Biologists and computer scientists combine in two Victorian Government projects to deliver quality outcomes for our health industry

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Image: Peter Georgeson (left) and Danny Park at work at VLSCI at Lab-14, the University of Melbourne.

Biologists sifting through piles of next generation sequencing data have a new tool now which eliminates one major step, thanks to the creation of UNDR ROVER, published this month in BMC Bioinformatics*. This fast and accurate DNA mutation detector for targeted DNA sequencing was created at the Victorian Government funded Victorian Life Sciences Computation Initiative (VLSCI) by Dr Daniel J. Park, Mr Roger Li, Mr Edmund Lau, Mr Peter Georgeson, Dr Tú Nguyen-Dumont and Dr Bernard J. Pope, all based at the University of Melbourne which hosts the VLSCI.

Any tool which can help researchers speed up and improve the analysis of their massive datasets is always welcome, so bioinformaticians are recognised when their tools are accepted and used by the global community. Publication of UNDR ROVER boosts VLSCI’s international reputation as a significant source of expertise and talent in bioinformatics.

Senior author Dr Bernard Pope, Project Leader and Lead Bioinformatician, Cancer and Clinical Genomics at VLSCI, said the project also gave third year maths major, Roger Li, (BSc, in 2014) the opportunity to be employed through BioMedVic’s Undergraduate Research Opportunity Program (UROP), another program supported by the Victorian Government. “Roger was a key contributor to this project and I am very pleased that he is a published author so early in his career,” said Dr Pope.

Roger is now working on his Masters in Software Engineering at the University of Melbourne and it was his innate mathematical talent as well as his developing computing skills which contributed to UNDR ROVER.

This team of bioinformaticians is working on detecting DNA mutations in targeted DNA sequence regions seen as having a likely connection to certain types of cancers. Just looking at targeted regions rather than the entire sequence can reduce the cost of the work and/or increase the number of samples studied.

By using existing knowledge of the targeted DNA locations, UNDR ROVER processes the output data without doing an interim analysis stage which often took up to 78% of processing time.

This research presents a tough challenge, and UNDR ROVER has just made one part of the data analysis a little easier and more cost-effective. Which is good news for patients, clinicians and health departments. And the beauty of this tool is that it is not organism specific. Any researcher wanting to analyse sequencing data from plants, animals, bacteria and, say, cancers, will find this tool handy in cutting out a major step in the usually complex process. Just start at the Hi-Plex sequencing platform.

Further background

Prof Melissa Southey’s Genetic Epidemiology Laboratory (GEL) at the University of Melbourne works on a range of cancer investigations in conjunction with the Cancer Council Victoria and VLSCI. First author on the paper, Dr Park, heads their Genomic Technology group and is also Lead, Melbourne Bioinformatics Platform at VLSCI. He and Dr Pope have a well-developed tool for this work called Hi-Plex – described in a 2015 paper and listed in the Top Ten Biotechniques Peer reviewed papers for 2015. They aim to build Hi-Plex into a useful and efficient platform for the kind of problems GEL are investigating. UNDR ROVER adds another layer to its functionality.

* BMC Bioinformatics is a journal focused on publishing original research articles in all aspects of computational methods used in the analysis and annotation of sequences and structures, as well as all other areas of computational biology (current journal impact factor of 2.58).