Chief Data Scientist
BSc(hons) PhD
Dr Jimmy Breen is the Chief Data Scientist of the Telethon Kids Indigenous Genomics research group in Adelaide. His group is the primary curator of multi-omic datasets produced in the South Australian PROPHECY (Predicting Renal, Ophthalmic, and Heart Events in the Aboriginal Community) Cohort study, a project aimed at assessing the levels of complications in Aboriginal people with Diabetes.
During his 17-year career as a Bioinformatician, Dr Breen has led data analysis for projects in many areas of genomics research, including agricultural genomics, plant host-pathogen research, ancient DNA, epigenetics and population genomics, and more recently, reproductive and cancer biology. As a PhD student and Postdoctoral Research Fellow, he led the first whole-genome assembly analyses (published in Plant Cell) of the Bread Wheat genome, analysed oral microbiome data for >48,000-year-old Neandertal (published in Nature), and lead data analysis for a NIH-funded Human Placenta Project investigating Pregnancy Complications in South Australia.
Since 2019 he has led the development of a clinical sequencing pipeline funded through an ‘Australian Genomics’ Cancer Flagship project (led by Professor Deborah White) and continues to work with the SAHMRI Acute Lymphoblastic Leukemia (ALL) Research Group
on clinical sequencing projects. He is also a member of the Australia-wide Zero Children’s Cancer (ZCC) ZERO2 ALL/Lymphoma Expert Group which develops Precision Medicine protocols for children with high-risk and non-high-risk cancer.
His group’s research interests include:
- Building secure genomics data infrastructure for Indigenous Healthcare
- Investigating complex diseases using high-throughput genome sequencing
- Developing Precision Medicine approaches for clinical diagnosis
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Publications
September 2023
Circulating epigenomic biomarkers correspond with kidney disease susceptibility in high-risk populations with type 2 diabetes mellitus
To investigate epigenomic indices of diabetic kidney disease (DKD) susceptibility among high-risk populations with type 2 diabetes mellitus.
Published research Aboriginal Health Indigenous Genomics Diabetes (Type 2)July 2023Progesterone receptor mediates ovulatory transcription through RUNX transcription factor interactions and chromatin remodelling
Progesterone receptor (PGR) plays diverse roles in reproductive tissues and thus coordinates mammalian fertility. In the ovary, rapid acute induction of PGR is the key determinant of ovulation through transcriptional control of a unique set of genes that culminates in follicle rupture. However, the molecular mechanisms for this specialized PGR function in ovulation is poorly understood.
Published research Indigenous Genomics Gene ExpressionFebruary 2023DraculR: A Web-Based Application for In Silico Haemolysis Detection in High-Throughput microRNA Sequencing Data
The search for novel microRNA (miRNA) biomarkers in plasma is hampered by haemolysis, the lysis and subsequent release of red blood cell contents, including miRNAs, into surrounding fluid. The biomarker potential of miRNAs comes in part from their multicompartment origin and the long-lived nature of miRNA transcripts in plasma, giving researchers a functional window for tissues that are otherwise difficult or disadvantageous to sample.
Published research Genomics Indigenous GenomicsOctober 2022RaScALL: Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL)
RNA-sequencing (RNA-seq) efforts in acute lymphoblastic leukaemia have identified numerous prognostically significant genomic alterations which can guide diagnostic risk stratification and treatment choices when detected early.
Children's Cancers Published research Genomics Indigenous GenomicsSeptember 2022Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in southern Armenia
Panicum miliaceum L. was domesticated in northern China at least 7000 years ago and was subsequentially adopted in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, where vast quantities archaeobotanical material were well preserved via desiccation.
Published research Genomics Indigenous GenomicsJuly 2022Haemolysis Detection in MicroRNA-Seq from Clinical Plasma Samples
The abundance of cell-free microRNA (miRNA) has been measured in blood plasma and proposed as a source of novel, minimally invasive biomarkers for several diseases. Despite improvements in quantification methods, there is no consensus regarding how haemolysis affects plasma miRNA content.
Published researchJune 2022Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens
Plant DNA preserved in ancient specimens has recently gained importance as a tool in comparative genomics, allowing the investigation of evolutionary processes in plant genomes through time. However, recovering the genomic information contained in such specimens is challenging owing to the presence of secondary substances that limit DNA retrieval.
Published researchJune 20223DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk
Genome-wide association studies (GWAS) have enabled the discovery of single nucleotide polymorphisms (SNPs) that are significantly associated with many autoimmune diseases including type 1 diabetes (T1D). However, many of the identified variants lie in non-coding regions, limiting the identification of mechanisms that contribute to autoimmune disease progression.
Diabetes (Type 1) Published researchMay 2022Placental Transcription Profiling in 6–23 Weeks’ Gestation Reveals Differential Transcript Usage in Early Development
The human placenta is a rapidly developing transient organ that is key to pregnancy success. Early development of the conceptus occurs in a low oxygen environment before oxygenated maternal blood begins to flow into the placenta at ~10–12 weeks’ gestation. This process is likely to substantially affect overall placental gene expression. Transcript variability underlying gene expression has yet to be profiled.
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Education and Qualifications
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Awards/Honours
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Active Collaborations