Instrumentation

The CHGI uses an extensive range of instruments and equipment in our quality control practices and sequencing workflow, in compliance with industry standards.

Sequencers and Analytical Platforms

We host a variety of sequencers and analytical platforms to help you maximize data output while minimizing cost. Our sequencers are located in our sequencing laboratory suite away from sample input and library preparation labs to minimize the risk of cross-contamination.

Coming soon: 10x Genomics Xenium Analyzer
Contact CHGI for more information.

Illumina NovaSeq 6000, image courtesy of Illumina, Inc.

Illumina NovaSeq 6000

We are proud to offer sequencing services on the first NovaSeq in Western Canada. Contact us for a consultation to plan your next project.

The NovaSeq 6000 is Illumina's latest sequencer. It offers massive throughput and project flexibility, as it can run two patterned flow cells at a time, with each capable of generating up to 3000 gigabases of sequence. It can sequence up to 48 human genomes at 30X coverage, but a variety of research goals are applicable. Patterned flow cells offer even spacing of sequencing clusters by employing nanowells at fixed locations, significantly increasing sequencing reads and data output.

Illumina NextSeq 500, image courtesy of Illumina, Inc.

Illumina NextSeq 500

The NextSeq is currently our preferred platform for smaller genome, exome, or transcriptome projects. This benchtop sequencer can be operated in high-throughput mode to generate up to 120 gigabases of sequence per run, with each run taking 1-2 days to complete.

Illumina MiSeq, image courtesy of Illumina, Inc.

Illumina MiSeq

The MiSeq benchtop sequencer is optimized for sequencing projects with lower diversity sequences, including 16S rRNA metagenomics, PCR amplicons, and small genomes. Sequencing runs take 1-3 days to complete and generate ~ 0.3-15 gigabases of sequence.

Illumina iSeq 100, image courtesy of Illumina, Inc.

Illumina iSeq 100

The iSeq 100 is Illumina's smallest benchtop sequencer. It is available for small-scale sequencing projects including bacterial and viral whole genome sequencing, targeted sequence of a set of genes, gene expression analysis, or 16S metagenomics. Primarily, we use it in our quality control workflow to ensure sequencing reads will be distributed equally among librarie, and that they will cluster efficiently before a NovaSeq run. The iSeq can generate up to 1.2 gigabases of sequence per run.

Oxford Nanopore MinION

Oxford Nanopore Technologies MinION

While we do not currently offer Nanopore sequencing as a service, we are happy to provide support for customers with their own MinIONs.

The CHGI participated in the MinION Access Program (MAP) to help develop single-molecule nanopore-based DNA sequencing. We have both the original MinION and MinION Mk1 devices. These small sequencers use 500 nanopores per run to sequence long reads of up to 60,000 bases. Please contact us if you have a project which might benefit from this powerful, but still evolving, technology.

Applied Biosystems 3730xl DNA Analyzer

Applied Biosystems 3730xl DNA Analyzer

The 96-capillary 3730xl DNA Analyzer is the gold standard for high throughput capillary genetic analysis and small-scale DNA sequencing. It's ideal for traditional Sanger DNA sequencing and DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, and mutation detection.


Library Preparation and Quality Control

To minimize sample cross-contamination, libraries are prepared in our laboratory suite located away from our next-generation sequencing instruments. The suite contains two air-locked isolated laboratories which are used for sample intake and pre-PCR reaction set-up. A third laboratory contains our RNase-free and post-PCR work areas.

10x Genomics Chromium iX

10x Genomics Chromium iX Controller

Under construction

Coming soon: 10x Genomics Chromium Next GEM single cell 3' library preparation

Contact CHGI for more information.

NanoDrop 2000 Spectrophotometer

Thermo Scientific NanoDrop 2000 Spectrophotometer

Although the NanoDrop can quantitate nucleic acids by UV absorbance, it can overestimate the amount of material present when low concentrations are used, or when contaminants are present. We use it more commonly to check the purity of samples.

Qubit 3.0 Fluorometer

Qubit Fluorometers

Qubits measure nucleic acid by fluorescence, and assays are highly sensitive and specific for DNA or RNA. The CHGI uses Qubit measurement in QC checks.

Synergy HTX Fluorescent Plate Reader

BioTek Synergy HTX Multi-Mode Microplate Reader

The Synergy HTX fluorescent plate reader is used for high-throughput fluorescent quantitation of nucleic acids.

TapeStation 4200

Agilent Technologies 4200 TapeStation

As the successor to the Agilent Bioanalyzer, the TapeStation measures the quantity, size, and integrity of nucleic acids with genomic DNA, DNA fragment, and RNA assays. It is frequently used in our QC checks.

Agilent Fragment Analyzer 5200

Agilent Technologies 5200 Fragment Analyzer

Geared towards higher throughput, the Fragment Analyzer also measures the quantity, size, and integrity of nucleic acids with genomic DNA, DNA fragment, and RNA assays, and is also used in our QC checks.

StepOnePlus Real-Time PCR System

Applied Biosystems StepOnePlus Real-Time PCR System

We use the StepOnePlus qPCR system as a QC check to accurately quantify libraries and ensure they will cluster before loading them on an Illumina sequencer.

Pippin Prep

Sage Science Pippin Prep

The Pippin Prep is suited for automated and targeted size selection of DNA fragments, from 90 bp to 1.5 kb, on precast agarose gel cassettes.

Hamilton Nimbus

Hamilton Robotics Microlab Nimbus

For large projects, we use the Nimbus as an automated pipetting workstation. The CHGI currently has two robots in use.

Covaris ML230 focused-ultrasonicator

Covaris Sonicators

The CHGI uses the ML230 Covaris sonicator for mid-throughput shearing of DNA samples, and both the S2 and S220 sonicators for smaller projects. They operate at high frequencies (500 KHz) using Adaptive Focused Acoustic Technology.


Retired Sequencers

Ion Torrent Personal Genome Machine

This instrument was removed from our services in January 2017, as most of its applications can now be performed on the Illumina MiSeq. The Personal Genome Machine used novel pH sensing semiconductor sequencing chips for rapid sequencing, producing up to 1 gigabase of sequence per run. The PGM was commonly used for sequencing Ampliseq gene panels, PCR amplicons, and small genomes.

Ion Torrent Personal Genome Machine

Life Technologies SOLiD 5500xl Genetic Analyzer

Successor to the SOLiD 4 System, the SOLiD 5500xl Genetic Analyzer was capable of higher throughput with a shorter run time. The CHGI operated two of these instruments which were capable of generating up to 45 gigabases of sequence per day. The SOLiD 5500xl platform and supporting products were discontinued by Thermo Fisher in 2016 as NGS technology evolved.

SOLiD 5500xl Genetic Analyzer

Life Technologies SOLiD 4 System

The SOLiD 4 System was the first sequencer acquired by the Centre for Health Genomics and Informatics in 2011. It could produce 6 gigabases of sequencer over 240 million reads per run, but the run time could take up to two weeks! Common applications at the time were targeted resequencing, gene expression studies, whole genome sequencing, ChIP-seq, and miRNA discovery.

SOLiD 4 System