GT-Scan Suite: Computationally guiding genome engineering
A double helix strand of DNA
The GT-Scan suite improves identification of unique genomic targets.
Software suite for the end-to-end design of CRISPR-based genome editing applications.
The challenge
Genome engineering is used for a wide range of applications across human health, environmental and agricultural spaces.
The possibilities are exciting – applications include editing tissues affected by genetic disease, developing novel diagnostics for current and emerging pathogens, and designing gene drives to protect crops.
However, finding the optimal spot to target in the genome is a complex optimisation task that requires substantial compute power and bespoke machine learning algorithms.
Our response
We worked with our research and clinical partners to create the GT-Scan suite. The software can make genome engineering more reliable as well as less time and resource consuming.
The suite is comprised of tools for prediction of CRISPR-Cas9 efficiency (TUSCAN), tissue-specific efficiency (GT-Scan2), and efficiency of insertion (CUNE).
VARSCOT improves safety by predicting the collateral damage (off-targets) for individual organisms and populations. GOANA quantifies the efficiency and outcome of a CRISPR-Cas9 experiment.
Benefits
The steps in the GT-Scan Suite
Flexible and cloud-based, the GT-Scan Suite allows the user to set the characteristics of targets and off-targets and ranks them, reducing collateral activity.
The GT-Scan suite is a fast and accurate design and analysis suite for genome editing activities.
TUSCAN and GT-Scan2 provide efficiency predictions for general and tissue-specific on-target activity that outperform current state-of-the-art tools by an average of 80%.
VARSCOT considers genetic variation between organisms when predicting collateral activity (off-targets). It can provide valuable insights for precision medicine and gene-drive applications.
The GT-Scan suite uses new developments in cloud computing. It is 95% cheaper to run than alternatives.
This combination of accuracy, specificity and high performance enables the GT-Scan suite to cater to the high precision market of human health, where specimens are precious and edits need to work the “first time, every time”.
GT-Scan suite also caters to the commodity market of livestock and crop applications – analysis can be performed quickly and scaled to suit genomes that are orders of magnitude larger than human.
The Australian e-Health Research Centre (AEHRC) is CSIRO's digital health research program and a joint venture between CSIRO and the Queensland Government. The AEHRC works with state and federal health agencies, clinical research groups and health businesses around Australia.