Simultaneous cell-free whole genome and epigenome sequencing to advance precision medicine in breast cancer

Blood tests to help personalize metastatic breast cancer care 

Biopsies are an important part of breast cancer care. They help determine the subtype of a patient’s tumour and guide decisions about the most effective treatment. But for people with metastatic breast cancer—where the disease has spread throughout the body—tissue biopsies can be risky, painful, or simply not feasible. 

To help address this challenge, Sasha Main (Princess Margaret Cancer Centre) will use new funding provided by a 2025 MOHCCN Health Informatics & Data Science Award to advance blood-based alternatives known as liquid biopsies. 

“When cancer cells die, they release DNA into the bloodstream, known as circulating tumour DNA,” explains Main. “Liquid biopsies let us analyze this DNA to look for genetic and epigenetic changes that could tell us more about an individual’s breast cancer, including how it behaves and how it might respond to treatment.” 

To advance this work, Main will contribute new data and develop computational tools, while also leveraging existing samples sequenced through the MOHCCN REFLECT cohort, part of the Network’s effort to create Canada’s largest and most complete cancer case resource. Using a new technology called 6-base sequencing, she will analyze both genetic and epigenetic changes in circulating tumour DNA to identify patterns that reveal breast cancer subtypes and predict treatment response.  

“This research could help pave the way for personalized treatment plans that don’t require invasive biopsies, while also expanding our understanding of treatment resistance,” she says. “Importantly, the computational tools and results from this work will be shared openly to support future research, providing a basis for further blood test studies to improve patient care.” 

Funding envelope 

As part of the Health Informatics and Data Science Award, Main will receive $40k over the next year from the Network, which is matched by her host institution for a total envelope of $80k.  

Main’s mentor, Dr. David Cescon, sees great promise in the work. 
 
“Sasha is an outstanding trainee who has led this work with clarity, drive, and a rare ability to bridge data science and clinical care. In close collaboration with a multidisciplinary team, she is applying new liquid biopsy technologies to uncover biological insights into treatment response and resistance.”