Genome-wide Analysis and Enrichment of Chimeric DNA Fragments in Plasma for Early Detection of Cancer

PROJECT SUMMARY Early detection of cancer leads to improved prognosis and relative survival. Cell-free DNA (cfDNA) has been used to detect cancer earlier in previous studies. However, without tumor tissue available, these methods rely on screening for commonly mutated loci in cancer-associated genes, such as TP53, or examining genome- wide alterations in methylation or fragmentation. These approaches have limitations. Examining single nucleotide variants in cancer-associated genes can have lower sensitivity if the tumor does not harbor a hotspot mutation. For genome-wide alterations, the shifts noted in cfDNA fragmentation or methylation are not cancer-specific and generally a result of cellular disruption. Thus, there is a need for a signature that is both specific to cancer and sensitive enough to be assayed from cfDNA. Structural variants (SVs) are a potential biomarker for early detection. SVs are the result of errors in DNA damage repair wherein there is an aberrant joining of two distant genomic loci, which results in a derivative chimeric DNA fragment with an identifiable breakpoint. Importantly, SVs occur in most cancer types and are less likely to be PCR-derived false positives compared to single nucleotide variants. However, tailoring a cfDNA assay to SVs is not without challenges. Identifying specific SVs with high confidence and precision is informatically difficult and requires high sequencing depth (>50x). Here, we hypothesize that genome-wide locus-agnostic detection and quantification of chimeric DNA molecules can be utilized as a multi-cancer biomarker for early detection. Chimeric molecules (CMs) contain the breakpoint of the SV they are derived from. This project seeks to develop laboratory and computational methods to detect CMs in plasma DNA, identify sources of technical noise that affect CM detection, and evaluate CMs as quantitative cancer biomarker (Aim 1). Furthermore, we plan to develop laboratory methods to enrich rare chimeric molecules from abundant non-chimeric DNA fragments to improve sensitivity for cancer detection and reduce associated sequencing costs (Aim 2). Together, these aims will lead to the development of an assay for screening and earlier detection across multiple cancer types. This will be accomplished in conjunction with the University of Wisconsin–Madison’s institutional support and robust academic resources. This project will provide the applicant with a comprehensive training program that includes personalized mentorship, avenues for presenting research findings, and opportunities for career development. Through these combined efforts, the applicant will evolve into an independent, proficient translational researcher who will specialize in biomarker development for diagnostic advancements.