Pan-cancer AI-driven Cell-free DNA Sequencing Platform for Reducing Disparities in Early Diagnosis, Molecular Characterization and Surveillance of Multiple Cancer Types
This project aims to address disparities in cancer outcomes by investigating the biology of cancers and the factors that contribute to aggressive cancers or lead to the development of treatment resistance. Researchers will introduce a minimally invasive liquid biopsy testing approach, which is essentially a blood draw, and utilize a new type of testing called fragmentomics to gather more information about a patient’s tumor and patterns of potential treatment resistance or cancer recurrence.
Collaborators: Amy Taylor, MD, assistant professor, Department of Medicine
The Challenge
Cancer remains a leading cause of death both nationally and in Wisconsin, and persistent disparities continue to limit equitable outcomes. While overall cancer incidence and mortality have declined, significant gaps remain by race, ethnicity, socioeconomic status and geography. In Wisconsin, African American patients experience higher incidence and mortality rates for colorectal cancer, along with some of the largest Black-white disparities in lung and breast cancer mortality in the country. At the same time, individuals living in rural areas are more likely to be diagnosed at later stages and have worse overall survival, reflecting ongoing barriers to timely and effective care.
These disparities are compounded by limitations in current cancer diagnostic and monitoring approaches. Traditional methods rely heavily on imaging and tissue biopsies, which can be invasive, costly and difficult to repeat over time. Many patients, particularly those in medically underserved or rural areas, lack access to advanced imaging technologies and specialized molecular testing such as next generation sequencing. Even when biopsies are obtained, they may not fully capture the complexity of metastatic disease, limiting the ability to guide treatment decisions effectively.
Together, these challenges highlight the need for more accessible, scalable and less invasive approaches to cancer detection, characterization and monitoring. Without innovations that can overcome infrastructure and access barriers, existing disparities in cancer outcomes are likely to persist or worsen.
Project Goals
The address these gaps, this project seeks to advance more equitable and scalable solutions for cancer diagnosis and care. The specific project goals are to:
Evaluate barriers to molecular testing in patients with newly diagnosed cancer
Validate blood based cfDNA fragmentomics as a method to improve equity in molecular testing
Implement novel cancer surveillance tools with cfDNA fragmentomics to identify recurrence and treatment resistance to reduce cancer disparities
Progress Update
This project has made progress in advancing both the scientific and community-engaged components of the work. Over the past year, the team has strengthened partnerships, expanded research capacity and continued to refine innovative approaches to cancer detection and monitoring.
A key area of progress has been community engagement. The team has worked closely with the UW Carbone Cancer Center African American Community Advocacy Board through ongoing meetings and collaborative discussions. These sessions have helped identify important barriers to participation in biospecimen research, including how to address historical mistrust in biomedical research and how to better support community members throughout the research process. These insights are directly informing the design of upcoming focus groups and patient-centered engagement strategies.
In parallel, the team has advanced the equity-focused aims of the project by developing and submitting a detailed IRB protocol for qualitative research. Plans are in place to launch focus groups that will gather direct feedback from patients on their understanding of and concerns about biospecimen donation. To support inclusive participation, recruitment materials have been developed using plain language to ensure accessibility across diverse literacy levels.
The project has also expanded its collaborative network, adding new partnerships with the Karmanos Cancer Center and the Moffitt Cancer Center. These partnerships broaden access to patient populations from medically underserved communities and support the long-term goal of scaling this work across institutions. Initial biospecimen samples have already been received from these partners, with analysis currently underway.
On the scientific front, significant progress has been made in refining the cell-free DNA (cfDNA) fragmentomics platform. The team successfully developed and published an updated analytical approach, demonstrating strong performance in distinguishing cancer types and subtypes using advanced machine learning methods. Importantly, these methods show promise for translation into clinical settings, including compatibility with existing commercial testing panels. Despite some delays related to regulatory approvals and staffing transitions, the team has continued to build momentum. Additional biospecimen samples have been collected; new staff have been onboarded and trained; and enhanced computing infrastructure has been implemented to support faster data analysis.
