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Health projects

Current projects

Extending whole genome analysis into healthcare

Led by Stephen Robertson and Louise Bicknell, University of Otago

Full genome sequencing is currently the most comprehensive method of arriving at a genetic diagnosis, but the full capability and infrastructure need to instigate this practice in New Zealand has yet to be established. Building on the completed Clinical Genomics project, this analysis extends to a broader range of potential genetic mutation types, and will develop methods to analyse datasets from whānau where key family members might not be available to participate. The project will also develop and run Genomics Wānanga – using a Te Ao Māori lens to teach genomics analysis to Māori medical students.

Aotearoa New Zealand Genomic Variome

Led by Phil Wilcox and Stephen Robertson, University of Otago

To use genomic medical diagnosis effectively and equitably, we need to understand genomic variation in New Zealand’s unique and increasingly diverse population. The aim of this project is to assemble genomic resources that catalogue genetic variants present in the genomes of individuals in our communities. This will support disease diagnosis and research into healthcare conditions relevant and important to Māori and Pacific people.

Epigenome-Wide Association Study Technology

Led by Greg Jones, University of Otago

Linking disease association with genetic, epigenetic or environmental factors may help better understand the health conditions of people taking part in New Zealand’s well-characterised cohort studies. However, New Zealand researchers need new pipelines and tools to do this. This project aims to streamline the analysis of population-level epigenetic datasets, in particular focusing on developing and establishing Epigenome-wide Association Study methods across several national research groups.

Identifying genetic drivers of Streptococcus pyogenes

Led by Joep de Ligt, ESR, and Paul Gardner, University of Otago

This project is focused on identifying genetic drivers of Streptococcus pyogenes isolated from children in Aotearoa New Zealand to better understand disease causality. The research looks at how very similar bacteria may have hugely different human health outcomes, ranging from asymptomatic carriage to severe disease, which are not fully explained by environmental and host factors.

Rakeiora: A pathfinder for genomic medicine in Aotearoa / New Zealand

Led by Cristin Print, University of Auckland, Phil Wilcox and Stephen Robertson, University of Otago, with Jennie Harré Hindmarsh, Ngāti Porou Hauroa, and Donia Macartney-Coxson, ESR

This pathfinder programme is to develop capability and infrastructure for research into personalised genomic data informed medicine.

Completed 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.