Our system is comprised of a variety of standard analysis workflows, each running a set of tools to accomplish a specific analysis task. These are organized into standard analysis pipelines, or packages, each composed of one or more consecutive workflows, for both accredited applications as well as research projects.
Validated pipelines for accredited assays
Our validated tumour-normal whole genome and transcriptome (WGTS) clinical case package includes 80X tumour, 30X normal whole genome and 100M paired end whole transcriptome in one integrated report. A lower coverage version of this package is also available when high tumour purity input is provided (40X tumour, 30X normal WGS, 100M PE WTS).
The report details oncogenic copy number variants (CNVs), somatic single nucleotide variants (SNVs), insertion-deletions (indels), structural variants (SVs), loss of heterozygosity (LOH), fusions, inferred cancer cell content (purity), genome-wide ploidy and fusions with OncoKb annotation and evidence tiers. All clinical reports are reviewed by board-certified geneticists (ACMG/CCMG).More about our accredited assays
RUO Analysis Packages
For research purposes (“Research Use Only”, or RUO), we offer various standard packages depending on the library types and project requirements. These are either configured to run in an automated analysis pipeline, or processed by one of our analysts through one of our standard protocols.
Standard analysis pipelines include:
- Whole Genome Analysis: Somatic, Tumour-only, or Germline calls
- Exome Analysis: Somatic, Tumour-only, or Germline calls
- Targeted Sequencing Analysis: UMI-extraction and collapse, error correction, and variant calling
- Transcriptomic Analysis: Expression and Fusion calls, Immune analysis
- Shallow Whole Genome Analysis: Copy number profiling, purity, and ploidy estimates
- cfMedip Analysis: Umi-extraction and collapse
Standard analysis protocols include:
- Whole Transcriptome
- Differential Expression Analysis
- Gene Set Enrichment
- Whole Genome or Exome
- Germline Joint Variant Calling
- Somatic Calls with a panel of normals (no matched normals)