genomics Unit offers different levels of service depending upon user needs, including experimental design, sample quality control, processing, and basic data analysis.

Services

1. ARRAY-BASED APPLICATIONS (Illumina)

DNA Methylation profiling analysis

Infinium Methylation EPIC v2 BeadChip (935k CpG sites) Infinium Mouse Methylation BeadChip (285k CpG sites) Infinium Methylation Screening Array (MSA) Beadchip (270k CpG sites)

SNP Genotyping and CNV (Copy Number Variation) analysis

Genome-wide Genotyping analysis with all currently available Illumina arrays including the new EX Platform BeadChips: Infinium Global Screening Array v4.0 (GSA v4) and Infinium Global Clinical Research Array-24 v1.0 (GCRA).

DNA extracted from fresh tissue, blood, PBMC, cell lines and saliva can be analyzed using these assays. Formalin-fixed paraffin-embedded (FFPE) samples are also eligible after passing a qPCR based FFPE QC test and undergoing a restoration procedure.

Equipment: Illumina iScan with Autoloader system, TECAN Freedom EVO liquid-handling robot & Infinium Automated pipetting system (IAPS) with ILASS

2. NEXT GENERATION SEQUENCING (NGS)

Illumina Sequencing by Synthesis (SBS) technology. Two platforms: MiSeqDx: for both research and in vitro diagnostic (IVD) assays. Throughput: 1–96 samples/run; read length up to 2 × 300 bp, màx 25M reads per run.

MiSeq i100 Plus: Optimized for medium-scale projects, offering up to 100 M paired-end reads per run (2 × 150 bp) and read length up to 2x 500 bp. Provides faster turnaround and cost-effective sequencing compared to MiSeqDx.

Applications:

Targeted resequencing
Small genome sequencing
Amplicon sequencing
Metagenomics (16S rRNA)
RNA-seq (small/medium projects)
Library QC

Equipment: Illumina MiSeqDx (diagnostic testing) & Illumina MiSeq i100 Plus (research projects)

3. PYROSEQUENCING

Applications

Quantitative analysis of DNA methylation levels
Determination of DNA variant allele frequencies (SNPs/ indels)

Equipment: Qiagen PyroMark Q48 Autoprep System

4. DNA EXTRACTION

DNA isolation from a range of sample types (primary cells, cell lines, frozen and paraffin-embedded tissues).

5. NUCLEIC ACID QUANTIFICATION

Nucleic acid quantification by spectrophotometry and fluorometry.

Equipment: Qubit 2.0 Fluorometer, QubitFlex & TECAN Infinite F Nano microplate reader

6. SAMPLE QUALITY CONTROL

Sizing and integrity analysis of DNA (genomic DNA & NGS libraries) and RNA are assessed by agarose gel electrophoresis and high-throughput automated electrophoresis platform.

Equipment: Agilent TapeStation 4200 system.