SOURCES SOUGHT
Q -- Request for Information on Slide Scanning and Automated Analysis of Immunohistochemical and In-Situ Assays
- 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-ESTB-2008-3201
- Point of Contact
- Richard L. Hartmann,, Phone: (301)496-8605, 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 that will permit the National Cancer Institute to develop a state-of-the science summary of available technology for digital pathology techniques. Specifically the technology review will focus on two topics: 1) scanning and creating digital image files of stained microscopic glass (both whole tissue sections and tissue microarrays) and 2) techniques for performing semi-automated or automated analysis of immunohistochemical stains, immunofluorescence stains or in-situ hybridization assays performed on tissue microarray sections. This information will be used for planning infrastructure development at the National Cancer Institute (NCI) and 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 scanning microscopic slides stained with hematoxylin and eosin or used for immunohistochemical/immunofluorescence or in-situ hybridization assays. 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: Molecular analysis of large numbers of tissue specimens collected in research studies is critical for translating advances in cancer biology to patient research and eventually improving public health and clinical practice. A critical challenge for achieving this goal is to identify methods for standardized, rapid, cost-effective analysis of tissue based assays based on technologies such as immunohistochemistry and in situ-hybridization. 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 to characterize large numbers of fixed human tissue samples collected in a range of studies. Meeting the aims of the AMP presents technical challenges related to tissue collection, tissue microarray production and assay standardization. Information related to best technologies for these procedures has been requested through a separate RFI. This RFI focuses specifically on methodologies needed to create digital images of pathology slides, develop matched databases of images and annotated information, and analyze images of tissue based assays. Developing these methods is critical for the large specimen / assay throughput anticipated for the AMP. Image scanning and archiving is necessary to facilitate web-based slide reviews, which permit data sharing among collaborators at remote centers. The capacity to sort images is also important for interpretation; for example, it is sometimes useful to simultaneously score the same tissue microarray core for several related markers simultaneously, rather than scoring each marker separately. Concurrent access to images of hematoxylin and eosin stained whole sections linked to cores, can provide the architectural clues necessary for making fine distinctions, such as separating non-invasive from invasive regions of a tumor. In summary, methods that permit relatively inexpensive, rapid preparation of image archives with flexible sorting capacity is central to the success of this effort. High resolution scanning of slides is useful for facilitating human scoring of tissue based assays; however, the ability to review such assays is inveitably limited by availability of trained staff, incomplete intra- and inter-observer agreement, and the capacity of human observers to quantitatively assess assay results such as percentages of cells stained or staining intensity. Semi-automated approaches that allow expert reviewers to train algorithms to complete these functions holds the potential to address these concerns partly, although concerns remain about computer-based methods for distinguishing target from non-target cells and artifacts from true signals. In addition, interpreting results in different cell compartments (nucleus, cytoplasm, cell membrane) can pose challenges for automation. Semi-automated systems would reduce workload by allowing an instrument to approximate the read of human experts, and future advances may permit better measurement than possibly by visual assessment. Ultimately, it would be desirable to relate assays signals to internal standards that reflect quantitative molecular content, rather than a pathologist’s subjective score. Complete automation might be needed to combined high numbers of specimens with assays for multiple different markers. Similar to the issues posed by semi-automated systems, advances in automation are tied to the capacity of instruments to actually achieve object identification and signal validation. Methods for simultaneously measuring co-expression of molecules in tissue by sing multiplexed assays with distinguishable signals (i.e. different fluorophores or chromagens) represents yet another opportunity to enhance this field of investigation. In summary, the NCI AMP will seek to combine best methodologies for tissue microarray construction with methods for image archiving, database construction and management and techniques for achieving high specimen throughput, cost effective, standardized assay scoring. The AMP 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: Respondents are invited to provide input related to any or all of the topics listed. I General Information (Optional) – contact information, including name, institution / organization, telephone and fax numbers and e-mail address; website URL II Scanning stained slides to capture digitized images and assembling digitized image archives suitable for searching and visual scoring using display on computer monitors Specifically, information is sought related to technologies for: <!--[if !supportLists]--> · <!--[endif]--> Scanning microscopic slides of whole sections or sections of tissue microarrays <!--[if !supportLists]--> o <!--[endif]--> Information concerning the capacity to automate scanning of multiple slides in queue without direct human – instrument interaction and level of throughput (e.g. slides / hour) <!--[if !supportLists]--> o <!--[endif]--> The resolution, storage requirements / characteristics of the digitized images generated <!--[if !supportLists]--> o <!--[endif]--> The suitability of such image files for posting on websites for multi-user, password controlled access <!--[if !supportLists]--> o <!--[endif]--> The suitability of these images for human scoring of immunohistochemical stains targeting antigens in nuclear, cytoplasmic or cell membrane cell compartments <!--[if !supportLists]--> o <!--[endif]--> The suitability of methods for achieving comparable results with assays that results in a fluorescent signal as opposed to a colorimetric signal and for detection with adequate optical resolution of small pinpoint signals (e.g. in situ-hybridization signals) <!--[if !supportLists]--> o <!--[endif]--> The suitability of technologies for producing images suitable for automated analysis using specific commercially available software or systems designed for automated assay scoring <!--[if !supportLists]--> o <!--[endif]--> The capacity to sort images, view multiple images simultaneously, and link images to databases containing clinical, pathologic, or epidemiologic annotation <!--[if !supportLists]--> o <!--[endif]--> Data related to loss of resolution secondry to variation in slide coverslips, mounting media for coverslips, tissue microarray transfer modalities (I.e. “tape transfer” techniques) and tissue edges III Automated and semi-automated methods for assessing immunohistochemical assays, immunofluorescence assays and in-situ hybridization assays performed using either chromagenic or immunofluorescence methods Tissue microarray technology provides a platform for cost effectively performing single batch assays on many tumor samples with histologic context. However, manually scoring high density arrays for multiple markers represents a huge workload and has limited reproducibility and quantitative validity. Achieving this goal is critical for translating biomarker discovery into clinical practice. Accordingly, NCI seeks information related to technologies available for semi-automated and automated assay scoring: <!--[if !supportLists]--> · <!--[endif]--> Technologies for semi-automated and fully-automated scoring of assays performed using tissue microarrays <!--[if !supportLists]--> o <!--[endif]--> Types of signals that can be analyzed: <!--[if !supportLists]--> § <!--[endif]--> Chromagenic, immunofluorescence or both <!--[if !supportLists]--> § <!--[endif]--> Immunhistochemistry, in-situ hybridization or both <!--[if !supportLists]--> § <!--[endif]--> Cell compartments: nuclear, cytoplasmic, membranous <!--[if !supportLists]--> o <!--[endif]--> Methods for setting cutpoints for positive signals – set by user based on algorithm or absolute cutpoints based on calibration or other methods <!--[if !supportLists]--> o <!--[endif]--> Validation data – based on comparison with pathologists’ reads; results of other assays (biochemical analysis, enzymatic activity, immunoblotting or Western blotting, etc.) or clinical outcomes (drug response, survival, etc.) <!--[if !supportLists]--> o <!--[endif]--> Ability to interactively mark areas for analysis on images <!--[if !supportLists]--> o <!--[endif]--> Instrument capacity to assess suitability of a tissue microarrray spot for scoring: assessment of appropriate cells, absence of artifact (e.g. stain background) <!--[if !supportLists]--> o <!--[endif]--> Type of output data (total cells assessed, percentage stained, intensity, etc.) and representation in tables, figures etc. <!--[if !supportLists]--> o <!--[endif]--> Capacity to interface with other computer software including commonly used biostatistical packages <!--[if !supportLists]--> o <!--[endif]--> Capacity of instrument: identify cells, epithelial cells or tumor cells <!--[if !supportLists]--> § <!--[endif]--> Technology used to to permit object identification: image analysis; co-expression of keratin, none, etc. <!--[if !supportLists]--> § <!--[endif]--> Speed of assessment 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 <!--[if !supportAnnotations]--> <!--[endif]-->
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