Garvan Summer Scholarship Program 2024/25

The Summer Scholarship Program, provides an exceptional opportunity for currently enrolled undergraduate students to engage in research projects during the summer of 2024/2025.

This program is designed to immerse highly talented undergraduates, particularly those in Science or related disciplines, in the research process. It aims to enrich your educational journey and inspire a deeper interest in research or related fields.

Participants will gain invaluable experience by working alongside our esteemed supervisors on meaningful research projects, providing a fantastic insight into the research process and helping you determine if a research career is right for you.

The program spans 8 weeks, offering 11 scholarship positions. Each scholarship is valued up to $5,000, with funding allocated at a rate of $625 per week based on the program's duration.

We encourage you to seize this opportunity to enhance your academic and professional development.

WHAT YOU WILL DO

Our range of projects for the Summer of 2024/2025:
Pan-Cancer analysis of fetal-like cells in tumours at spatial resolution

We discovered that fetal-like cells in liver cancer play an essential role in immune suppression (Sharma et al., Cell 2020) and impact clinical outcomes in patients treated with immunotherapy (Li et al., Nature Cancer 2024). However, whether such cells exist in other cancers and play any role in their response to therapy remains unknown. This project utilises pan-cancer spatial transcriptomic data to investigate which other tumours exhibit fetal-like properties in the microenvironment.
- What you will learn_ On this project you will specifically learn how to explore spatial transcriptomic data to identify fetal-like cells in the tumour microenvironment. This project will also allow fellows to work on the interphase of developmental biology, cancer genomics and computational science.
- Prerequisites_ R, Python

Decoding the epigenetic principles of early embryonic development.
During embryonic development, gene expression dynamics are tightly controlled by the epigenome. This includes cytosine DNA methylation, DNA wrapping around histone-containing nucleosomes, and post-translational histone modifications. These epigenetic marks function to activate or repress gene transcription, ultimately enabling the development and regulation of diverse cell and tissue types. Using the latest single-cell epigenome and transcriptome sequencing technologies, this project will investigate the fundamental epigenetic mechanisms driving the complex organization of tissues in a developing embryo. These findings will provide a necessary foundation for exploring how aberrant changes to the epigenome drive congenital disorders associated with improper organ development and positioning, such as heterotaxy syndrome and dextrocardia.
- What you will learn _This project would suit a motivated individual familiar with the basic principles of gene expression and next-generation sequencing, who has a keen interest in analysing data from cutting-edge sequencing technologies.
- Prerequisites _R, Unix shell

Evaluation and finetuning of phenotype concept recognition tools
- What you will learn_ In this project, you will use this dataset to evaluate the performance of current state-of-the-art HPO phenotype concept recognition tools. If time permits, we can also use this dataset to finetune an existing tool.
- Prerequisites _Python (required), familiarity with NLP and LLMs (helpful)

Building a polygenic risk prediction pipeline for whole genome sequence data
- and low-coverage WGS, long-read WGS, genotyping array, and a blended genome-exome approach).
- Prerequisites _Unix, Python/R

Developing a Novel Diagnostic Method for the Muscle Disease FSHD Using Long-Read Sequencing
Facioscapulohumeral muscular dystrophy (FSHD) is a hereditary disorder causing progressive muscle weakness. Current diagnostic methods are slow, complex, and often yield inconclusive results. This project aims to develop a streamlined diagnostic test for FSHD using Oxford Nanopore Technologies (ONT) long-read sequencing, which is the only technology equipped to read through the challenging D4Z4 repeat region on chromosome 4. In addition to genotyping key regions, ONT sequencing allows simultaneous profiling of DNA methylation, a critical feature for diagnosing FSHD. By integrating both genetic and epigenetic markers, we will design a single, comprehensive test that improves accuracy, reduces testing time, and resolves unsolved cases. The student will implement a bioinformatics pipeline for analysing both genetic and epigenetic data, helping to optimise the test and validate it using clinical samples.
- What you will learn_
- Prerequisites _GitHub for hosting the comparison and automation with GitHub actions Bash, Python, and R for running tools and visualisation Enthusiasm for genomics data analysis

Understanding the heterogeneity of breast cancer
Breast cancer is known to be geneticall