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

We offer 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

1) Infinium Methylation EPICv2 BeadChip. Allows the interrogation of over 935,000 methylation sites quantitatively across the human 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.

2) Infinium Mouse Methylation BeadChip. Interrogates > 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. The assay achieves > 98% reproducibility for technical replicates and shows a high correlation with whole-genome bisulfite sequencing data.

SNP Genotyping and CNV (Copy Number Variation) analysis

Our unit offers Genome-wide Genotyping analysis with all currently available Illumina arrays: Infinium Global Screening Array, Infinium Omni5-4 Beadchip, Infinium CytoSNP-850K BeadChip, Infinium Global Diversity Array-8 Kit, Infinium OmniExpress-24 BeadChip, etc.

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

2. NEXT GENERATION SEQUENCING (NGS)

The MiSeqDx is used for targeted sequencing of DNA libraries using Sequencing by Synthesis (SBS) technology. It can be used for basic research purposes or for in vitro diagnostic (IVD) assays. It reaches a throughput of 1–96 samples/run depending on the assay, and gives a read length of up to 2 × 300 bp.

Applications

• Targeted resequencing

• Small genome sequencing

• Metagenomics (16S rRNA)

Equipment: Illumina MiSeqDX (for diagnostic testing)

3. PYROSEQUENCING

Pyromark uses pyrosequencing 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.

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 & TECAN Infinite F Nano microplate reader.

6. SAMPLE QUALITY CONTROL

Integrity and RNA contamination of DNA are assessed by agarose gel electrophoresis.