PROJECT SUMMARY Ovarian cancer is the deadliest gynecological cancer, in part because there is no widely used screening test and 80% of tumors are diagnosed at a late stage. Though ovarian cancer screening has the poten>al to diagnose tumors at early stages when pa>ent outcomes are far be?er (90% survival for stage I cancer vs. <20% for stage III/IV), recent screening trials of protein biomarkers have failed to show a mortality benefit. This has highlighted three main challenges in ovarian cancer screening: (1) Avoiding false posi>ve results leading to unnecessary procedures in a disease with low popula>on prevalence, (2) Achieving high enough sensi>vity to be a clinically useful test, and (3) Ensuring accessibility and pa>ent compliance with screening. Much of my early PhD work, and work in my mentor’s lab, has pioneered high performance blood tests that use cell-free DNA fragmenta>on pa?erns to detect cancer. These fragmentomic assays can detect subtle changes to DNA shed from tumor cells even using low-coverage sequencing of <1mL of blood, and their non-invasive nature makes them accessible and appealing to pa>ents. Given the cri7cal clinical need, the overarching goal of my work is to advance our understanding of ovarian tumorigenesis and develop an accessible, high-performance liquid biopsy for ovarian cancer screening. A limita>on of current liquid biopsies is that they don’t incorporate informa>on from the ~50% of the genome comprising repeat elements, which have long been implicated in carcinogenesis but have been difficult to study due to incomplete genome references and technical genome alignment challenges. In preliminary work, I show a novel approach I developed that allows the study of repeat landscapes in short-read sequencing and that has iden>fied over 800 new elements not previously implicated in cancer. The ability to use this approach in short-read sequencing opens the door to studying repeat landscapes in cell-free DNA, where most fragments are 150-180bp in length. I propose three specific aims: In Aim 1, I will expand this approach to develop novel bioinforma>cs approaches enabling the study of repeat elements in cell-free DNA. In Aim 2, I will develop and test sensi>ve and specific cell-free DNA liquid biopsies for ovarian cancer. In Aim 3, I will characterize genomic changes to repeat elements during ovarian tumorigenesis, from normal >ssue to pre-cancerous lesion to tumor. Successful execu7on of these aims has the poten7al to advance our understanding of the role of the so-called “dark genome” in ovarian tumorigenesis, change the paradigm for liquid biopsies by illumina7ng cancer-related changes to repeat elements, and apply these discoveries to a screening technology for ovarian cancer. This work may also serve as a basis for future pan-cancer screening methods. The proposed work will provide me with outstanding mentorship and scien>fic training in basic and transla>onal science and help me advance my career as a future physician-scien>st and independent inves>gator.

PROJECT NARRATIVE Ovarian cancer is the deadliest gynecologic cancer with 80% of tumors diagnosed at a late stage though there is dras9cally higher survival for early-stage disease. This study proposes to develop novel methodologies to study the >50% of the genome comprising repeat elements in the context of ovarian tumor evolu9on and cell-free DNA, and to use genome-wide approaches to enable a non-invasive screening technology for ovarian cancer. Development of accessible screening and characteriza9on techniques for ovarian cancer has the poten9al to revolu9onize clinical prac9ce for this devasta9ng disease.