GSI uses Illumina sequencing technology for the majority of our projects, in addition to internally developed systems. These systems are open source and managed by our development team. For more nuanced details on how we use our technology and software, explore our project initiation options and discover how you can benefit from our modern sequencing systems.
A detailed list of our technologies and systems, and their uses and functions, can be found below.
Lab Equipment
| Equipment | Usage |
| Illumina NovaSeq 6000 | DNA Sequencer |
| Illumina NovaSeq X Plus | DNA Sequencer |
| Illumina NextSeq 2000 | DNA Sequencer |
| Illumina MiSeq | DNA Sequencer |
| Hamilton Star Liquid Handler | Increases library prep capacity |
| PerkinElmer Sciclone G3 Liquid Handling Workstation | Increases library prep capacity |
| Agilent Fragment Analyzer | Automated parallel capillary electrophoresis to QC nucleic acids |
| Agilent 4200 Tapestation | High-throughput automated eletrophoresis platform for nucleic acid sample QC |
Analysis Pipeline
| Pipeline | Description |
|
Illumina Fastq Generation |
Generation of fastq files from Illumina run folders . Delivery of fastq files is included as part of the sequencing costs. |
| Whole Genome, Somatic Variant Calling Pipeline |
Generation of somatic variant calls from whole genome libraries. This requires that each tumour sample has a matched normal (generally blood or tumour adjacent). |
|
Whole Transcriptome RNASeq Analysis Pipeline |
Generation of expression and gene fusions information from whole transcriptome libraries. |
|
WGTS (Whole Genome Transcriptome Sequencing) Pipeline |
This is the Whole Genome Somatic Variant Calling + Whole Transcriptome RNASeq Analysis Pipelines. These are run together from DNA and RNA isolated from samples from a single Donor/Case |
|
Whole Exome, Somatic Variant Calling Pipeline |
Generation of somatic variant calls from whole exome libraries. This requires that each tumour sample has a matched normal (generally blood or tumour adjacent). |
|
Whole Genome or Whole Exome Tumor-only Variant Calling Pipeline |
Generation of variant calls from tumor-only whole exome libraries, without a matched normal. |
|
Targeted Sequencing Panel Variant Calling Pipeline |
Generation of variant calls from high depth sequencing of small targeted panels. UMI incorporation allows improved deduplication and error correction. |
|
Shallow Whole Genome Analysis Pipeline |
Shallow whole genome (< 1X) copy number calling |
|
Whole Genome and Exome Germline Variant Calling Pipeline |
Germline variant calls are generated from each sample separately. Joint genotyping is run across a set of samples. |