Tracking gene expression changes in cancer using simple blood tests

Hello everyone! We are excited to host our July event online. Looking forward to seeing you all!

Dineika is a senior postdoctoral fellow at the Peter MacCallum Cancer Centre where she leads a bioinformatics team within the Molecular Biomarkers and Translational Genomics lab. Her current research revolves around circulating tumour DNA which can be captured from the bloodstream of cancer patients. These are fragmented pieces of DNA released from tumour cells which carry mutations, methylation and other alterations of the cancer genome. Therefore, a simple blood test gives us a window to study the cancer, offering a non-invasive alternative to often painful tumour biopsies. Dineika develops innovative methods to analyse circulating tumour DNA and use it as a non-invasive biomarker to detect the presence of cancer and track how tumours evolve and become resistant to therapy. Her ongoing passion is to translate these methodologies to the clinic under the mantra of ‘bench to bedside’.

Circulating tumour DNA in the blood of cancer patients can be used to investigate somatic alterations such as mutations and copy number events of the cancer genome as well as epigenomic signatures such as methylation. However, the assays in clinical use cannot capture tumour gene expression even though we now know that tumours escape cancer therapy by changing their transcriptome as well as their genome. I will present a new method we have developed named SNIPER (Serial Non-Invasive Plasma gene Expression Reconstruction) that can be applied to serial blood tests to study how tumours change their gene expression as they evolve. I will discuss results from applying SNIPER to 180 blood samples across Breast cancer, Melanoma, Lung cancer and blood cancers and show how we have adapted tools such as limma and gProfiler for this non-standard data type.