Biospecimen and Pathology Core
- Ensures efficient and highly coordinated procurement, use, storage and analysis of clinically-, molecularly- and epidemiologically-annotated human biospecimens related to breast cancer
- Offers a unique collection of biospecimens with pre-analytic and analytic variables (derived questionnaires) from ethnically diverse populations of patients, including populations of African ancestry in the city of Chicago as well as Nigeria, Cameroon and Ugand
- Implemented a Universal Consent Form, that allows patients to select various levels of participation (questionnaires, use of blood, tissue, saliva, urine, stool, organoids, imaging, access to medical records) within our medical center and abroad
- Manages dedicated recruiters to obtain informed consent from patients. This effort resulted in remarkably high consent rates with less than 5% of patients approached declining participation
- Is fully integrated with other cores and uses ONCO-D to integrate its workflow and data with the Analytics and the Genomics and Informatics Cores for all SPORE projects.
- Prioritizes procurement of biospecimens from women with aggressive breast cancers, specifically women of African ancestry which enables establishment of a physiologically relevant ethnic/racial breast cancer model of patient derived organoids
- Collaborates with outstanding scientists and leaders in computational biology and data science, and provides high-quality services and access to unique ethnically diverse resources from Sub-Saharan Africa and the Southside of Chicago
- Serve all three SPORE translational projects, as well as the Developmental Research and Career Enhancement Programs, and all future studies and investigations conducted within the UChicago Interdisciplinary Breast Cancer SPORE
- Interacts closely with leaders of each of the research projects in the specification of aims and hypotheses, the delineation of endpoints, in performing sample size and power calculations, and in the selection and description of proposed statistical methods. The study designs and statistical analyses proposed for each of the projects are detailed as well as in the individual project write-ups.
- Assists study design and analysis, including methods for the acquisition, management, and integration of data collected in the SPORE, as well as interactions and cross-talk with the other main cores
Genomics & Informatics Core
- Serves all three SPORE translational projects and all future studies and investigations conducted within the UChicago Interdisciplinary Breast Cancer SPORE
- Leverages existing innovative institutional resources
- Amnis is a novel framework which will be used to monitor the entire data production process, as a laboratory information management and sample tracking system, and it will enable genomics results reporting and interpretation, as a tool for integrative data analysis.
- ONCO-D, established since the previously funded UChicago Breast Cancer SPORE, integrates data generated by different research groups and stored in disparate sources
- University of Chicago shared resources, including enterprise clinical data warehouse, that are specialized in collecting different human subject data.
- Builds informatics tools that leverage and unify data from these institutional resources
- Uses a series of pre-built bioinformatics pipelines for standard analysis to minimize development time and enable fast turnaround
- Staffed with expert bioinformaticians and computer scientists to develop custom analysis pipeline using parallelization library and resource allocation tools built in-house to optimize workflow