Core B: Biospecimen and Pathology Core

Project Summar/Abstract The Biospecimen/Pathology Core, Core B, will provide outstanding leadership, expertise in biospecimen sciences, pathology, and technology to maximize biospecimen analyses and data sharing. Experts in brain, breast, and prostate pathology will ensure well-annotated biospecimens are optimally acquired, preserved, distributed, and analyzed. This includes acquisition of prospective and retrospective biospecimens from properly-consented patients being treated at the University of California San Francisco (UCSF) Hospitals and Clinics and at partnering institutions and seeing that these patients’ confidentiality is protected and that patient identifiers (protected health information or PHI) is never released to researchers. Leveraging the expertise and resources at UCSF and University of California Davis, including the UCSF Brain Tumor SPORE, UCSF Prostate SPORE (Prostate Cancer Tissue Bank/PCTB), and the Breast Oncology Program and ISPY2, the Biospecimen/Pathology Core for the UCSF SPORE will pursue the following Aims: Aim 1: To provide pathology and biospecimen expertise to ensure optimal sample quality and extraction of maximal, high-quality data from each biospecimen. This includes performing quality control assays on archived biospecimens and extraction of appropriate quantitative and semi-quantitative parameters from whole slide images. Aim 2: To provide state-of-the-art tissue-based analytical techniques as needed by the Projects, including spatial transcriptomics and proteomics, mass cytometry (CyTOF), imaging mass cytometry (IMC), multiplexed ion beam imaging (MIBI), multiplexed in situ hybridization and immunoassays, and quantitative whole slide image analysis. In addition, the Core will provide routine procedures, including tissue microarray construction and DNA/RNA extraction. Aim 3: To acquire, preserve, and store high-quality patient biospecimens that are fully annotated with respect to preanalytical parameters, demographics, and clinical pathology and molecular data. This includes tumor tissue and blood components. Aim 4: To provide consistent oversight and tracking of biospecimens, their acquisition parameters, and their molecular characterization to ensure stringent compliance with Project needs and with regulations governing informed consent and patient confidentiality. Impact. These aims are accomplished by the efforts of a dedicated team of pathologists and lab technologists from the Biospecimen Core. High quality, well-annotated biospecimens are essential to the success of all SPORE projects.