SOURCES SOUGHT
Q -- Information on Tissue Microarray Technologies
- Notice Date
- 4/18/2008
- Notice Type
- Sources Sought
- NAICS
- 621511
— Medical Laboratories
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 6120 Executive Blvd., EPS Suite 600, Rockville, Maryland, 20852
- ZIP Code
- 20852
- Solicitation Number
- SS-ETSB-2008-3202
- Point of Contact
- Richard L Hartmann,, Phone: (301) 496-8620, Michael P. Marino,, Phone: (301)435-3801
- E-Mail Address
-
Richard.Hartmann@nih.gov, Michael.Marino@nih.gov
- Description
- This Request for Information (RFI) is intended to provide source material for a state-of-the science summary of available tissue microarray technology and for planning infrastructure development at the National Cancer Institute (NCI). It should not be construed as a solicitation or as an obligation on the part of the Federal Government, the National Institutes of Health (NIH), and the NCI. The NCI does not intend to award a cooperative agreement, grant, or contract on the basis of responses to this RFI or to otherwise pay for the preparation of any information submitted or for the Government's use of such information. Based on the response to this RFI, the NCI may issue a Request for Proposals (RFP) at an undetermined time in the future or use the information to guide purchases of equipment, adaptation of specific methodologies or conduct specific methodologic research. THERE IS NO SOLICITATION AVAILABLE AT THIS TIME, no basis for claims against NCI shall arise as a result of a response to this Sources Sought notice or the NCI's use of such information as either part of our evaluation process or in developing specifications for any subsequent requirement. In addition, this notice is also being utilized as market research. The NCI is specifically interested in determining the types of organizations available in the marketplace that provide these technologies. In particular, the NCI is seeking qualified small business concerns [including Small Disadvantaged Businesses (SDB), Woman-owned Small Businesses (WOSB), Historically Underutilized Business Zone (HUBZone) Small Businesses, Veteran-Owned Small Businesses (VOSB) and Service-Disabled Veteran-owned Small Businesses (SDVOSB] which provide these technologies. Based on the responses received from this announcement, an acquisition may be solicited as a Total Small Business Set-Aside. Purpose: This Notice is a time-sensitive Request for Information (RFI) on state-of-the-science technologies, methodologies and protocols for tissue microarray production, sectioning, slide preparation and slide storage with maintenance of molecular stability. This RFI will provide source information needed to summarize technologies that can be employed by the National Cancer Institute to develop an Applied Molecular Pathology (AMP) laboratory that will analyze tissue biomarkers in large numbers of extremely valuable formalin fixed paraffin embedded tissues collected in epidemiologic studies, clinical trials and other investigations. It is envisioned that the AMP will play a critical role in helping NCI advance its mission of translating biomarker discovery into human populations. Responses (no longer than 25 pages in MS Word or pdf format) may be submitted via e-mail to Mr. Michael P. Marino, Contract Specialist, NCI, at Michael.Marino@nih.gov. All responses must be received by 3:30 PM (Eastern prevailing time) on May 16, 2008. Background: Respondents are invited to provide input related to any or all topics. Molecular analysis of large numbers of tissue specimens collected in epidemiological and clinical studies is critical for relating advances in cancer biology to cancer etiology and pathogenesis, population-based prevention, cancer surveillance, clinical practice and other key areas with direct implications for patients. It is recognized that meeting this goal presents unique challenges, foremost of which is the identification of best available technology for rapid, cost-effective, standardized performance of assays on routinely collected formalin fixed paraffin embedded tissues. To meet these goals, NCI is developing a high throughput Applied Molecular Pathology (AMP) laboratory that will use tissue microarray technology in combination with other high throughput methods. Meeting the aims of the AMP presents technical challenges. Tissue based research often uses archival material that has been collected, fixed, and prepared using non-standardized and sometimes suboptimal protocols. Variable processing procedures are often encountered in multi-center studies, which are especially challenging for tissue microarray construction which results in the inclusion of specimens from multiple sources in single tissue microarray blocks. In addition, most facilities currently produce tissue microarrays manually, which limits throughput, limits uniformity in construction and creates need for technologists with specialized skills. Therefore, methods for pre-processing tissue blocks prior to tissue microarray preparation as well as standardizing tissue microarray construction itself are needed. Since the multitumor (sausage) tissue block (Battifora H Lab Invest 1986) and the tissue microarray (Kononen J Nat Med 1998) were described, advances have allowed laboratories to build tissue microarrays with enhanced features including: 1) inclusion of small targets, such as normal structures and non-invasive lesions; 2) standardized core placement with high density; 3) flexibility in core diameter; and 4) sectioning with high levels of core retention. Advances have been made that permit sectioning of tissue microarray blocks with minimal tissue loss related to preliminary sectioning ("facing" the block) and methods have been proposed to improve transfer of cut sections to glass slides with preservation of core spacing and minimal background when viewed microscopically. These improvements permit the exploratory use of tissue microarrays in applications that have stringent technical requirements such as assessment of multiple markers simultaneously (dual or multiplex staining); fluorescence or chromogenic in-situ hybridization and potentially other types of assays or assay combinations (quantum dots, combined immunohistochemical and nucleic acid probes, etc.). Nonetheless, many assays require pre-treatment to unmask targets, resulting in loss of tissue cores in sections. Tissue microarrays may be particularly susceptible to this problem because each core represents a small area for slide contact compared with a whole tissue section. In summary, the NCI AMP will apply best methodologies for tissue microarray construction and utilization to support NCI studies and will provide an environment for testing and developing new methodologies in collaboration with extramural academic and industry partners. This activity will function as the translational vehicle for the discovery pipeline driven by molecular profiling and basic science efforts. Information Requested: I General Information (Optional) - contact information, including name, institution / organization, telephone and fax numbers and e-mail address; website URL II Information Technology - software for inventory, tracking and data recording. Intake of thousands of blocks from multiple sources related to different projects is an important challenge for high throughput pathology, given that receipt is often continuous, unpredictable in timing and may include loaned blocks that must be returned to sources within promised timeframes. Information is sought related to software and approaches for: •Tracking source (donor) tissue blocks, microscopic slides prepared from such blocks, tissue microarray blocks and stained and unstained tissue microarray slides •Software for building tissue microarray maps •Software for recording assay interpretations with easy exportable functions into commonly used statistical packages such as SAS, Stata and others permitting creation of relational databases that combine assay data with epidemiological, clinical and pathologic data III Quality Assurance - measures for assessing source (donor) blocks Tissue microarray quality may be limited by the poorest quality specimens selected for inclusion within blocks. For example, in automated approaches, a single problematic block may lead to instrument malfunction which can result in damage to the microarray block under construction. Poor quality blocks may also contribute tissue cores that pose problems later in the process during assay performance or scoring of arrays secondary to spot loss. Information is sought re: •Procedures for assessing tissue block quality prior to tissue microarray preparation •Techniques for assessing tissue thickness within blocks •Specialized paraffins for re-embedding donor blocks to avoid shattering and cracking during tissue microarray preparation and that provide uniform sets of optimized donor blocks for target core extraction IV Tissue Microarray Devices, related technology and procedures Most tissue microarrays are constructed by microscopically examining slides of hematoxylin and eosin stained sections of source (donor) blocks, identifying and marking targets on these slides, aligning marked slides and corresponding blocks and then using devices to manually remove tissue cores from corresponding target areas in the blocks. Source blocks with faint tissue outlines (often adipose rich) may pose problems for matching regions of interest on slides to blocks, especially for small targets. This approach also assumes that targets that appear satisfactory based on one 5 micron section will yield cores of 2 mm or more in length with target preservation. This problem is exacerbated given that target cores transferred to tissue microarray blocks may be placed at varying depths within recipient blocks, requiring repeated sectioning of the tissue microarray block to reach a depth at which all cores are represented. Similarly, nucleic acid extraction from tissue cores with variable representation of targets through the z-axis may yield disappointing results. Information is requested regarding: •Devices for manual tissue microarray construction •Robotic devices for automated or semi-automated tissue microarray construction •Paraffins for use in preparing tissue microarray blocks •Procedures for "curing" tissue microarray blocks prior to sectioning •Strategies for ensuring equal depth of placement of cores in tissue microarray blocks •Devices for sectioning tissue microarray blocks to minimize tissue wastage •Procedures for transferring sections of tissue microarray blocks to glass slides that optimize / maintain core orientation, produce maximal optical transparency when mounted on slides, create minimal artifact / interference with regard to immunohistochemistry, in-situ hybridization and other tissue based assays and provide excellent slides for scanning and potential automated image analysis for assay interpretation •Methods for increasing adhesion of cut sections to slides, thereby reducing tissue shedding when sections are treated to expose assay targets such as antigen unmasking ("antigen retrieval") for immunohistochemical assays or exposure of nucleic acids for hybridization techniques •Novel methods for increasing assays sensitivity with minimal target unmasking procedures (e.g. mild antigen retrieval methods), thus preserving adhesion of tissue microarray sections to slides •Best practices for removing tissue cores for extraction of nuclei acids with maintenance of targets through full-thickness of cores (z-axis) and potential for high sample throughout without inter-specimen contamination V Archiving and storage of cut unstained tissue microarray sections Amassing data indicate that many antigens degrade in cut unstained tissue sections mounted on glass slides when stored at room temperature under ambient conditions. This recognition has prompted recommendations to dip cut unstained sections in paraffin, store in anoxic conditions (nitrogen gas; vacuum) or store slides at cool temperatures. Information is sought related to: •Best techniques for storing cut unstained tissue sections mounted on glass slides to maintain antigen preservation for immunohistochemical assays •Data related to length of antigen preservation when cut sections are stored under alternative antigen preserving conditions such as those listed above Additional comments relevant to this RFI, and addressing issues that are not specifically mentioned above, are also encouraged. How to Submit a Response: Please limit your responses to 25 pages or less. Brevity and structured format (such as bulleted items) are encouraged whenever applicable to aid in processing. The Government prefers that responses be submitted in MS Word or Adobe Acrobat pdf format via e-mail to: Michael P. Marino Contract Specialist E-mail: Michael.Marino@nih.gov If using U.S. Postal Service: Michael P. Marino Contract Specialist National Cancer Institute Office of Acquisitions Epidemiology, Therapeutics and Sciences Branch 6120 Executive Blvd MSC 7194 EPS/6037 Bethesda, MD 20892-7194 If using a hand-delivery or courier service: Michael P. Marino Contract Specialist National Cancer Institute Office of Acquisitions Epidemiology, Therapeutics and Sciences Branch 6120 Executive Blvd, Room 6037 Rockville, MD 20852 Responses will be accepted through 3:30 PM (Eastern prevailing time) on May 16, 2008. All information provided will be processed and analyzed confidentially. Respondents will not be notified of the results of this RFI. Inquiries: Inquiries concerning this Notice may be directed to: Richard L. Hartmann Contracting Officer Telephone: 301-496-8605 E-mail: Richard.Hartmann@nih.gov
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