The GSC's technology platform is a high-throughput, large-scale DNA and RNA sequencing and analysis facility that has been designed to maximize analytical capacity, diversity, efficiency, scalability and flexibility. The platform is one of the largest of its type in Canada and is well recognized internationally.
Nucleic acid extraction and library construction services include FFPE genome, PCR-free genome, low input DNA, bisulphite, chromatin immunoprecipitation (ChIP), mRNA (strand specific), ribodepletion, miRNA, TCR/BCR, exome and custom capture.
Sequencing services include whole genome, whole transcriptome (ribosomal depleted, or polyA RNA), epigenome, ChIP, exome capture (exons only, or UTR included), miRNA, long reads and linked read as well as customized sequencing.
Bioinformatics services include somatic analysis, cancer immunogenetics, epigenetic analysis, structural variant analysis, expression analysis, germline analysis and genome assembly as well as bespoke analysis and data handling.
Oxford Nanopore MinION
Oxford Nanopore PromethION
Whole genome sequencing is used for interrogating single-nucleotide variants (SNVs), insertions and deletions (indels), structural variants (SVs) and copy number variants (CNVs) in coding and non-coding regions of the genome.
Genomic DNA is ligated to adapters without amplification creating the best quality and least biased whole genome.
We specialize in human sequencing but can sequence any species from bacteria to mammalian and large plant genomes.
Various genome coverages are available—30-40X is recommended for human germline analysis and 80X for somatic analysis.
Formalin-fixed paraffin-embedded (FFPE)
We have optimised plate-based FFPE nucleic acid extraction and library construction, these libraries are amplified and have shorter inserts due to sample quality.
Due to the variable quality of FFPE samples, this sample type routinely requires more sequences to be generated to reach the same coverage levels as non-FFPE samples.
We also offer amplified whole genome sequencing, in particular for limiting samples, eg., circulating DNA or small biopsies.
Phase genome / Linked read
Utilising the 10x Genomics Chromium platform we can offer linked reads and phased genome sequencing, this only requires ng amounts of genomic DNA input.
Whole transcriptome RNA sequencing is a next generation sequencing technique that measures the abundance of RNA transcripts and the presence of mutations or fusion transcripts in a sample. It is a powerful tool for understanding dynamics in the transcriptome, including gene expression level differences between different physiologic conditions or changes that occur during development or over the course of disease progression.
Ribosomal RNA depleted
Stranded total RNA-seq with ribosomal depletion selectively removes ribosomal RNA from total RNA samples by hybridization. A complete transcriptome profile is produced that can be utilised for expression studies, alternative splicing, novel isoforms and expressed structural rearrangements.
This can be performed on human or mouse samples and also functions well with lower quality RNA such as those extracted from FFPE tissue samples.
PolyA+ messenger RNA (mRNA)
Stranded mRNA-Seq is a popular tool for estimating gene expression levels and comparing differential gene expression in model organisms.
mRNA-Seq (PolyA+ selection) can provide valuable information about alternatively spliced isoforms and can help identify novel fusion transcripts.
Micro RNA (miRNA)
miRNA analysis provides the ability to discover, measure and compare expression levels of known miRNAs and other small non-coding RNA species.
Using the 10x Genomics Chromium system we can provide single cell sequencing services, including 3’ polyA RNA sequencing and whole genome sequencing aimed at copy number profiling.
Epigenetics is used to describe heritable genetic modifications that are not attributable to changes in the primary DNA sequence. Epigenetic modifications play a crucial role in gene expression, and thereby underpin the development, regulation and maintenance of the normal cell. Lifestyle, nutrition and environmental factors can all lead to epigenetic changes. Two of the most commonly studied epigenetic modifications involve the binding of proteins to DNA and the methylation of cytosine (C) nucleotides in the context of a CpG dinucleotide. Because the expression of miRNAs can impact epigenetic mechanisms, they can also contribute to epigenetic changes.
Chromatin immunoprecipitation (ChIP)
ChIP is a powerful experimental approach enabling the identification of proteins associated with specific regions of the genome.
Histone modifications can impact gene expression by altering chromatin structure. Histone H3 modifications include methylation of lysine residues 4 (H3K4me1 and H3K4me3), 9 (H3K9me3), 27 (H3K27me3) and 36 (H3K36me3) and acetylation of lysine residue 27 (H3K27ac). Quantitative detection of these histone ‘marks’ provides useful information on the epigenetic regulation of cellular processes.
We recommend sequencing the narrow, or punctate, marks (H3K4me3 and H3K27ac) with 50 million reads and the broad marks (H3K4me1, H3K9me3, H3K27me3, H3K36me3) and input chromatin control with 100 million reads.
Whole genome bisulphite (WGBS)
WGBS is a sequencing technology used to determine the DNA methylation status of individual cytosines by treating the DNA with sodium bisulfite before sequencing. The chemical compound sodium bisulfite converts unmethylated cytosines into uracil. The cytosines that have not converted to uracil are methylated. After sequencing, the unmethylated cytosines are read as thymines.
A sequencing depth of 30X is recommended.
Methyl capture is a targeted approach to bisulfite sequencing.
We target over 3.3 million CpG dinucleotides, interrogating biologically important methylome targets using hybridization oligonucleotide probes. This approach supports both screening and biomarker discovery in the methylome.
Whole exome sequencing (WES) consists of sequencing only a specific subset of the genome, the exons, which represent the entire protein coding part of the genome. WES can be used to study genetic variations involved in inherited as well as in sporadic disorders, including cancers, and provide an alternative to whole genome sequencing. We offer two types of exome capture protocols as well as custom gene/feature panels.
Covering 39 Mb of the human genome, representing the coding exons of 19,396 genes, we offer the xGen Exome Research Panel (v1.0) from Integrated DNA Technologies.
Exons plus UTRs
Covering 89 Mb of the human genome, including coding exons and 5’ and 3’ untranslated regions (UTRs), we offer the SureSelect Human All Exon (V6+UTR) exome from Agilent.
We can also provide custom gene/feature panels.
Please contact us to discuss your project requirements.
Custom projects and additional services are available upon request, including submission of constructed libraries. Please connect with us to explore the possibilities.