Genomic Technologies

Team members

Ira Deveson   JHammond_crop.png  
Ira Deveson James Ferguson Jillian Hammond  
TAmos_crop.png Igor_crop.png Hasindu_crop.png  
Timothy Amos Igor Stevanovski Hasindu Gamaarachchi  

Mission statement

The KCCG Genomic Technologies program aims to ensure that the Garvan Institute is at the cutting edge of the rapidly evolving genomics technology landscape by evaluating new sequencing platforms, developing new molecular and computational tools for genome analysis, and translating these into clinical and commercial settings.

Background

The Genomic Technologies Group extends and complements the Garvan Institute's capabilities in genomic, transcriptomic, and epigenomic research by evaluating new technologies for clinical and research applications.

As genome sequencing technologies continue to advance and diversify, it is essential to constantly evaluate, implement, and develop the most informative and efficient genomic data generation methodologies. Harnessing the capabilities of the latest technologies allows researchers to answer questions with greater ease, explore new areas of biology, and develop more effective diagnostic tests.

At the moment, routinely used DNA sequencers generate large amounts of data to achieve accurate genome reconstruction, yet still struggle or fail to resolve important genomic features implicated in disease aetiology, such as haplotype estimations, large structural variations, epigenetic marks, copy number variations, and characterisation of repetitive elements, which make up more than 40% of the human genome.

The latest generation of sequencing technologies, such as Oxford Nanopore Technologies, Pacific Biosciences and 10X Genomics, facilitate many beneficial applications for genomic research. These include the following:

  • Ultra-long sequencing reads (up to 1Mb);
  • Single-cell full-length isoform sequencing;
  • Direct and automatic detection of epigenetic modifications (e.g., 5-methylcytosine);
  • Direct RNA sequencing without conversion to DNA;
  • High portability;
  • Rapid turnaround of results; and
  • Real-time, interactive, and dynamic acquisition.

The Genomic Technologies program is developing methods and applications involving the latest genome sequencing technologies, with a strong focus on bioinformatics, to complement existing high-throughput sequencing capabilities and maintain the Garvan Institute’s position as a global leader in genomics research. In addition to its core research capacity, the program also provides a range of application specific sequencing solutions that integrate the latest genomic sequencing platforms.

 

Core activities

Nanopore sequencing service

Hosting cutting-edge sequencing instruments from Oxford Nanopore (PromethION and GridION), the KCCG offers fee-for-service nanopore sequencing and analysis to researchers across Australia and the globe.

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The PromethION is Oxford Nanopore’s largest instrument to-date and enables long-read sequencing of whole human genomes as routine practice.

 

 

 

In addition to this commercial sequencing service, the Genomic Technologies program regularly assists internal and external collaborators in developing new sequencing methods and advanced data analysis solutions to tackle pressing questions in biology.

Genomic research

Rapid sequencing and analysis of human coronavirus

We are leveraging our expertise in Oxford Nanopore sequencing to inform Australia’s response to the novel human coronavirus outbreak. By sequencing the complete genome of coronavirus isolated from infected patients in Eastern NSW, we are studying how the virus evolves and spreads through the community. DNA sequencing with nanopore devices is cheap, fast and portable, enabling real-time viral surveillance. Our work in this area is contributing to a national and international network studying the transmission and evolutionary dynamics of coronavirus.

Targeted long-read sequencing

Sequencing an entire genome is unnecessary when investigating the features of a single (or a handful) of genes of interest. In such cases, a targeted sequencing strategy is usually more productive and cost-effective. We test and develop new approaches to efficiently select for specific genomic targets, in order to profile these with improved resolution and lower cost per sample. To do so, we employ new molecular tools to enrich for genetic targets of interest and advanced computational methods for programable selective sequencing on Oxford Nanopore devices. Such approaches are enabling us to accurately diagnose neurological disorders underpinned by tandem repeat expansions, detect functional copies of the HIV virus harboured in patient genomes and much more.

Synthetic controls for genomics

With new DNA sequencing platforms and genomics tools emerging every day and clinical translation underway in many areas, it is critically important to understand their accuracy and reproducibility. We work on the development and application of synthetic reference standards, known as ‘sequins’, that can be used to routinely measure the performance of next-generation sequencing assays. Sequins provide critical information to optimise and quality assure genomic assays for research and clinical applications.

Transcriptomics research

Single cell, single molecule sequencing

Single cell sequencing offers unprecedented resolution of gene activity throughout normal tissues and tumours. However, most single cell methodologies are limited by only being able to sequence the extremity of genes, thus lacking information about the upstream sequence. We are developing and applying new software for the analysis of long-read sequencing data from single cells, which can elucidate the entire sequence of individual gene transcripts instead of a small fragment. The higher sequence error rate of nanopore sequencing (compared to short read data), hinders the effective identification of cell barcodes (i.e., molecular tags) in single cell data. Barcodes are required to separate sequence data into the individual cells they originate from. Therefore, much information is lost using classical sequence-based approaches. By developing algorithms to analyse the raw signal instead of the processed sequence data, we can deconvolute single-cell barcodes with greater accuracy, enabling unparalleled views of the molecular inhabitants of individual cells.

Transcriptional mechanisms of vertebrate sex determination

Unlike mammals, whose sex is determined by the inheritance of X and Y chromosome, many reptiles and fish employ environmental sex determination. We are studying the molecular mechanism of sex determination in Australian lizard species with temperature-dependent sex. Gene-regulation events in the developing embryo can lead to male or female development depending on incubation temperature. Besides understanding this fascinating system, this work will also help us predict and mitigate the impact of climate change on the viability of these species.

Product Development and Clinical Applications

Portable, real-time genome analysis

Devices from Oxford Nanopore have enabled cheap, portable and rapid DNA sequencing. However, the realisation of these opportunities has been limited by need for high-performance computing for the analysis of the resulting DNA. We are developing novel computational tools for rapid – even real-time – analysis of nanopore sequencing data on laptop computers and smartphones. Such tools will be critical to the adoption of Oxford Nanopore devices for genome analysis in the field or the clinic.

Circulating tumour DNA sequencing

Cancer cells release fragments of DNA into the circulatory system that may be detected by targeted DNA sequencing. Circulating tumour DNA sequencing can inform cancer detection, molecular stratification, therapeutic monitoring and post-treatment surveillance, and avoids the need to invasive tissue biopsies. We are working the US FDA-led Sequencing Quality Control consortium to evaluate the accuracy and reproducibility of commercially available assays for circulating tumor DNA sequencing. This study will assess the suitability of participating assays for clinical translation, and establish best-practice guidelines for this exciting field.

 

Collaborations

Garvan collaborations

Synthetic controls for genomics ('sequins')
A/Prof Tim Mercer, Transcriptome Research

Single-cell, single-molecule sequencing
Prof Chris Goodnow, Immunogenomics
A/Prof Alex Swarbrick, Tumour Progression
A/Prof Joseph Powell, Garvan-Weizmann Centre for Cellular Genomics 

Tumour evolution and therapeutic resistance
Prof David Thomas, Genomic Cancer Medicine
Dr Arcadi Cipponi, Genomic Cancer Medicine 

External collaborations

Kirby Institute, UNSW Sydney
A/Prof Rowena Bull, A/Prof Fabio Luciani

Institute for Applied Ecology, University of Canberra
Prof Arthur Georges, Dr Clare Holleley

Peter MacCallum Cancer Centre
Prof Sarah-Jane Dawson, Dr Stephen Wong

US Food and Drug Administration
Dr Joshua Xu, Dr Binsheng Gong

Oxford Nanopore Technologies