TYPE OF SUPPORT
Research Background
Recent developments in spatial omics technologies allow interrogation of gene expression and protein abundance down to the single cell and subcellular level, localized across tissue. In turn this allows researchers to interrogate hypotheses that draw on transcriptomic (or proteomic) information in a spatial context. e.g examination of differences of celltype composition or gene expression across the tumour microenvironment, or regional effects of drug treatment.
Furthermore, these techs are rapidly improving and developing, covering more genes, generating more data, and enabling more advanced analysis techniques. A cosMX SMI machine (bruker) was installed at Griffith University's Gold Coast campus in late 2023, opening the door to such spatial transcriptomics experiments at Griffith and beyond.
The team responsible, lead by Nic West and Amanda Cox, engages in both service provision (Griffith centre for genomics) and research (Mucosal immunology research group).
With the new tech in house, they were presented with the need to establish workflows for quality control and service delivery, and the opportunity to apply these novel technologies and techniques in their own research and collaborations.
QCIF Role
QCIF has engaged with the group with a 0.6FTE bioinformatician for some years now. This provides not only on-demand bioinformatics expertise, but access to the entire QCIF-hosted skillset – including statisticians, software developers and AI experts.
This embedded model facilitates a deep understanding of the focus and priorities of the group – even one with a dual focus on research and service provision. This ensures flexibility for practical contributions and productive analysis centered on research needs within operational context.
Tasks include:
Involvement in development of cosMX QC, data delivery and and data management SOP (Standard Operating Procedures )
Spatial omics analyses for internal and collaborative research projects, both academic and commercial
Consultation with clients and collaborators on experimental design
Consultation with clients and collaborators on analysis
Consultation and upskilling with in-house bioinformatician
Contribution to papers, conferences
Research Outcome & Impact
Established data pipelines accessible to team members
Templates for QC and data deliveray of simple projects
Extensive data analysis in several collaborations, both academic and commerical.
Guidance for clients in the design and analysis stage to facilitate their analyses
Our long-term collaboration with this group has built a strong foundation of trust and shared expertise. As we look ahead, we're excited by the possibilities to deepen our impact, leveraging embedded bioinformatics and QCIF’s broader capabilities to support innovative research and expand collaborative opportunities.
Dr Sarah Williams, Senior Bioinformatician, QCIF
