Pathology Network Shared Resource (PNSR)

A variety of biospecimens are available from the Pathology Network Shared Resource (PNSR). Fresh and frozen tissues are collected by the tissue procurement lab. Formalin Fixed Paraffin Embedded tissue and tissue microarrays (TMAs) are built using the remnant blocks from the Paraffin Archive Resource (PAR). All tissue used for research is collected under remnant tissue protocol I 115707. The BioRepository Bank provides resources to investigators with IRB-approved protocols.

The following biospecimens are provided by the PNSR.

DNA and RNA

DNA and RNA are isolated from tumor and matching non-tumor tissues in the biobank. DNA and RNA are primarily extracted from frozen tissue samples, but DNA can be extracted from formalin-fixed paraffin-embedded tissue as well. All samples are QC’ed after extraction to confirm that high quality DNA.

Please note that the numbers reported on this link are approximate. Please contact PCFAdmin@RoswellPark.org for a further assessment of samples available for your project.

DNA frozen

Genomic DNA is isolated using the Gentra DNA Purification Kit. QC: 260/280 ratios are evaluated and DNA is run on an agarose gel to confirm the presence of high molecular weight product.

RNA frozen

RNA is isolated using a Trizol extraction procedure. QC: 260/280 ratios are examined and an RNA aliquot is run on the Agilent bioanalyzer to evaluate RNA integrity. Specimens with an RNA Integrity Number (RIN) of seven or greater are generally suitable for expression analysis while those with a value of five to seven yield less than optimal results for array studies. Specimens with a RIN less than five are not suitable for array studies but may yield results for RT-PCR.

FFPE tissue

Formalin-fixed paraffin-embedded (FFPE) blocks from surgical pathology tissues are archived and can be accessed for research purposes. Our archive of paraffin tissues is extensive, having approximately more than 200,000 cases dating back to 1993 that can be electronically searched and used for research purposes.

Fresh and frozen tissue

Fresh and frozen remnant tissues are from surgical specimen. These tissues can be stored and distributed for research purposes. Our biospecimens are procured by certified Pathologist Assistants and then stored in -80C freezers that are protected by state-of-the-art monitoring systems and 24/7 emergency contact schedules.

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Requests for fresh or frozen tissues are guided by the Laboratory Information Management System (LIMS) and are integrated with other shared resource facilities, (e.g., the Genomics Shared Resource).

The number of biospecimens available in the biobank varies by disease site and their utilization, which is subject to TRG approval and prioritization. Specific details for samples in the biobank including inventory, surgical events, tumor dimensions, and the numbers of tissues procured, banked, and distributed per disease site are available on the LIMS dashboard at https://rpcilims.roswellpark.org/.

TMA library

Tissue microarrays (TMAs) are constructed by using a hollow needle to remove very small tissue cores from multiple tumors of interest which are then inserted into a recipient paraffin block in an arrayed fashion. This format permits the screening of a large number of patient samples on a single slide. TMAs are an efficient and effective way to screen potential biomarkers and are typically used in conjunction with immunohistochemical (IHC) staining or fluorescent in situ hybridization.

The PNSR has constructed more than 200 different TMAs representing a wide variety of disease and tissue types. Currently, our TMA library contains over 60 breast TMAs, 42 TMAs from gastrointestinal tissue, and 73 with prostate tissue. Several other tissue types for which TMAs are constructed include lung, head and neck cancers, gynecological cancers, brain cancers and melanoma.

PNSR has a large collection of assembled TMA blocks available representing a diverse selection of disease and tissue types. Please contact PCFAdmin@RoswellPark.org for a list of currently available TMAs.

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Please contact PCFAdmin@RoswellPark.org for questions regarding biospecimens availability for your project.

The Imaging and Analysis lab uses an Aperio^® AT2 slide scanner. Slide scanning permits investigators to easily access their digital images of slides from anywhere using Aperio^® eSlide Manager, a web-based digital pathology information management system. Annotation of the digital slides can be conducted via a digital platform using Aperio^® ImageScope. This allows researchers to create digital images for publication as well as facilitate inter-institutional collaboration by providing rapid and easy sharing of digital image information.

AT2 system

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The AT2 is an ultra-fast, high-capacity scanning system with powerful 400-slide capacity. This system creates digital images from glass slides with superior image quality and includes the following features:

• 20X and 40X scanning magnification capabilities
• Create digital slides in multiple formats (SVS, JPEG, TIFF, composite web slide)
• View and edit digital slides with the user-friendly and freely downloadable ImageScope viewing software
• Connect multiple, remote parties through digital slide conferences.

ImageScope software

ImageScope is a freely downloadable viewing software for digital slide viewing. ImageScope is easy to use and puts a host of powerful capabilities at your fingertips.

• View digital slides from any workstation on the network; this eliminates the need to physically transport glass slides instantly pan and zoom to any region of the slide.
• Built-in web conferencing: real-time digital slide sharing and discussion in multiple remote locations.
• View multiple digital slides concurrently.
• Apply image adjustments in real time for contrast, brightness and gamma.
• Analyze entire digital slides or selected regions.
• Add graphical and text annotations to digital slides.
• Use the built-in ruler to make on the spot measurements.
• Save a region or selected regions of a digital slide to a file.
• Allows researchers to create digital images for publication as well as facilitate inter-institutional collaboration by providing rapid and easy sharing of digital image information.
• ImageScope also enables side-by-side coordinated viewing of multiple slides, something that cannot be done with traditional glass slides. In addition, Aperio's SmartSync™ feature makes it easy to compare different sections from the same tissue block, even when sections are rotated or translated with respect to one another.

Leica eSlide Manager (eSlide)

eSlide is a web-based digital pathology imaging and information management system. Access to eSlide can be granted by contacting Erika Van Dette at Erika.VanDette@RoswellPark.org or Leighton Stein at Leighton.Stein@RoswellPark.org.

Download the application form for a user account. The form must be filled out and submitted to the eSlide administrator at PRNImaging@RoswellPark.org. A brief eSlide tutorial session can be scheduled free of charge with Leighton Stein.

Automated image analysis

Image analysis is a service also provided by the Pathology Network Shared Resource (PNSR). Algorithms can be tailored to fine tune the cellular, nuclear, and stain parameters, creating an optimized algorithm macro for each antibody target and tissue type to select the cells of interest. The original digital slide image is never modified. Rather, an annotation layer with the markup image and quantitative data is created and linked to the digital image. Currently, we have one full-time employee with expertise in digital slide analysis. The PNSR performs image analysis for slides stained by IHC only. Nuclear, cytoplasmic and membranous expression can be scored individually or in any combination. Vascular analysis can be performed and tailored to calculate specific vessels by tweaking vessel size parameters. Some dual stains can also be analyzed with this system depending on the type of stains and target. To inquire about this service contact Dr. Wiam Bshara at Wiam.Bshara@RoswellPark.org.

The Clinical Research Laboratory Services (CRLS) consists of a team of laboratory professionals dedicated to managing all aspects of biospecimens related to clinical trials. CRLS coordinates tissue feasibility for clinical trials and provides services for processing, storing, and the shipment of specimens for clinical trials.

All staff members are IATA certified to ship biological specimens and serves as a point of contact for addressing laboratory specimen related concerns. Team members function in lab and office areas dedicated to clinical research activities. Additionally, CRLS staff facilitates specimen testing and reporting, provide budgets, and review studies for lab implementation for clinical trials at Roswell Park.

The CRLS team is comprised of two labs. The labs are located in the Gratwick Basic Science Building, which is dedicated to tissue management and in the Cell & Virus Building which manages non-tissue specimen.

CRLS performs the following tasks:

• Processing of various specimen types, i.e., blood, urine, body fluids and bone marrow
• Storage of specimens
• Shipment of specimens (same day and/or batch)
• Specimen transport
• Tissue feasibility determination
• Form and specimen requisition completion
• Facilitate specimen testing and reporting
• Facilitate budget completion
• Study reviews for lab implementation
• Protocol development

Please contact CRSLabAdminTeam@RoswellPark.org for a project specific cost estimate.

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The Histology Facility is a centralized lab that provides services for standard tissue processing and embedding, cryotomy, microtomy, general histology staining, antibody optimization, and immunohistochemistry (IHC). The Histology team also perform laser microdissection and sterile needle coring to isolate DNA from tumor samples. Histology staff work closely with the Biomedical Research Informatics Shared Resource and other core labs within the Pathology Network Shared Resource to identify samples sets, and then perform the required staining for research studies that use IHC. The lab uses several autostainers for consistent and high-throughput IHC staining. Antibody staining procedures and IHC slides are regularly reviewed by a pathologist for quality control. Histology continually works to expand our repertoire of antibody staining protocols and we currently have over 500 procedures.

The following histology services are provided by the Histology Facility:

• Immunohistochemical staining
• Antibody optimization for immunohistochemistry
• Hematoxylin and eosin staining
• Special histological staining (e.g., GMS, Masson’s Trichrome, PAS)
• Cryotomy
• Microtomy
• Paraffin embedding
• Standard tissue processing
• Sterile needle coring for DNA/RNA isolation

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Please contact Cassandra Whalen at 716-845-3006 or at Cassandra.Whalen@RoswellPark.org for a project specific cost estimate.

The SKY/FISH facility was established in January 2000, through the support of the J.H. Cummings Foundation, to provide comprehensive cancer cytogenetics services.

Services include conventional chromosome analysis such as G-banding (Human tissue only) and fragile site analysis as well as more specialized techniques such as Spectral karyotyping (SKY) and fluorescent in situ hybridization (FISH). These techniques are useful in identifying chromosomal abnormalities on a global scale or more specific gene level mutations in a variety of species such as human, mouse and rat.

The following are SKY/FISH detailed services:

• Spectral karyotyping (SKY) to identify chromosomes or chromosomal segments that are structurally and numerically altered in cells.
• G-Banding analysis (Human samples only) to identify chromosome number as well as chromosome aberrations including translocations, insertions, deletions or duplications in cells.
• Fluorescence in-situ hybridization (FISH) analysis using up to three-fluorescent colors to detect and localize genes, gene sets, fusion genes, telomere-specific sequences, centromere-specific sequences and specific chromosomal regions.
• Combined analysis by SKY and FISH to determine whether rearrangement, deletion or amplification occurs in genes encoding tumor suppressors, cell cycle factors, factors involved in immunological responses, DNA-damage responses, drug resistance, transgene expression, etc.
• Quantification of gene copy number in transgene research material. This method is also useful for investigators who want to identify transgene locations.
• Chromosome aberration and fragile site analysis.
• Planning of inter-disciplinary projects utilizing SKY/FISH technology, data interpretation and technical education and guidance for standard cytogenetic protocols.

Investigators interested in the use of the facility may contact Leighton Stein at 716-845-3213 or at Leighton.Stein@RoswellPark.org to discuss scheduling and procedures.

Cost estimates for services and biospecimens are prepared on a project specific basis. If you would like a cost estimate, please contact PCFAdmin@RoswellPark.org. CCSG members are eligible to receive discounted pricing.

A general inventory of all tissues in the biobank is available through the LIMS dashboard.

Translational Research Group (TRG) approval is required for the use of tumor biospecimens from the PNSR.

Requirements for TRG approval vary by the TRG. Some TRGs require a formal presentation before approval is granted, while other TRGs may grant approval via email. Contact the appropriate TRG representative for guidance regarding the approval process.

Please contact PCFAdmin@RoswellPark.org to organize an amendment for your current BDR protocol.

Yes. Please include the following statement in the acknowledgements section of your manuscript: Biospecimens or research pathology services for this study were provided by the Pathology Network Shared Resource, which is funded by the National Cancer Institute and is a Roswell Park Comprehensive Cancer Center Cancer Center Support Grant shared resource.