The Abramson Cancer Center BioRepository (ABR) is a shared core laboratory comprised of four integrated components that together enable the collection of tumor and normal tissue samples from surgical resections and radiology guided biopsy (supporting clinical trials), blood collections (buffy coats, serum and plasma), and liquid biopsy (ctDNA, CTC, soluble proteins and extra-cellular vesicles). This integrated Shared Resource leverages uniformity of quality across a breadth of biosamples and enhanced efficiencies gained through use of a universal consent. The tumor tissue, blood collection and liquid biopsy material collections are supported by a new prospective universal consent allowing for collection of blood and tissue (at time of surgery), patient re-contact, "omics" study of the collected biosamples, and linkage to electronic health records for outcome-related translational research.
ABR combines the services formerly provided by two Shared Resources and an institutional core; namely, Tumor Tissue and Banking (TTAB; formerly institutional); Liquid Biopsy (formerly the Circulating Tumor Material Developing Shared Resource); and Radiology Biopsy services (formerly part of the Cancer Imaging Shared Resource). The ABR was developed in response to the needs of ACC members across the basic, clinical, and population science Programs for increased access to tissue and blood products to accelerate translational and clinical research. This new Shared Resource, directed by Dr. Michael Feldman (Vice Chair, Department of Pathology and Laboratory Medicine [PLM]), provides efficiencies of consenting, sample collection and processing under a single unified consent at the time of patient registration for population level collections. Blood samples are collected at the time of a scheduled clinical blood draw to avoid unnecessary venipuncture. For patients undergoing tumor resection or non-tumor surgeries, capturing consent in the EHR allows tissue collection workflows to be linked to operating room schedules. The Radiology Biopsy Service performs all image-guided biopsies associated with clinical trials. In turn they work with the ABR tissue processing staff to make sure that both clinical and research pathology processing needs are simultaneously met. A "work list" of patients is generated daily for ABR technicians in HUP pathology collection areas to interface with HUP Anatomic pathology teams to allow for both population-level and specialized tissue collection without compromising clinical care. Circulating tumor material processing is a critical component of the ABR, and both population-level and specialized services are provided. By combining these services and specimen management, we developed a more cost-effective and simplified workflow for biosample collection broadly across the ACC rather than through disease-focused collection teams. This new process facilitates access to a much wider variety and number of biospecimens for ACC members, addressing the changing scientific needs of ACC membership and demand for biosamples.
- Collection and distribution of biosamples
- Histology – cutting FFPE or OCT embedded samples as slides or rolls
- Histopathology quality control of material with pathologist review
- Biosample shipping
- Collection, banking and distribution of plasma, serum or DNA from buffy coats
- DNA extraction from buffy coats
- Viable PBMC collection and cryopreservation, in collaboration with the Human Immunology Core (HIC) based on individual research protocol needs
Liquid biopsy services:
- Extraction of cell-free DNA from plasma, measure concentration
- ctDNA droplet digital PCR (ddPCR)
- Extra-cellular vesicle enrichment and molecular analysis
- Circulating tumor cell (CTC) collection and analysis
Radiology biopsy service:
- Medical and technical consultation with investigator to define biopsy protocol and pathology tissue collection
- Procurement of tissue and integration with tissue banking team for sample cryopreservation. Often, with the same clinical operators, samples needed for both research and routine clinical needs (if any) may be obtained during the same procedure.
Technologies and Major Equipment
The Liquid Biopsy Service offers services on several diverse platforms. CTCs are enriched, enumerated, and phenotyped on the CellSearch platform. QIASymphony uses plasma as input for extraction of cell-free DNA. The Raindance and Bio-Rad ddPCR platforms can be used for high-sensitivity ctDNA-based mutation detection. Dynex D2 provides semi-automated ELISA analysis of soluble proteins from plasma or serum. A dedicated clean room environment is used for molecular analysis of sparse input materials such as from CTCs or ctDNA. ABR also offers histopathology embedding, IHC services, microtomy, and cryomicrotome through use of the PLM pathology tissue analytic core.