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
Discovery Early Career Researcher Award - Grant ID: DE150101117
Funder
Australian Research Council
Funding Amount
$327,000.00
Summary
The functional impact of new genes acquired through retrotransposition. Novel copies of genes often arise through retrotransposition of processed messenger RNAs. Many thousands of gene copies have arisen over evolutionary time and some of these have retained functionality while diverging from the parental gene leading to new paralogs under different regulatory regimes. Through analysis of whole-genome sequence data, we are now able to identify very recent gene copies that are not present in the ....The functional impact of new genes acquired through retrotransposition. Novel copies of genes often arise through retrotransposition of processed messenger RNAs. Many thousands of gene copies have arisen over evolutionary time and some of these have retained functionality while diverging from the parental gene leading to new paralogs under different regulatory regimes. Through analysis of whole-genome sequence data, we are now able to identify very recent gene copies that are not present in the reference genomes for various species, giving us the opportunity to explore the effects of new copies on the regulation of the original gene and the surrounding genomic environment into which the new copy is inserted. This project aims to address these important open questions through computational and biochemical approaches.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE130100614
Funder
Australian Research Council
Funding Amount
$375,000.00
Summary
Novel statistical algorithms and methods to quantify and partition pleiotropy between complex traits in populations. A fundamental question in biology is how common genetic effects are shared between traits or groups. For example, is cognition or human behaviour genetically identical across genders or across human population groups? This project will address these questions using multiple independent genome-wide association studies.
Discovery Early Career Researcher Award - Grant ID: DE190100116
Funder
Australian Research Council
Funding Amount
$415,737.00
Summary
Cell types and cell states revealed by single-cell regulatory networks. This project aims to use single-cell gene regulation networks to predict cell types. Computational approaches are needed to recapitulate how the over 37 trillion cells program the shared genome sequence in a human body to create astoundingly diverse forms and functions. This project integrates millions of high-resolution single-cell gene expression profiles with large-scale population regulatory data to systematically recons ....Cell types and cell states revealed by single-cell regulatory networks. This project aims to use single-cell gene regulation networks to predict cell types. Computational approaches are needed to recapitulate how the over 37 trillion cells program the shared genome sequence in a human body to create astoundingly diverse forms and functions. This project integrates millions of high-resolution single-cell gene expression profiles with large-scale population regulatory data to systematically reconstruct gene regulatory networks. These networks are the molecular basis for understanding human cells. This projects outcomes intend to include the first reference single-cell regulatory database and novel methods and software to predict individual cells. This project will contribute to advancing Australia's capabilities in single-cell, precision medicine, and big biological data analysis leading to significant scientific, societal and commercial benefits.Read moreRead less
Using population resequencing data to investigate the evolutionary role and functional impact of inversion polymorphisms. The project will use population re-sequencing data to generate high resolution haplotype maps of inversion polymorphisms in multiple human populations comprising more than 5,000 individuals. These maps will be used to impute inversion polymorphsisms in genotyped samples of more than 100,000 individuals, facilitated by development of novel algorithms for mapping inversion poly ....Using population resequencing data to investigate the evolutionary role and functional impact of inversion polymorphisms. The project will use population re-sequencing data to generate high resolution haplotype maps of inversion polymorphisms in multiple human populations comprising more than 5,000 individuals. These maps will be used to impute inversion polymorphsisms in genotyped samples of more than 100,000 individuals, facilitated by development of novel algorithms for mapping inversion polymorphism from population sequence data. Finally, the project will use this map to assess the functional impact and evolutionary role of inversions, by assessing their effect on quantitative traits and assessing measures of selection and population differentiation. Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE170100428
Funder
Australian Research Council
Funding Amount
$368,968.00
Summary
Diversity and evolution of methanogens. This project aims to discover methane-metabolising microorganisms and link their metabolic capabilities to cryptic parts of the carbon cycle. To date, only a small fraction of microbial diversity has been characterised, so there are significant gaps in our understanding of carbon cycling, while the metabolic capabilities of undiscovered and widely distributed microorganisms involved in methane metabolism remain unknown. This project will study these microo ....Diversity and evolution of methanogens. This project aims to discover methane-metabolising microorganisms and link their metabolic capabilities to cryptic parts of the carbon cycle. To date, only a small fraction of microbial diversity has been characterised, so there are significant gaps in our understanding of carbon cycling, while the metabolic capabilities of undiscovered and widely distributed microorganisms involved in methane metabolism remain unknown. This project will study these microorganisms’ metabolic pathways using DNA sequencing, bioinformatics and cultivation techniques. By understanding these microorganisms’ metabolisms, researchers expect to assess how they affect global carbon cycling and climate change.Read moreRead less
Mapping recombination blocks in Brassica. DNA technology provides new ways to study genomes. Understanding how the genome behaves during plant breeding will help design strategies for the breeding and selection of improved crop plants.
Australian Laureate Fellowships - Grant ID: FL150100038
Funder
Australian Research Council
Funding Amount
$2,982,714.00
Summary
Reconstructing the universal tree and network of life. Reconstructing the universal tree and network of life: This fellowship project aims to obtain 100 000 genome sequences and systematically organise these into natural phylogenetic relationships comprising both vertical inheritance and lateral transfers. One of the challenges in biology today is to reconstruct the complete evolutionary history of life on Earth. A major hurdle to this goal is our inability to culture most microbial species whic ....Reconstructing the universal tree and network of life. Reconstructing the universal tree and network of life: This fellowship project aims to obtain 100 000 genome sequences and systematically organise these into natural phylogenetic relationships comprising both vertical inheritance and lateral transfers. One of the challenges in biology today is to reconstruct the complete evolutionary history of life on Earth. A major hurdle to this goal is our inability to culture most microbial species which comprise the bulk of evolutionary diversity. The framework developed in this project seeks to replace the current incomplete classification of microorganisms to provide fundamental insights into ecology and evolution. It is hoped that the outcomes of the project can be applied to manage risk and capture opportunities in important Australian industries including agriculture, mining and biotechnology.Read moreRead less