Biomarker Developmental Laboratory (BDL)

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Project Summary/Abstract – Biomarker Developmental Laboratory The Biomarker Developmental Laboratory for the proposed BCC will develop and validate genomic and proteomic assays for the detection of ovarian cancer in uterine lavage samples. The genomic assays will analyze the cellular pellet from uterine lavage for genome wide hypomethylation. This genome-wide approach increases the clinical sensitivity of the biospecimen sampling. Machine learning methods will be applied to optimize the aggregation of the methylation signal across the genome accounting for the unknown fraction of sample derived from ovarian/fallopian tube cancer cells and the remaining fraction mostly comprised of uterine epithelial cells. Proteomic analysis of the uterine lavage fluid using proximity extension assays (PEAs) have a superior analytical sensitivity to mass spectrometry. Analysis of samples from a training cohort of cases and controls by PEA will identify upregulated proteins from the tumor and its microenvironment. Supervised biostatistical classifiers will define an optimal panel of up to 21 PEA biomarker proteins. The optimal panel will undergo Custom Panel development for absolute quantitation under the direction of the BRL (biomarker reference laboratory). The training samples will be re-assayed, and a classifier developed combining the custom panel proteins and the aggregated methylation signal to form a combined classifier. The combined classifier will be tested in uterine lavage samples from an independent validation cohort. If the classifier is validated, the classifier will be applied to the cervical swabs – same biospecimen as a Pap smear – to determine its performance in a readily accessible and patient acceptable sample.