The team has been instrumental in the early adoption and application of next generation sequencing (NGS) technologies. These technologies, although well positioned to detect single nucleotide DNA variations and small insertions or deletions, are limited in detecting large chromosomal rearrangements. These structural variations, which may include millions of nucleotides of heterogeneity within a genome, are significant in driving prostate cancer development, while little is known about their heritability.
The team is actively involved in assessing and adopting technologies that can detect the ‘hard-to-detect’ genomic variation, including large structural variations, further facilitated by the need to improve de novo assembly. The team has therefore established two laboratories.
NGS Long-Read Laboratory
The laboratory is focused on utilizing technologies that are capable of generating ‘long reads’ as apposed to the more commonly used ‘short read’ NGS technologies. The laboratory currently houses two Ion Personal Genome Machine (PGM) Systems, which enables the team to generate over 400-base shotgun sequencing reads.
Genome Mapping Laboratory
The laboratory houses the BioNano Irys System, currently the only System within Australia (Read an interview with Prof Vanessa Hayes about it here). The Irys NanoChannel technology allows for the visualization of whole human and cancer genomes by capturing linerised DNA molecules hundreds of kb in length. The team is working in close collaboration with San Diego company BioNano Genomics to improve both DNA isolation and downstream analysis pipelines.