Urine based circulating tumor DNA analysis

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Urine is an underappreciated source for systemic circulating tumor DNA in patients with non-genitourinary cancers. Based on recent data suggesting that blood-based HPV DNA testing is useful for disease monitoring in HPV positive oropharynx cancer patients, we identified non-metastatic HPV positive oropharyngeal cancer patients as an excellent model system to examine the potential of urine-based transrenal DNA analysis. Our preliminary data suggests that our newly developed urine-based HPV test could have biomarker performances comparing favorably to blood-based HPV testing. The specific objectives of this application are to establish that urine is a suitable source for HPV DNA in non- metastatic HPV positive oropharynx cancer patients, and that at-home urine based molecular testing is feasible for these patients. Specifically, we will compare sensitivity and specificity of pre-therapy urine-based HPV testing to tissue gold standard testing in a cohort of newly diagnosed non-metastatic oropharyngeal cancer patients. Recurrence detection lead time of urine-based HPV testing will be compared to clinical routine care in the same cohort after curative intent treatment. Controls will include blood-based HPV testing, pharyngeal swab-based HPV testing and blood based personalized ctDNA sequencing panel testing. Additional control cohorts will include cervical and anal cancer patients as well as cancer-free patients with recently diagnosed oncogenic HPV infections. Using in vivo fluorescence imaging techniques, we will generate fundamental knowledge on renal handling of cell free DNA and determine the impact of chronic kidney disease and other patient, disease and iatrogenic factors on cell free DNA excretion.