Preparing Australia For Genomic Medicine: A Proposal By The Australian Genomics Health Alliance
Funder
National Health and Medical Research Council
Funding Amount
$25,000,000.00
Summary
The sequencing of the human genome brings the possibility of more accurate identification of the underlying basis of many diseases. This technology has moved so rapidly, however, that clinical access has been limited. In this application, a national alliance of clinicians, researchers, health economists and policymakers will evaluate the case for clinical genomics across inherited disease and cancer, determine how best to deliver this to the patient and train a capable workforce.
Sequencing and assembling microbial community metagenomes in real-time. This project aims to assemble metagenomes directly from environmental samples using nanopore sequencing. Short-read approaches to metagenomics cannot assemble mixed genomes from an environmental sample, so focus on describing which species and genes are present. Long-read nanopore sequencing enables the assembly of full genomes of multiple species in a sample. Assembling complete genomes in important resources such as water ....Sequencing and assembling microbial community metagenomes in real-time. This project aims to assemble metagenomes directly from environmental samples using nanopore sequencing. Short-read approaches to metagenomics cannot assemble mixed genomes from an environmental sample, so focus on describing which species and genes are present. Long-read nanopore sequencing enables the assembly of full genomes of multiple species in a sample. Assembling complete genomes in important resources such as water and soil should lead to deeper understanding of the dynamics, variation and transfer of genetic material within these resources’ microbial communities, strategies to manage microbial diversity, and improved productivity and long-term sustainability for these resources.Read moreRead less
Understanding How Azithromycin Prevents Exacerbations In Severe Asthma
Funder
National Health and Medical Research Council
Funding Amount
$697,273.00
Summary
In some people with severe asthma, conventional inhaler treatments are not able to control the disease so there is a need for new treatment options. We have recently completed a large clinical trial which showed that very low doses of a common antibiotic help prevent asthma attacks in this situation. However, not much is known about how the antibiotic is working. This study will help us understand how the antibiotic is working and which people respond best.
Understanding somatic mutation in plants: new methods, new software, new data. Somatic mutations accumulate as plants grow, affecting everything from short-term ecological interactions to long-term evolutionary dynamics. These mutations have important consequences for plant industry and conservation, but because they are so hard to measure almost nothing is known about them. This project aims to develop new methods and software to detect, analyse, and compare the genome-wide history of somatic m ....Understanding somatic mutation in plants: new methods, new software, new data. Somatic mutations accumulate as plants grow, affecting everything from short-term ecological interactions to long-term evolutionary dynamics. These mutations have important consequences for plant industry and conservation, but because they are so hard to measure almost nothing is known about them. This project aims to develop new methods and software to detect, analyse, and compare the genome-wide history of somatic mutation in individual plants, providing an unprecedented level of detail into an important but understudied source of biological variation. By applying these methods to an iconic experimental population, This project aims to provide the first insights into the genome-wide causes and consequences of somatic mutation in plants.Read moreRead less
Glucocorticoid Resistance In Paediatric Acute Lymphoblastic Leukaemia
Funder
National Health and Medical Research Council
Funding Amount
$394,721.00
Summary
Glucocorticoids are among the most effective drugs used in the treatment of many haematological malignancies, including leukaemia, lymphoma and multiple myeloma. However, the development of tumour cell resistance to these drugs remains a significant problem, and clinically relevant mechanisms of glucocorticoid resistance remain poorly understood. This project aims to define mechanisms of resistance to glucocorticoids and develop new drugs to reverse resistance.
Diet influences the selective advantage of mitochondrial DNA mutations. This project aims to examine critical mechanisms that affect mitochondrial DNA variation within species. It aims to test the hypothesis that mitochondrial DNA haplotypes have the potential to be under nutritionally induced balancing selection as a consequence of cellular signalling and/or Adenosine triphosphate (ATP) production by mitochondria. Diet can vary both seasonally and geographically and is a key environmental param ....Diet influences the selective advantage of mitochondrial DNA mutations. This project aims to examine critical mechanisms that affect mitochondrial DNA variation within species. It aims to test the hypothesis that mitochondrial DNA haplotypes have the potential to be under nutritionally induced balancing selection as a consequence of cellular signalling and/or Adenosine triphosphate (ATP) production by mitochondria. Diet can vary both seasonally and geographically and is a key environmental parameter that influences the ability of a species to colonise new habitats. The project plans to characterise the functional links between specific mitochondrial DNA haplotypes, mitochondrial functions and organismal traits. The expected outcome is a more precise grasp of the processes influencing genetic variation within and among species, which would inform current issues in ecology and genetics.Read moreRead less
Elucidating the genetic basis of newly evolved metabolic functions in yeast. Elucidating the genetic basis of newly evolved metabolic functions in yeast. This project intends to research how complex metabolic pathways originate and evolve. This project will use cutting edge genome sequencing and molecular techniques to elucidate the heritable genetic basis of Baker’s yeast, which has been the selectively evolved to use xylose as a sole carbon source: something vital for second generation biofuel ....Elucidating the genetic basis of newly evolved metabolic functions in yeast. Elucidating the genetic basis of newly evolved metabolic functions in yeast. This project intends to research how complex metabolic pathways originate and evolve. This project will use cutting edge genome sequencing and molecular techniques to elucidate the heritable genetic basis of Baker’s yeast, which has been the selectively evolved to use xylose as a sole carbon source: something vital for second generation biofuel production that wild yeast cannot do. This project will combine detailed molecular characterisation of highly adapted yeast strains with a novel "molecular palaeontology" approach to trace the evolutionary process and identify functionally significant loci under selection. Detailed characterisation of this trait will accelerate the development of future yeast strains and test fundamental evolutionary theories.Read moreRead less
Mining large negative correlations for high-dimensional contrasting analysis. Negative correlations are widely embedded in real life applications, but in-depth research has rarely been conducted due to its high level of complexity. This project aims at efficient algorithms and frontier theory for finding large negative correlations, to enable smart information use in bioinformatics to promote Australia's leading role in data mining research.
Commensal benefits: genomic basis for suppressing plant pathogens with Pseudomonas biocontrol species. Food security is an issue of mounting significance due to unpredictable climate trends and increasing global population growth. A feature of paramount importance to reliable crop production is the capacity to control plant diseases. This project investigates natural plant colonising bacteria as a tool for protecting plants from disease.
Deep correction of DNA sequencing errors by data mining algorithms. This project aims to investigate the many layers of error correction problems in the terabytes of genomic sequence data, and aims to solve these problems by novel data mining algorithms. High-throughput sequencing platforms have generated massive amounts of useful raw data, but also made widespread errors. The new algorithms are capable of correcting errors at deeper layers to further enhance data quality. Expected outcome inclu ....Deep correction of DNA sequencing errors by data mining algorithms. This project aims to investigate the many layers of error correction problems in the terabytes of genomic sequence data, and aims to solve these problems by novel data mining algorithms. High-throughput sequencing platforms have generated massive amounts of useful raw data, but also made widespread errors. The new algorithms are capable of correcting errors at deeper layers to further enhance data quality. Expected outcome includes the knowledge advancement of genomic data industry and interdisciplinary collaboration between biotechnology and data mining. This also provides significant benefit for genomic decisions in forensics and personalised medicine which demand accurate genomic information.Read moreRead less