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BWH Specimen Bank

Director: Bry, Lynn, M.D., Ph.D.

Location: LB2-232 Amory Building, Department of Pathology, Brigham & Women's Hospital, 75 Francis Street, Boston, MA 02115

Summary:

"The Specimen Bank provides materials to investigators with IRB-approved protocols. Staff are available to assist with selection of samples appropriate for downstream applications, development of processing protocols or preparation of derivatives from clinical materials.

IT Staff are also available to assist researchers with creation of queries for prospective sample collection or queries to select samples from specific cohorts.

Our goal is to drive quality research in an efficient and cost-effective manner. Each year we provide tens of thousands of samples to area researchers."

Getting started: Partners investigators and study staff may request a Crimson user account to help manage studies and collected materials.

Affiliations:

People:

Resources:

Protocols

  • Buffy coat processing protocol ( Protocol )

    Acceptable Tube Types:

    If you plan to extract nucleic acids from materials, Purple-top and Yellow-top tubes are most commonly used.

    Purple top tube (EDTA anti-coagulant). Commonly 4.0 or 10mL volume tubes for collection of whole blood.
    Green top tube (lithium heparin anti-coagulant). Commonly 4.0, 5.0 or 10mL tube. Note the heparin anti-coagulant interferes with many nucleic acid extraction protocols
    Blue top tube (sodium citrate anti-coagulant. Commonly 3.0, 5.0 or 10mL tubes for collection of whole blood. Used primarily for coagulation testing.
    Yellow top tube (ACD, acid-citrate-dextrose anti-coagulant). Uncommon sample, but often received as 10mL tube.

    Standard Procedure:

    Spin at 3000rpm for 10 minutes at room temperature (25*C).
    Use a sterile pipette to pull off plasma, leaving no more than 0.5mL of plasma over the cell interface.
    Note the buffy coat/yellowish layer over the packed RBC layer.
    With a single-use pipette, collect as much of the yellow layer as possible (generally in <0.5mL volume), avoiding taking significant amounts of plasma or RBCs.
    Transfer the buffy coat to a sterile pour-off tube or cryovial.

    Variations (added per request to study protocol):

    Spin time: Can be modified from 10 minutes.
    Spin temperature: Can be modified from 25*C (4*C-42*C).
    Storage conditions: ambient, 4*C, -20*C, -80*C.
    Alternate collection tube, including:
    Eppendorf tubes: 1.8mL, 2.0mL.
    Screw capped tubes: 2.0mL, 10mL.
    Cryovials: specify volume, size (1", 2").

  • Plasma processing protocol ( Protocol )

    Acceptable Tube Types:

    Purple top tube (EDTA anti-coagulant). Commonly 4.0 or 10mL volume tubes for collection of whole blood.
    Green top tube (lithium heparin anti-coagulant). Commonly 4.0, 5.0 or 10mL tube.
    Green top tube with serum separator gel (lithium heparin anti-coagulant). Commonly 5.0 or 10.0mL volume.
    Blue top tube (sodium citrate anti-coagulant. Commonly 3.0, 5.0 or 10mL tubes for collection of whole blood. Used primarily for coagulation testing.
    Yellow top tube (ACD, acid-citrate-dextrose anti-coagulant). Uncommon sample, but often received as 10mL tube.


    Standard Procedure:

    Spin at 3000rpm for 10 minutes at room temperature (25*C).
    Use a sterile pipette to transfer plasma to a pour-off tube. Do not contact the buffy-coat layer overlying the packed red cells.
    Cap the aliquot tube, record sample/volume in Crimson application and label.


    Variations (added per request to study protocol):

    Spin time: Can be modified from 10 minutes.
    Spin temperature: Can be modified from 25*C (4*C-42*C).
    Storage conditions: ambient, 4*C, -20*C, -80*C.
    Aliquotting: Can request >1 aliquot in other tube type. Available tube types include the following:
    Eppendorf tubes: 0.6mL, 1.8mL, slim tube.
    Screw capped tubes: 0.6mL, 2.0mL, 10mL.
    Cryovials: specify volume, size (1", 2").

  • Processing of microbial isolates protocol ( Protocol )

    Acceptable Samples:

    Solid media for bacterial and yeast species, frequently completed culture plates from the microbiology lab.
    Collection of anaerobic, BL-3, fungal and virology isolates must be discussed with the specimen bank director regarding best means of collection.

    Standard Procedure:

    Collect plates after completion of the culture.
    Verify that the isolate is in pure culture, else set up new sheep's blood agar plate with the strain and incubate at 37*C in 5% CO2 atmosphere or per appropriate conditions.
    Once a pure culture has been verified, create duplicate frozen stocks of the isolate in cryovials with Tryptose Soy Broth media (TSB) and microbeads for adsorption of bacterial cells.
    Use a swab to obtain a heavy inoculum of pure material from the plate and suspend in each vial.
    Invert vials 5 times to mix and coat beads with bacteria.
    For non-fastidious organisms, pipette off excess broth and discard.
    For fastidious organisms leave excess TSB in the vials.
    Store vials at -80*C.

    Variations (added per request to study protocol):

    Isolates can be frozen under other conditions, including with 20-50% glycerol in the media, or in media other than TSB.
    Other containers: standard cryovials, 2" crovials.
    Additional aliquots (>2).
    Agar slants can be made on chocolate agar or other media as needed, for pickup or shipment of isolates.
    Special labeling of the tube (microbial species, sample source, etc.) as allowed in the investigator's IRB protocol.

  • Serum processing protocol ( Protocol )

    Acceptable Tube Types:

    Red top tube (no anti-coagulant). Commonly 5.0 or 10mL volume tubes for collection of whole blood.
    Tiger top tube with serum separator gel. Commonly 10mL volume tube for collection of whole blood.
    Gold top tube with thrombin pro-coagulant. 2.5, 3.5 and 5.0 mL tubes for collection of whole blood.
    Gold top tube with thrombin pro-coagulant and serum separator gel. 2.5, 3.5 and 5.0mL tube volumes for collection of whole blood.

    Standard Procedure:

    Spin at 3000rpm for 10 minutes at room temperature (25*C).
    Use a sterile pipette to transfer serum to a serum aliquot tube.
    Cap the aliquot tube, record sample/volume in Crimson application and label.

    Variations (added per request to study protocol):

    Spin time: Can be modified from 10 minutes.
    Spin temperature: Can be modified from 25*C (4*C-42*C).
    Storage conditions: ambient, 4*C, -20*C, -80*C.
    Aliquotting: Can request >1 aliquot in other tube type. Available tube types include the following:
    Eppendorf tubes: 0.6mL, 1.8mL, slim tube.
    Screw capped tubes: 0.6mL, 2.0mL, 10mL.
    Cryovials: specify volume, size (1", 2").

Services

  • BWH tissue repository service ( Storage service )

    Handles requests for fresh or fixed tissues, or paraffin-embedded sections.

    Please direct requests for fresh, frozen or paraffin-embedded tissues/sections to the BWH Tissue Repository at (617) 732-6780, or email to WRICHARDS @ partners.org

    Archived tissue specimens from HMS-affiliated institutions may also be searched in the Virtual Specimen Locator

  • Crimson application support serivice ( Support service )

    The Crimson application was developed by the BWH Pathology department to facilitate support of research investigations at Partners-affiliated institutions.

    Crimson fills a key gap in existing clinical and research systems by tapping into discarded sample streams within Pathology Departments to allow prospective collection of materials for designated research use or to develop retrospective repositories around specific diseases or organ systems.

    * Prospective query and collection of samples under an IRB protocol.
    * Management of patient consent status on collected materials.
    * Ability to collect materials on cohorts of consented patient or queries forwarded from the RPDR (Research Patient Data Registry).
    * Ability to receive and process samples submitted from consented patients.
    * Management of downstream processing and testing of materials.
    * Core application from which study users may download sample data and results.

    Partners investigators and study staff may request a Crimson user account to help manage studies and collected materials.

  • Diagnostic and clinical testing service ( Material analysis service )

    The test menu of the BWH Clinical Laboratories is available to investigators. The Specimen bank and Clinical Trials Unit in the BWH Clinical Labs also perform specialized testing for novel biomarkers.

    * 24X7 operations for specimen handling and diagnostic testing.
    * Clinical Trials Unit to handle high-volume clinical testing for NIH or pharma-sponsored trials.
    * Download of clinical and research results in the Crimson application.

  • Diagnostics development service ( Data analysis service )

    Resources and expertise are available to help investigators evaluate markers with potential use as diagnostic tests.

  • Medical/pathology informatics support service ( Support service )

    Our group developed the Crimson Application. Partners investigators may request users accounts on this web-based application to manage their studies, samples and patients. IT Staff are also available to assist researchers with creation of queries for prospective sample collection or queries to select samples from specific cohorts.

  • Microbial isolates service ( Storage service )

    Clinical isolates may be collected for investigators performing epidemiological studies, basic research into microbial pathogenesis and virulence, or studies of microbial resistance to antibiotics.

    Requirements:
    * Studies must have a COMS# (HMS Committee on Microbiological Safety) in place to receive materials.
    * All requests are subject to review and approval by the microbiology laboratory director prior to the collection and release of materials.
    * Requests for data to be associated with isolates, including antibiograms, sample of origin, or diagnosis codes must be included in the study's IRB protocol.
    * If patient identifiers are to be included, then all patients must be consented for the study and registered in the Crimson system prior to release of isolates.


    The following represent common types of isolates identified in the Clinical Microbiology Laboratory:

    * Aerobic and facultative anaerobic bacterial pathogens including Staphyloccoal, Streptococcal species, Escherichia coli, and other Gram-negative organisms.
    * Toxigenic BL-2 level pathogens such as Shigella and clostridial species require approval by the microbiology lab and proof that the requesting investigator maintains appropriate facilities to store and handle such isolates.
    * Microaerophilic organisms including Campylobacter species.
    * Strict anaerobes such as Bacteroides and Prevotella
    * Candida and other monomorphic yeasts.

    ** BL-3 materials including Mycobacterium tuberculosis and fungal isolates require review and approval of the request by the microbiology lab, and proof from investigators that they maintain appropriate facilities within the Longwood Medical Area for the storage and handling of such materials.

    ** Viral lysates from clinical cell cultures for CMV, HSV I and II, Adenovirus.
    ** Primary source materials (blood only) containing CMV, EBV, HIV or HCV. These materials are collected after completion of viral antigen or viral load studies.

    *** Discarded blood from patients with malarial or babesial infection.

  • Open repositories service ( Storage service )

    The Specimen Bank maintains a series of open repositories for use by Partners or HMS-affiliated investigators.

    Ability to search online for available samples.

  • Prospective sample collection service ( Storage service )

    Crimson queries against a rolling window of samples accessioned in the clinical laboratories (5000+/day at BWH). Investigators with IRB protocols approved to use Crimson for sample collection may define queries to locate materials of use.

    Fill in the Services Request Form to inquire about use of prospective collection for your study, or to request a quote for services.

    The IRB page discusses how to document use of the Crimson application in protocols.

  • Sample processing service ( Material processing service )

    The central facility offers service for handling consented patient samples.

    Dedicated staff and equipment can process materials to specific study or sponsor requirements.

    Offshift and weekend processing available (coordinated with BWH Lab Control).

    The following protocols describe standard processing performed in the Specimen Bank. Each protocol notes variations that can be made for a particular study's SOP (standard operating procedure).

    * Serum Processing
    * Plasma Processing
    * Buffy Coats
    * Microbial Isolates

    Please see protocols for details.

  • Sample selection consultation Service ( Support service )

    Bank staff can assist with selection of samples for desired analyses, development of processing protocols, and preparation of derivatives.


Web Links:

Last updated: 2015-11-19T12:59:47.994-06:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016