Cancer Institute Biorepository (CIB)
The Cancer Institutional Biorepository (CIB) is a password-protected, HIPAA-compliant, custom database under the Electronic Research Application Portal Rapid Database Generator (eRAP RDG) that is a 21 CFR Part 11 compliant web-based interactive tool for data entry and reporting.
CIB, in combination with Freezerworks, supports the biorepository to annotate, manage, and search donor and sample (tissue and fluid) information, consent status, clinical annotations, and sample tracking. CIB is integrated with the Mount Sinai Data Warehouse, specimen management system (Freezerworks), anatomic pathology Information System (PowerPath) and e-consent database. The CIB/eRAP BRP disease/normal database contains both de-identified and patient information linked to our BRP ID# and a Freezerworks ID.
What is Annotated in CIB:
For donors: we track demographic and consent information linked to MRN , DOB, Name, and sample summary
For samples: we track sample information, Accession #, Disease group, Anatomical location, ischemia time, diagnosis as well as parts of the pathology report
For slides: we track tissue annotations based on histopathologic criteria including tumor content (epithelial vs stroma), non-tumor stroma, inflammatory infiltrates, necrosis, normal adjacent tissue, and autolysis
For aliquots: we track available sample derivatives for tissue (OCT, NUNC,FFPE, slides…) or fluids (urine, blood, blood derivatives such as plasma or serum).
Public Data Sets (Unrestricted)
- 1,000 Genomes Project
- Genome Aggregation Database (gnomAD)
- Genome-wide Association Study (GWAS) Summary Stats
- Genotype-Tissue Expression (GTEx) Project
- Linkage Disequilibrium (LD) Score Regression Data
- Reference Genome
- The Cancer Genome Atlas (TCGA)
- UK Biobank (UKBB)-Linkage Disequilibrium (LD)