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22 Nov 2023

Genomics Health Futures Mission funds medical research at Garvan

Four Garvan researchers will lead projects to harness genomics for improved diagnosis and treatment of disease.

Clockwise from top left: Professor Joseph Powell, Professor Stuart Tangye, Dr Kishore Kumar and Dr Ira Deveson
Clockwise from top left: Professor Joseph Powell, Professor Stuart Tangye, Dr Kishore Kumar and Dr Ira Deveson

Four research teams led by the Garvan Institute of Medical Research have been awarded grants totalling $11.6 million from the Medical Research Future Fund Genomics Health Futures Mission. The grants will support projects that develop genomics for improved diagnosis and treatment of various diseases, such as Parkinson’s disease, inflammatory bowel disease and rare genetic disorders.

Announced recently by Mark Butler, Federal Minister for Health and Aged Care, the funded projects will build on existing research in genomics – the study of all our genes – to benefit patients. Funding will allow researchers to detect genetic diseases, diagnose rare conditions faster, predict responses to treatment, and assess disease risks to guide prevention.

“Garvan is a world-leader in genomics and thus uniquely positioned to unravel the genetic factors that contribute to disease – which will ultimately guide the development of precision treatments,” says Professor Benjamin Kile, Executive Director of the Garvan Institute. “With the support of the MRFF, our researchers will leverage advanced technologies and expertise to enable earlier diagnosis, personalised therapies, and improved management of some of the most debilitating conditions that affect Australians.”

 

Accelerating diagnosis of inborn errors of immunity – Professor Stuart Tangye

Inborn errors of immunity (IEI) are a group of rare genetic disorders causing abnormal immune system function, increasing susceptibility to infections, autoimmune diseases, allergies and some cancers. Early diagnosis is vital for improving quality of life, but currently, only 30-40% of affected individuals receive a definitive molecular diagnosis, which would open the door to precision treatments.

Professor Stuart Tangye will lead a four-year project to double the rate of diagnosis for IEI using a comprehensive 'multi-omics' approach, merging data on genes, gene expression and activity, protein and immune cell function, and blood biomarkers. This will offer insight into the genetic and molecular causes of IEI, enabling faster, more accurate diagnoses.

The team will develop and leverage advanced tools, such as next-generation DNA and RNA sequencing, bioinformatics and functional genomics pipelines, and sophisticated immune cell analysis. It will also build a national database of IEI cases to promote collaboration, share knowledge and resources and ultimately accelerate the discovery of new genes causing IEI and treatments for affected individuals.

“Every patient deserves an accurate diagnosis and precision treatment,” says Professor Tangye. “By combining multiple approaches and diverse types of biomedical data, we can gain invaluable insights into the molecular mechanisms underlying IEI and find answers for patients and their families. With this project, we hope to increase the molecular diagnostic rate for IEI patients across Australia to 70% by 2025.”

 

Predicting which patients respond best to IBD treatment – Professor Joseph Powell

Inflammatory bowel disease (IBD) affects millions of people worldwide, causing chronic inflammation in the digestive tract that can lead to debilitating ongoing abdominal pain, diarrhoea and weight loss. Biologic therapies – genetically engineered drugs that target specific parts of the immune system – have revolutionised IBD treatment but they do not work for all patients.

Professor Joseph Powell will lead a four-year project to develop a test predicting patients’ responses to IBD biologic therapy, enabling personalised treatment. The test will be based on multi-omic data, integrating biological information such as genes, proteins, and metabolites with clinical and demographic information to create comprehensive patient profiles.

The project will analyse cellular data from the flagship OneK1K project. Using machine learning, the team will identify shared patterns in treatment response to form predictions that help clinicians choose the most appropriate therapy for an individual.

Predictive models for treatment response could also inform future research into new treatments and personalised medicine for other complex diseases.

“Our approach could lead to major progress in IBD diagnosis and treatment. Harnessing the power of machine learning and multi-omics data could improve outcomes, decrease side effects, and enhance quality of life for millions living with IBD worldwide,” says Professor Powell.

 

Unravelling the genetic causes of Parkinson’s disease – Dr Kishore Kumar

Parkinson’s disease is a progressive neurological disorder affecting movement and cognitive functions that results from the gradual degeneration of brain cells producing dopamine. With no known cure, early diagnosis is important for timely intervention, potentially slowing progression and improving patients’ quality of life.

Dr Kishore Kumar will lead a research project aimed at improving the genetic diagnosis of monogenic Parkinson’s disease and identifying disease-causing variants in known and previously unknown genes. Uncovering genetic causes can enhance our understanding of the disease’s underlying mechanisms, provide insights into potential therapies, and improve diagnostic accuracy.

Dr Kumar’s team will analyse DNA samples from 1,000 Parkinson’s patients, making it one of the largest registries of Parkinson’s worldwide. The researchers will employ advanced genetic testing techniques and cutting-edge data analysis tools to uncover hidden insights into the disease.

“Identifying the genetic causes of this disease is pivotal in unravelling the mysteries of its underlying mechanisms and guiding us towards potential treatments,” says Dr Kumar. “Our comprehensive database will not only increase the likelihood of discovering new genes and variants linked to the disease but also improve the way we diagnose and manage Parkinson’s disease.”

 

Improving rare disease diagnosis with long-read sequencing – Dr Ira Deveson

Rare genetic diseases affect millions worldwide but are difficult to diagnose due to complex genetic causes, rarity, and overlapping symptoms. While gene sequencing advances have accelerated the diagnostic process, around half of all patients with rare disease still fail to receive a diagnosis.

Dr Ira Deveson will lead a three-year project establishing a national program for long-read sequencing, addressing challenging unsolved cases and improving rare genetic disease diagnosis. Standard gene tests analyse short segments of DNA before assembling them into a full sequence. This ‘short-read’ method may miss large or complex genetic changes that can also cause disease. Cutting-edge long-read sequencing technologies provide a more complete picture of a person’s genes, detecting complex genetic variants that traditional sequencing methods might miss.

The project involves evaluating and optimising long-read sequencing for prospective clinical use, as well as determining best practices for sample preparation, sequencing, and analysis to generate high-quality, reliable data.

By incorporating long-read sequencing into rare genetic disease diagnosis, the researchers aim to raise diagnosis rates, enabling more patients to receive accurate diagnoses and treatments. Identifying new variants and disease mechanisms may uncover new therapies for these conditions.

“We believe long-read sequencing technologies will hold the key to unlocking some of the most challenging unsolved cases of rare genetic diseases, changing how we diagnose and treat these conditions,” says Dr Deveson. “Our national program for long-read sequencing will not only increase the overall diagnostic rate but also contribute to the discovery of new genetic variants and future treatment approaches for people with rare diseases.”