QIMR Berghofer Medical Research Institute Summer Research projects
Improving diagnostic processes for regulatory region variants
Project duration, hours of engagement | 6 weeks between 13 January and 21 February in 2025 36 |
Location: | Herston: QIMR Berghofer MRI |
Description: | Hereditary disease diagnosis has improved dramatically in recent times due to improvements in genomic sequencing technology. The majority of work however has centered on the diagnosis of gene variants in the protein coding region of the genome. The non-coding region of the genome remains an unexplored and underdiagnosed area. In particular, variants in regulatory regions have a high likelihood of impacting gene function and causing disease, but few have sufficient available information to determine if they cause disease in a patient. This project centers on translating research methods into evidence informed clinical process for non-coding variant interpretation. There are many bioinformatics tools that are being used in a research context to identify and understand non-coding variants and predict variant impact on function, however their accuracy and best use in clinical application is not well understood. This project aims to identify improved methods for diagnostic evaluation of non-coding variants through computational prediction of variant impact. To achieve this we will investigate some of the many bioinformatics tools available, identifying which are applicable to non-coding variant diagnostics. We will prioritise the most practical tool/s (we have already developed an extensive database of potential tools) and use a set of established non-coding disease variants to assess the clinical reliability of these tools for genetic variant interpretation. This project will evidence applicability of new methods for non-coding variants in inherited disease diagnosis, and develop processes or the appropriate use of these tools in a clinical setting. |
Expected outcomes and deliverables: | Students will learn processes relevant to applied genomic diagnostics, specifically in variant curation. Scholars may gain skills in data collection, analysis and bioinformatics, but do not necessarily need to be an expert bioinformatician as this project is focussed on the aspect of clinical translation. Tools used will be selected based on the student’s prior-experience/ability. In this project students will have an opportunity to inform clinical genomics process and may also be asked to produce a report or oral presentation at the end of their project. This work is intended to contribute to a publication. |
Suitable for: | Students would require a basic understanding of human genetics and would benefit from some understanding in genomics, basic statistics or bioinformatics. An interest in learning bioinformatics/data skills would be favourable. This is a dry lab/computer based project (no wet lab). |
Primary Supervisor: | Professor Amanda Spurdle, amanda.spurdle@qimrberghofer.edu.au The supervisor MUST be contacted by students prior to submission of an application. |
Improving bone marrow/stem cell transplant outcomes through pre-transplant modulation of donor T cell function
Project duration, hours of engagement | 6 weeks between 13 January and 21 February in 2025 36 |
Location: | Herston: QIMR Berghofer MRI |
Description: | Donor stem cell/bone marrow transplantation (allo-SCT/BMT) is an important curative therapy in the treatment of blood cancers, however its application is limited by serious complications such as graft-versus-host disease (GVHD) that have a significant impact on patient mortality and quality of life. Early inflammatory responses during treatment initiate a cascade of adaptive immune responses that manifest as acute and/or chronic tissue damage in >50% of transplant recipients. GVHD treatment options are relatively limited and focused on immunosuppression and steroidal therapy, which are problematic due to opportunistic infection and refractory disease, therefore new therapies are urgently needed. Donor-derived T cells are known to be the key drivers of GVHD pathology but are also critical to maintain ongoing anti-tumour immunity, also known as Graft-versus-leukaemia (GVL) effects, which prevent cancer relapse in these patients. Identifying novel ways to target GVHD whilst maintaining GVL is key to improving patient outcomes. We propose that in vivo screening of potential therapeutic targets via manipulation of donor T cells pre-transplant will accelerate therapeutic development in this area. In this study, we will utilise recent advances in CRISPR-mediated gene therapy to modulate T cell function in naïve primary T cells for allo-SCT. This will involve optimisation, testing and validation of CRISPR gene editing of novel targets in naïve mouse T cells in vitro prior to transplant into allogeneic mice. |
Expected outcomes and deliverables: | Students will develop new skills in techniques relevant to immunology research such as immune cell isolation, gene modification and exposure to in vivo models of inflammatory disease. This is an ideal opportunity to gain experience in the laboratory and will aid in future career choices (e.g. Honours, PhD & beyond). |
Suitable for: | We are looking for students with a strong interest in immunology who are keen to learn new techniques relevant to the field, e.g. immune cell isolation, in vitro cell culture, PCR etc. |
Primary Supervisor: | Associate Professor Kate Gartlan, kate.gartlan@qimrberghofer.edu.au The supervisor MUST be contacted by students prior to submission of an application. |
Iron deficiency and implications for healthcare costs
Project duration, hours of engagement | 6 weeks between 13 January and 21 February in 2025 36 |
Location: | Herston: QIMR Berghofer MRI |
Description: | Background: Iron is an essential mineral nutrient for human health. Iron deficiency occurs when the body does not have enough mineral iron and this can be caused by inadequate dietary intake of iron, malabsorption, increased iron requirements (such as in pregnancy) or as a comorbidity to an underlying condition. Untreated, iron deficiency is associated with impaired development in children, adverse effects on cognitive and physical performance in adults, and poorer maternal and infant outcomes in pregnancy. Aim: To understand and quantify the economic burden of iron deficiency to the Australian health system. Methods: This project involves a literature search and scoping review of the evidence on the health and economic consequences of iron deficiency, specifically to the health system. Informed by the literature searches, an estimation of costs using population attributable fractions or other suitable costing method will be employed. The project will be working with researchers at the Health Economics and Molecular Nutrition labs at QIMRB. |
Expected outcomes and deliverables: | Scholars may gain skills in literature searching and synthesis, data collection, epidemiology and have an opportunity to contribute to a publication from the research. Students may also be asked to produce a report or oral presentation at the end of their project. |
Suitable for: | Introductory statistical/mathematical skills, excellent written communication, an interest in public health and economic burden, ability to synthesize and summarise data succinctly, attention to detail. |
Primary Supervisor: | Associate Professor Louisa Collins, louisa.collins@qimrberghofer.edu.au The supervisor MUST be contacted by students prior to submission of an application. |
How does osteopontin in milk affect neonatal microbiobe composition, the metabolome, and immune development to protect from disease?
Project duration, hours of engagement | 6 weeks between 13 January and 21 February in 2025 36 |
Location: | Herston: QIMR Berghofer MRI |
Description: | Factors in the milk, such as sugars, microbes and growth factors promote growth and immune development. This is partly achieved via the assembly of the gut microbiome. Infants who are breast-fed are at lower risk than those who are fed formula, although the underlying mechanisms are unclear. We have shown that osteopontin in milk confers protection against infection and that this is mediated by an increase in the number of dendritic cells and regulatory T cells, an effect that appears to be downstream of changes to the microbiome and metabolome (metabolites in serum). We are now seeking to elucidate the specific microbes, metabolites and cellular pathways that link OPN to immune development. |
Expected outcomes and deliverables: | You will learn several skills in relation to the conduct of rigorous biomedical research. You will be taught how to excise and process tissue from mice, and trained to perform a number of cellular and molecular techniques (flow cytometry, immunohistochemistry, ELISA, etc). You will be supervised in the lab by a postdoc and PhD students. If appropriate you will be co-authored on publications, and outstanding students will be encouraged to stay on for Hons and PhD. |
Suitable for: | Those with an interest in immunology or microbiology, and a willingness to learn. |
Primary Supervisor: | Associate Professor Simon Phipps, simon.phipps@qimrberghofer.edu.au The supervisor MUST be contacted by students prior to submission of an application. |
Genetic epidemiology of endometrial cancer
Project duration, hours of engagement | 6 weeks between 13 January and 21 February in 2025 36 |
Location: | Herston: QIMR Berghofer MRI |
Description: | Lab Background Project Aims Approaches |
Expected outcomes and deliverables: | The applicant will learn how to use a high performance computing cluster to manipulate and analyse large genetic datasets. They will gain experience using coding languages such as R, Python and Bash on a Linux operating system. They will also learn how to interpret results of various statistical models they will perform and how to present their findings. The applicant will have the opportunity to engage with many of the researchers at QIMR Berghofer as well as present their results at the end of their project. There will be opportunity for the applicant to be involved in publication of their findings. |
Suitable for: | Background in Biomedical Science Basic understanding of genetics Interest in learning how to handle big data |
Primary Supervisor: | Associate Professor Tracey O'Mara, Tracy.OMara@qimrberghofer.edu.au The supervisor MUST be contacted by students prior to submission of an application. |
Metabolism of endometrial cancer
Project duration, hours of engagement | 6 weeks between 13 January and 21 February in 2025 36 |
Location: | Herston: QIMR Berghofer MRI |
Description: | Endometrial cancer is the most common gynaecologic malignancy in developed countries. While often caught early due to symptomatic bleeding, advanced or recurrent endometrial cancers have limited treatment options and poor outcomes. In contrast with many cancers, the incidence and mortality of endometrial cancer is steadily increasing, largely due to increasing rates of obesity, the strongest risk factor for this disease. However, the specific metabolic alterations, their functional roles in tumour progression, and potential as druggable targets remain poorly characterised. Endometrial cancers have a high degree of heterogeneity that is hard to mimic in 2D cell culture system. In our laboratory, we use endometrial organoids as a 3D model that recapitulate the tumour heterogeneity. Organoids can be derived from normal, pre-neoplastic and cancer endometrial tissue and they preserve genomic and phenotypic traits from the tissue of origin, making them a powerful system for disease modelling and therapeutic screening. Overall Aim: To obtain a better understanding of the metabolism of endometrial cancer in the case of association with patients with high-BMI. Approaches: Employing endometrial organoids from healthy and cancer patients as a model to study the effects of altered metabolism on the endometrial epithelium. To use molecular biology and imaging techniques to assess the effects of altered metabolism on healthy and cancer endometrial organoids. |
Expected outcomes and deliverables: | The applicant will learn cell culture techniques, including of 3D and patient derived models. They will also use be exposed to a range of molecular biology and imaging techniques. The applicant will have the opportunity to contribute to publications and also present their work at our lab meeting at the end of their placement. |
Suitable for: | Students that have completed molecular biology/biochemistry subjects. |
Primary Supervisor: | Associate Professor Tracey O'Mara, Tracy.OMara@qimrberghofer.edu.au The supervisor MUST be contacted by students prior to submission of an application. |
Genomics of mosquito populations in space and time – finding optimal control solutions
Project duration, hours of engagement | 6 weeks between 13 January and 21 February in 2025 36 |
Location: | Herston: QIMR Berghofer MRI |
Description: | Dengue and Zika fever are dangerous viral diseases transmitted by the mosquito Aedes aegypti. This mosquito is found around the global tropics, and different parts of the world face different control challenges. In Singapore, this mosquito is generally found in low numbers throughout a year, but there are still regular dengue outbreaks across the country. In a collaborative work with the Singapore’s Environmental Health Institute, we have obtained an unprecedented mosquito collection that spans multiple locations and time periods, which allows us to use genome-wide sequencing data to understand the changes that mosquito populations undergo under natural conditions (different seasons, extreme weather events) and man made suppression. The key objective is to use these vast genomic datasets and computer simulations to determine how effective existing interventions are and which emerging technologies could significantly improve the control of this dangerous mosquito. |
Expected outcomes and deliverables: | This project entails bioinformatics processing of NGS data and analyses of genome-wide SNP variation from thousands of individually-barcoded and geo-located mosquitoes. You will gain bioinformatics and “big data” management skills, ranging from scripting to streamline data QC, genome alignment, variant and genotype calling, to skills in population-genomic analyses and simulation modelling (in R, Python). You will also have an opportunity to learn molecular biology techniques such as customized Next Generation genome Sequencing. These skills in NGS data generation and analyses are highly transferable and marketable, enabling you to competently enter a competitive job market in biotechnology. |
Suitable for: | Suitable for students with interests and background in one or more areas: genetics and genomics (human or animal/plant), population ecology, big data management and analysis, epidemiology, computational biology (simulation modelling) |
Primary Supervisor: | Dr Gordana Rasic, gordana.rasic@qimrberghofer.edu.au The supervisor MUST be contacted by students prior to submission of an application. |
Sex-specific lethality and sterility for mosquito biocontrol
Project duration, hours of engagement | 6 weeks between 13 January and 21 February in 2025 36 |
Location: | Herston: QIMR Berghofer MRI |
Description: | Dangerous arboviruses such as dengue, Zika and chikungunya, that infect hundreds of millions of people and kill hundreds of thousands around the globe each year, are primarily transmitted by females of the mosquito Aedes aegypti. Due to rapidly evolving mosquito resistance to commonly used chemical insecticides that can also pose risks to human health and the environment, there is a critical need to find sustainable alternatives to chemical control of mosquito vectors. Alternative strategies such as genetics-based technologies are being increasingly considered. As only female mosquitoes bite and transmit arboviruses, technologies that exploit genes with female specific negative effects are preferable over other approaches. Yet, few such genes are known in Aedes mosquitoes. We have recently identified several genes that we hypothesize have sex specific lethality or sterility upon disruption. The key objective of this project is to functionally validate the usefulness of these gene candidates for a novel genetics-based biocontrol technology. |
Expected outcomes and deliverables: | This project covers a wide range of techniques in molecular biology, experimentation with insects and NGS data generation and analyses. A combination of these skills is very rare, and will ensure you are highly-competitive in the academic and industry job markets in Australia and abroad. |
Suitable for: | Suitable for students with interests and background in one or more domains of: gene expression analyses (RNA-seq, qRT-PCR, FISH, Northern Blot), genetic engineering, animal/plant rearing and experimentation, insect biology |
Primary Supervisor: | Dr Gordana Rasic, gordana.rasic@qimrberghofer.edu.au The supervisor MUST be contacted by students prior to submission of an application. |