The BioRepository & Precision Pathology Center (BRPC) (https://brpc.duke.edu) has facilitated biospecimen collection and processing for over 10,000 Duke patients participating in clinical trials. In addition, the Duke BRPC has obtained broad consent from over 7,000 patients for blood and leftover cancer tissue donation to research. Through the BRPC, researchers can access over 60,000 dedicated research specimens and tens of millions of leftover pathology tissue and blood. The BRPC has been College of American Pathologists (CAP)-accredited since 2013 and has an excellent working relationship with the CAP-accredited DUHS Clinical and Anatomic Pathology Laboratories. This partnership supports all forms of biobanking with simultaneous protection of patient care. Tissue biospecimens with specific genomic variants can be identified using a dedicated database of all clinical next generation sequencing results. If biospecimens outside of Duke’s vast collections are required, BRPC also serves as the Southern Division of the NCI’s Cooperative Human Tissue Network and can facilitate access to research biospecimens from the national network.
The BRPC is housed in the Duke Clinics building on the main Duke biomedical campus and occupies 5,839 ft2 of floor space in the Department of Pathology. This area provides five offices and space for biorepository specimen processing, clinical trial specimen processing, specialized tissue research services, and biospecimen storage at room temperature, -80C and -150C. Biospecimen procurement and preliminary processing often occurs at the point of care (biopsy suite, surgical pathology laboratory, phlebotomy station, autopsy suite) within DUHS and/or CLIA-certified Clinical Laboratory and Pathology Department space. Thus, the BRPC team works in partnership with the Duke Clinical Laboratories to obtain fresh, frozen, and formalin-fixed paraffin-embedded human tissue and fluid samples from Duke patients. The BRPC obtains broad consent from patients for blood and tissue sample donation and procures, processes and banks both liquid and tissue biospecimens, supports Duke’s “living biobank” by providing tissue for creation of patient-derived xenografts and primary tumor cell culture and organoid cultures, and implements bioinformatic and clinical strategies for precise sample and model annotation. The BRPC houses 16 computer workstations connected to the electronic health record as well as the state-of-the-art biobanking system LabVantage (branded CoreResearch@Duke). Two-dimensional barcode label printers, paraffin block printers, and barcode readers support this CAP-accredited biorepository. The BRPC was the 20th in the United States to receive prestigious College of American Pathologists’ (CAP) Biorepository Accreditation in 2013. The BRPC is also home to the Research Immunohistology Laboratory. With the Research Immunohistology Laboratory, BRPC offers an entire spectrum of tissue technologies to investigators: histology, immunohistochemistry, in situ hybridization, tissue microarray, laser capture microdissection, whole slide imaging, image analysis, and spatial profiling/spatial transcriptomics.
Within the BRPC laboratory space there are reagents and standard laboratory equipment for tissue and liquid biospecimen processing, nucleic acid extraction, and quality assurance including a gel documentation system and a NanoDrop® ND-1000. The laboratory also has a BioAnalyzer station for nucleic acid QC. There is an Arcturus XL laser capture microdissecting platform as well as a TMA Master semi-automated tissue microarrayer. Biospecimen storage is supported by room temperature racks and drawers (FFPE blocks and glass slides), eight -80C freezers, and one liquid nitrogen storage unit. All cryogenic storage is monitored under the standard university alarm system but is also under constant temperature surveillance using Sensaphone Wireless temperature monitoring equipment. Histology is supported by multiple paraffin tissue processors, embedding stations, microtomes, cryostats, and a slide staining station, as well as an Olympus BX46 trinocular brightfield microscope equipped with a 64 megapixel, shifting-pixel digital camera. Multiplexed immunohistochemical and immunofluorescent analysis are conducted using three different platforms: Leica autostainer, BioCare, and a Ventana Discovery Benchmark instrument. The laboratory performs whole slide imaging on the Leica Aperio AT2 and Leica GT450 instruments, stores resulting images on a dedicated PathCore server, and conducts image analysis using Visiopharm’s Oncotopix Analysis Platform. The laboratory also houses a NanoString GeoMx Digital Spatial Profiler instrument, which detects and quantifies multiplexed protein and RNA targets with spatial resolution on slides from formalin fixed, paraffin embedded (FFPE) tissues or frozen tissues.
BRPC EQUIPMENT
Within the BRPC laboratory space there are reagents and standard laboratory equipment for tissue and liquid biospecimen processing, nucleic acid extraction, and quality assurance including a gel documentation system and a NanoDrop® ND-1000. The laboratory also has a BioAnalyzer station for nucleic acid QC. Histology is supported by multiple paraffin tissue processors, embedding stations, microtomes, cryostats, and a slide staining station, as well as an Olympus BX46 trinocular brightfield microscope equipped with a 64 megapixel, shifting-pixel digital camera. Multiplexed immunohistochemical and immunofluorescent analysis are conducted using three different platforms: Leica autostainer, BioCare, and a Ventana Discovery Benchmark instrument. The laboratory performs whole slide imaging on the Leica Aperio AT2 instrument, stores resulting images on a dedicated PathCore server, and conducts image analysis using Visiopharm’s Oncotopix Analysis Platform. There is an Arcturus XL laser capture microdissecting platform as well as a TMAMaster semi-automated tissue microarrayer. Biospecimen storage is supported by room temperature racks and drawers (FFPE blocks and glass slides), eight -80C freezers, and one liquid nitrogen storage unit. All cryogenic storage is monitored under the standard university alarm system but is also under constant temperature surveillance using Sensaphone Wireless temperature monitoring equipment. There is also a NanoString GeoMx Digital Spatial Profiler for highly multiplexed spatial profiling of protein and RNA targets.
BRPC EQUIPMENT
Duke South Hospital Clinics (Department of Pathology)
- 3- Twin Guard® Series Panasonic –86°C Upright Ultra-Low Temperature Freezers
- 6- Revco Ultima II –86°C Upright Ultra-Low Temperature Freezers
- 1- VWR –86°C Upright Ultra-Low Temperature Freezer
- 1- American Scientific –86°C Upright Ultra-Low Temperature Freezer
- 1- Revco –86°C Upright Ultra-Low Temperature Freezer
- 1- Liquid Nitrogen Storage Unit
- 1- Biological Safety Cabinet
- 2- Refrigerators, -4°C, with freezer compartments, -20°C
- 1- Sensaphone Wireless Temperature monitoring equipment
- 1- Leica Autostainer XL
- 1- Biocare Autostainer
- 1- Ventana/Roche Discovery Autostainer
- 1- Leica Bond RX Autostainer
- 1- TBS Coverslipper RCM-7000
- 3- Thermo Microtomes Model HM 355S
- 1- Leica Microtome RM-2125
- 1- Leica Microtome RM-2235
- 1- Leica Microtome RM-2135
- 2- Leica Cryostats CM-1800
- 1- Thermo Cryostat NX-70
- 3- Sakura Tissue Processors VIP E-300
- 2- Sakura Embedding Centers Model 4710
- 1- Sakura Tissue-Tek Vacuum Infiltration
- 11- Olympus BH2 Microscopes
- 1- Olympus BX46 Binocular or Trinocular Microscope
- 1- Nikon DigitalSight DS-L3 Microscope Camera
- 1- 3D Histech TMA Master II Tissue MicroArrayer
- 1- Applied Biosystems® ArcturusXT™ Laser Capture Microdissection System
- 1- Beckman Coulter Allegra X-12R Refrigerated Centrifuge
- 3- Beckman Coulter Microfuge-18 Tabletop Centrifuges
- 1- ThermoScientific Nanodrop ND-1000 Spectrophotometer
- 1- Picopure 2 Plus Water Purification System
- 1- Promega Maxwell semiautomated nucleic acid extractor
- 1- Leica AT2 Whole Slide Imager
- 1- Leica GT450 Whole Slide Imager
- 1- Leica Aperio GT450 SAM Server
- 1- Visiopharm Oncotopix Image Analysis Suite
- 1- NanoString GeoMx Digital Spatial Profiler
- 1- Agilent BioAnalyzer
- 1- BioMatrix Inc Pipette/Balance Calibration
- 2- Thermo HeraCell Incubators
BRPC GEOMX PIPELINE INFORMATION (nCounter):
Access to and use of the NanoString GeoMx Digital Spatial Profiler is available to any Duke Investigator through the joint collaboration of the BioRepository & Precision Pathology Center (BRPC) and Microbiome Shared Resource (MSR) CORE laboratories. The GeoMx DSP is housed within the BRPC laboratory space where all wet laboratory functions are performed, including tissue processing, slide cutting, slide staining, region of interest (ROI) selection, and oligonucleotide tag capture. Capture plates are then transported to the MSR laboratory where hybridization and detection on the nCounter instrument. Oligonucleotide tags with their quantitative counts are then imported back into the GeoMx platform for integration with the slide images and ROI selections for spatially-resolved protein or RNA expression. Investigators then access the GeoMx remotely to analyze their data.
BRPC GEOMX PIPELINE INFORMATION (Illumina):
Access to and use of the NanoString GeoMx Digital Spatial Profiler Cancer Transcriptome Atlas is available to any Duke Investigator through the joint collaboration of the BioRepository & Precision Pathology Center (BRPC) and Sequencing and Genomic Technologies Shared Resource (SGT) CORE laboratories. The GeoMx DSP is housed within the BRPC laboratory space where all wet laboratory functions are performed, including tissue processing, slide cutting, slide staining, region of interest (ROI) selection, and oligonucleotide tag capture. Capture plates are then transported to the SGT where the oligonucleotides are sequenced on an Illumina next generation sequencer. DNA oligonucleotide sequences contain ROI indices mapping them back to their tissue location, an RNA target identification sequence matching them to their ISH probes, and a unique molecular identifier (UMI) to deduplicate reads. Sequenced oligonucleotides are processed then imported back into the GeoMx platform for integration with the slide images and ROI selections for spatially-resolved RNA expression. Investigators then access the GeoMx remotely to analyze their data.