Swarbrick Lab

We are leaders in applying cellular genomics to oncology. Single-cell and spatial omics are revolutionising our understanding of cell biology, immunology and genomics, and promise to fuel a new generation of biological insights and treatments for cancer.

Together with our clinical collaborators, we have an active fresh tissue collection program, building unique cohorts of tissue sampled throughout disease progression:

• Early disease, both untreated and undergoing neoadjuvant therapy
• Metastatic disease, sampled at relapse and during adjuvant therapy
• At death from cancer, we collect multiple metastatic deposits from consenting participants through our Monarch autopsy program.

We apply advanced methods to permit high-plex multiomic single-cell and tissue analysis to these cohorts, measuring whole transcriptomes, hundreds of protein markers and targeted genome sequences from thousands of cells per sample. These studies reveal deep insights into the mechanisms of disease, along with new candidate biomarkers and drug targets.

Novel biomarkers or treatment strategies undergo rigorous preclinical testing in mouse- and patient-derived models of disease. We lead one of Australia’s largest patient-derived xenograft programs, with more than 70 models of disease. The most promising candidates proceed to early phase clinical trials. For instance, as exemplified in our paper in Nature Communications, we used single-cell genomics to discover the mechanism of Hedgehog signalling in breast cancer, validate the efficacy of anti-Hedgehog drugs (smoothened inhibitors) in PDX models and then conduct a first-of-kind phase 1 clinical trial.

Data and code sharing

We make all data publicly available following its publication.

Processed data for each of our studies is generally available on GEO or Zenodo, as indicated in each study. Also, scRNA-seq data is generally available from the Broad Institute's Single Cell Portal together with relevant meta data and, in some cases, multimodal data such as CITE-seq.

Raw genomic and transcriptomic data is stored at the European Genome Archive. To comply with requirements of our funding agency, ethics committee and the EGA, we need to set up a data access agreement between our organisations before providing raw data. This may require legal review by your institution. To access processed data from our studies, or apply for access to raw data, please see the additional information available at: swarbricklab.com/data-and-code-access.

Code for lab publications is hosted on GitHub. These repositories also include annotations and other metadata. Please use GitHub ‘issues’ to raise questions about code or data files referred to in the code.

For additional queries regarding data access, please contact John Reeves at j.reeves@garvan.org.au.