Project Description

Dr Devika Ganesamoorthy

The University of Queensland

Genotyping tandem repeats with high throughput sequencing

Long read bioinformatics and applications

Wednesday 3 July 2019

Dr Devika Ganesamoorthy is an early career researcher at The University of Queensland. She obtained her PhD in Molecular Biology from the University of Melbourne in 2014. She has a strong interest in genomics and her major research focus has been on the development and assessment of high throughput genomic methods to assess genomic variation. She has extensive expertise and skills in Nanopore long-read sequencing technology and has explored the method for various applications. She is currently a postdoctoral researcher in A/Prof. Lachlan Coin’s group at the Institute for Molecular Bioscience in The University of Queensland, where she is presently working on various projects including human genomic variation and cancer genomics.

Tandem repeats comprise significant proportion of the human genome, including coding and regulatory regions. They are highly prone to repeat number variation and nucleotide mutation due to their repetitive and unstable nature, making them a major source of genomic variation between individuals. There are almost 1 million tandem repeats in the human genome, however only few of these regions have been investigated in terms of disease association. Genome-wide analysis of tandem repeats is hindered due to the limitations in analysis techniques and lack of high throughput analysis methods. Recent advances in high throughput sequencing technologies provides an opportunity to explore this class of genomic variation that has been under-studied in genomic research.

We have developed novel targeted sequencing approaches to facilitate high throughput analysis of tandem repeats in large-scale association studies. These targeted approaches can be used in combination with short-read Illumina sequencing or long-read Nanopore sequencing technology. We have also developed novel genotyping tools (GtTR and VNTRTyper) to improve the analysis of TRs from both long-read and short-read sequencing data. The genotyping estimates from these tools are comparable to the accuracy of PCR genotyping. These targeted approaches and analysis tools will assist us to explore the impact of tandem repeat variations in complex traits and common diseases.