The software and hardware solutions enabling CRISPR-based gene editing

#STEM #bioinformatics #cloud #crispr

The software and hardware solutions enabling CRISPR-based gene editing
Dr. Jake Bradford, Queensland University of Technology

Abstract

CRISPR-Cas9 has become a leading tool for gene editing, due to the ability to make very targeted modifications in virtually any genome of interest. The technology relies on using a customisable “guide RNA” whose sequence controls where the modifications will be made. However, designing these guide RNAs is not trivial. Identifying sequences that are unique enough not to lead to off-target modifications is particularly important. It is also computationally challenging. A given genome could have millions of potential CRISPR sites, and brute-force approach of the off-target evaluation would require comparing each site with every other site. In this presentation, I will provide a historical perspective of the computational techniques used to assess off-target risk, and provide details of how advanced data structures originally developed for searching web-scale collections of data can accelerate this task. I will also discuss how cloud computing can be leveraged for a scalable analysis of entire genomes.

Bio 

Dr Jake Bradford is an early career researcher in the School of Computer Science at the Queensland University of Technology. He was awarded his PhD in 2022, which focused on using algorithmic approaches for improving the safety and efficiency of the CRISPR-Cas9 gene editing technology. Having a background in software engineering, a significant contribution of his research included software that is scalable to extremely large genetic data. His research in this space is on-going, and is now being adapted to modern cloud computing environments where its availability can be greatly increased at a very low cost. His research is being used to assist with engineering new gene editing technologies for the biotechnology and livestock industries, and assists with designing CRISPR-based experiments for understanding molecular pathways of reef-based organisms.