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Onco-Genomics Services

Next Generation Sequencing (NGS)

  • NGS services utilize both NovaSeq X+ and NovaSeq 6000 for low cost high capacity sequencing, a NextSeq 500 for smaller rapid runs and an iSeq 100 for quality control and validation. Sequencing services are supported by expertise in manual library prep and automated library prep on a PerkinElmer Zephyr G3 NGS and Hamilton Vantage.
  • For RNA-seq, Kapa RNA Hyper and Illumina TruSeq workflows support a range of input amounts.
  • DNA-seq libraries for fragmented DNA submissions like ChIP are supported by Kapa DNA Hyper and DNA Evo. For metagenomics and whole genome studies enzymatic fragmentation workflows are available with additional sample cleanup to provide efficient library conversion.
  • SARS-CoV-2 genome sequencing is available using ARTIC amplicon sequencing (NEB).
  • Hybridization capture workflows for whole exome sequencing and targeted panels are considered on request.
  • Aside from in-house library prep, the OGSR provides a sequencing only NGS service, where users can provide their own NGS libraries or library pools for sequencing following in-house quantification and fragment analysis.

Single Cell Genomics

  • Single cell and single nuclei gene expression profiling is run on a 10x Genomics Chromium single cell controller supported by sample QC on a Nexcelom K2 imaging cell counter. Services are available for all 10X Genomics protocols including 3’ and 5’ gene expression and T cell and B cell receptor sequencing and “feature barcoding” applications including cell surface antibodies.
  • DNA sequencing multi-omics studies are run on a Mission Bio Tapestri with many off-the-shelf panels for cancer driver mutations and applications for CNV and cell surface marker studies.
  • A dual rotor Miltenyi GentleMACS tissue dissociator is available for loan to investigators to assist with sample prep for single cell studies and nucleic acid extraction.

Spatial Omics

  • Whole-section spatial genomics is available using the Visium platform from 10X Genomics which captures transcripts using arrays of oligo spots on special microscope slides. Fresh frozen and FFPE sections can be used with histopathology support from the Cancer Modelling Shared Resource. A CytAssist system is available in the OGSR for tissue section transfer and imaging. Oligo spots provide 55µm resolution equivalent to 10-30 cells.
  • High resolution regional sampling of sections is available using the nanoString GeoMX digital spatial profiler. This platform supports whole transcriptome studies of human and mouse tissues along with smaller targeted transcript panels and antibody panels. Data output employs NGS for target counting or nCounter scanning for low density studies. Region of interest selection and morphology guided sectioning can select for cell populations as low as 200 – 300 cells at 1 µm resolution.
  • In situ single cell spatial omics will be available towards the end of 2023 on the nanoString CosMX platfrom. This platform will employ 1,000-plex transcript panels and 100-plex antibody panels quantifying hundreds of targets per cell at sub-cellular resolution.

Gene Expression and Molecular Quantification Assays

  • The nanoString nCounter® platform is a complete solution for detecting and counting large sets of molecules using solution-phase hybridization, immobilization and fluorescence barcode counting. OGSR runs an nCounter Gen2 Analysis System designed for core facilities and can operate at a throughput of 24 samples per day.
  • Digital PCR (dPCR) services are available using a QIAgen QIAcuity One. dPCR is suited to applications such as genotyping, viral load counting and transcript quantification. Assays are typically run using hydrolysis probes (Taqman) and can be multiplexed using three channel detection. Validated hydrolysis qPCR assays can usually be transitioned easily to dPCR.

Nucleic Acid Extraction, Quantification, and Quality Control (QC)

  • RNA and DNA extraction services are available for cells, tissues, biofluids, and FFPE. Homogenization can be carried out using cryo-fractionation (Covaris CryoPrep) or grinding (Miltenyi GentleMACS) in sealed single-use vessels. Standard extraction procedures run on a Thermo KingFisher Apex mag-bead extractor and manual extractions are also available. Phase separation extraction is not available.
  • Sample quantification is available using Qubit or Quant-iT dye-based systems or micro-volume spectrophotometry using NanoDrop.
  • Fragment analysis, including services to determine RNA integrity, are available using Agilent 2100, or 5200 systems. Both systems are capable of analysis of low or standard input RNA or DNA samples (~1 - 100 ng) with fragment sizes up to about 6Kb.