Environment projects
Environmental Metagenomics
Led by Kim Handley, University of Auckland
A powerful way of studying microorganisms is by direct sampling of their collective genomes from the environment. This helps determine the role of organisms and their impact on environmental health. This project will generate a high quality database of mixed genomes from DNA collected from a stream to determine its health and genetic potential. The aim is to develop national capabilities and contribute to improved environmental monitoring approaches using genomics.
High Quality Genomes
Photo: Birgit Rhode
Led by David Chagné, Plant & Food Research, and Thomas Buckley, Manaaki Whenua - Landcare Research
High quality genome (sets of DNA) sequences of organisms that are important to New Zealand are needed for conservation purposes and breeding within our primary industries. Assembling high quality genomes is a challenge as many genomes are large, variable or very complex. This project developed the capability and distributed tools needed to routinely generate high quality genome assemblies. These tools will accelerate protection of our threatened species and improve knowledge for primary production species.
Health projects
Cell-Free Genomics
Led by Parry Guilford and Mik Black, University of Otago
Plasma genomics has the potential to enhance our ability to diagnose and treat cancer and other non-communicable diseases. Cell-free plasma samples are easily accessible from patients, and there may be effective ways to use such samples to monitor patient responses to cancer therapy, and eventually screen for multiple types of cancer. This project will develop pipelines for data analysis, quality control and clinical reporting of plasma genomic data, leading to the more rapid implementation of plasma genomics into clinical practice.
Clinical Genomics
Led by Stephen Robertson, University of Otago
This pilot project gave laboratory scientists the opportunity to analyse genomic datasets from patients with real clinical problems, with the ability to deliver results back to patients. The initiative targeted disadvantaged communities to ensure equitable access to the latest technologies. This work further develops Aotearoa’s capability to implement genomically informed healthcare in collaboration with clinicians and diagnostic laboratories.
Culture-Independent Genomic Typing of Bacterial Pathogens
Led by Una Ren, ESR
Once a disease-causing microorganism is identified in a particular patient, food or environmental sample, it takes further clinical laboratory work to determine the “typing” data that describes the organism’s characteristics, such as what antibiotics it is resistant to or where it came from. This project will develop a metagenomics-based test to determine the typing information for a specific pathogen directly from the clinical sample. This will allow use of faster diagnostic tests without compromising the ability to monitor infectious diseases.
Genomic Translational Oncology
Led by Cristin Print, University of Auckland
Genomic translational oncology is developing rapidly around the world, changing our understanding of cancer biology and approaches to treatment. This project will adopt overseas learnings in the use of genomics to assist people with cancer, while being mindful of New Zealand differences and opportunities. The aim is to develop a cohesive set of protocols and methods, and upskill clinical and research leaders, to enable the progressive induction of translational genomics into New Zealand’s oncology practice and cancer research.
Primary production projects
Better Breeding Values
Led by Dorian Garrick, Massey University, and Michael Lee, University of Otago
Primary industries rely on genetic improvement to maintain sustainability and increase efficiency and profitability, in order to remain competitive and mitigate risk. This project developed next-generation tools and approaches to help manage the complexity of using genomic data to predict breeding values.
High Quality Genomes
Blueberries, photo by Elisabeth Joly
Led by David Chagné, Plant & Food Research, and Thomas Buckley, Manaaki Whenua - Landcare Research
High quality genome (sets of DNA) sequences of organisms that are important to New Zealand are needed for conservation purposes and breeding within our primary industries. Assembling high quality genomes is a challenge as many genomes are large, variable or very complex. This project developed the capability and distributed tools needed to routinely generate high quality genome assemblies. These tools will accelerate protection of our threatened species and improve knowledge for primary production species.
Bioinformatics projects
Bioinformatics Capability (1)
Led by Mik Black and Peter Dearden, University of Otago, Kim Handley, University of Auckland, Rudiger Brauning, AgResearch, and Miles Benton, ESR
This project co-ordinates the bioinformatics aspects of Genomics Aotearoa projects. The focus is on establishing and providing underpinning computational / bioinformatics infrastructure and training.
Te Ao Maori projects
Te nohonga kaitiaki
Led by Maui Hudson, University of Waikato
Te nohonga kaitiaki are guidelines for genomic research with taonga species that align with cultural expectations of appropriate ethical behaviour. These guidelines support Genomics Aotearoa researchers to work appropriately with Māori / Iwi communities in the generation, storage and use of genome sequences for taonga species and indigenous plants and animals.