Childhood cancer affects around 1000 children in Australia each year, however due to the low case numbers and the unique molecular profile, research into paediatric cancer has lagged that of adult cancer. For this reason, paediatric specific approaches are critically required to help improve survival rates and to reduce the long-term effects of treatment on kids with cancer.
The ACRF Child Cancer Liquid Biopsy Program extends the personalised medicine approach developed through the ZERO Childhood Cancer program[1] and leverages a dataset of approximately 400 patients’ samples to create disease specific approaches to uncover the genes responsible for disease in a minimally invasive way. The program takes a multi-modal, data driven approach to developing non-invasive liquid biopsy in paediatric cancer.
Here we describe aspects of our approach that focus on using advanced single-cell and genomic cytometry to the provide a minimally invasive way to assess circulating tumour cells (CTCs) and other cellular aspects of childhood cancer using liquid biopsy. Particularly how we are integrating technologies, including microfluidic devices for rapid cell enrichment and characterisation, ultra-low volume liquid dispenser and high-parameter cell sorter for cell isolation coupled with the latest error corrected Next Generation Sequencing approaches to devise a recipe to handle data layers involving CTCs or ctDNA. The preliminary results consist of three parts: 1) assessment of the impact of Streck BCT on blood samples regarding RNA content loss and epitope integrity; 2) development of one 27-colour and two 10-colour backbone immunophenotyping panels for in-depth characterisation of CTCs and immune cells; and 3) identification of CTCs in cerebrospinal fluid through single cell RNA sequencing. Together, these results highlight the importance of understanding pre analytical factors when implementing liquid biopsy into a personalised medicine.