SOURCES SOUGHT
A -- NHGRI Protein Reagent Validation
- Notice Date
- 7/31/2015
- Notice Type
- Sources Sought
- NAICS
- 541711
— Research and Development in Biotechnology
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Heart, Lung and Blood Institute, Rockledge Dr. Bethesda, MD, Office of Acquisitions, 6701 Rockledge Dr RKL2/6100 MSC 7902, Bethesda, Maryland, 20892-7902
- ZIP Code
- 20892-7902
- Solicitation Number
- HHS-NIH-NHLBI-RDSS-03-IM
- Archive Date
- 9/1/2015
- Point of Contact
- Iris Merscher, Phone: 3014350365
- E-Mail Address
-
iris.merscher@nih.gov
(iris.merscher@nih.gov)
- Small Business Set-Aside
- N/A
- Description
- This is a Research and Development (R & D) Sources Sought notice (RDSS). This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this notice is to obtain information regarding the availability and capability of all qualified sources to perform a potential requirement. Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. I. BACKGROUND: The Protein Capture Reagent Program (PCRP) is a pilot project aimed to develop, optimize and scale renewable protein affinity reagents for use in biomedical research and clinical applications. Multiple ICs participate in the PCRP, and the program is coordinated by two ICs: the National Human Genome Research Institute (NHGRI) and the National Institute on Deafness and Other Communication Disorders (NIDCD). The major component of the pilot program is to produce high-quality, high-utility affinity reagents against human transcription factors (hTFs) as a test set of proteins. Deliverables from the production centers include hTF as target antigens and the corresponding affinity reagents in both monoclonal (mAb) and phage display recombinant Fab (rAb) form. Three production grants were awarded: a single antigen center in 2010 and two affinity reagent centers in 2011: - "Production Of Human Proteins To Be Used For Generating Affinity Reagents" (U01) RFA-RM-10-007 ; one three-year award supplemented to continue through 2015, and was made to Dr. Stephen Anderson, Rutgers University ("antigen center"). - "Production of Affinity Reagents for Human Transcription Factors" (U54) RFA-RM-10-017; five-year awards were made in September 2011 to Dr. Tony Kossiakoff, University of Chicago to produce Fab recombinant antibodies (Recombinant Antibody Network - RAN center) and to Dr. Jef Boeke, Johns Hopkins University (JHU) to produce mouse monoclonals. The award later transferred to Drs. Seth Blackshaw and Heng Zhu (2013), JHU when Dr. Boeke left the institution. The groups developed a working target list for human transcription factors and divided the list with each center tasked with producing their portion of the antigens. The majority of the hTF antigens were produced by Rutgers as hTF protein domains expressed and purified from Escherichia coli using a variety of tags. Antigens were purified using a variety of custom purification procedures and shipped to five different sites: two sites within the JHU center for protein chips and mouse injection, and three sites within the RAN center for phage display. Each of the affinity production centers has its own validation pipelines as well as some internal antigen production. While ostensibly the pilot endeavor appeared straightforward, there were bottlenecks at almost every juncture of the production process: - solubility expression issues with Avi-tagged antigens - difficulty with stringent antigen requirements for phage display recombinants - difficulty with optimizing standard operating procedures (SOPs) for Ab production and validation The Rutgers, JHU and RAN pipelines are described on the PCRP data portal website (http://proteincapture.org/). The affinity centers capture reagents must pass primary and secondary levels of various validations in order to be considered "passing reagents" of high enough quality to be posted on the data portal. Specifically, JHU primary validation of mouse monoclonals is via a human protein (HuProt) array specificity measurement, with secondary validation via immunoprecipitation (IP) and/or Western Blots (WB). Other value-added measurements include immunocytochemistry (ICC), chromatin immunoprecipitation followed by parallel sequencing (ChIP-Seq, collaboration with Hudson Alpha Institute) and affinity measurement via a proprietary Oblique-Incidence Reflectivity Difference (OIRD) device. The RAN recombinant affinity reagents must pass primary validation via affinity measurement with competitive enzyme linked immune-assay (ELISA), and secondary validation via spiked IP. Other value added measurements include immunoprecipitation - mass spectrometry (IP-MS), cellular localization with immunofluorescence (IF) in 6 cell lines, and ChIP. The PCRP program currently has a collaboration with the National Cancer Institute (NCI) contractor Leidos Biomedical to cross-validate 50 mAbs and 50 rAbs with six standard assays: WB (recombinant and cell lysate), Indirect ELISA (titration and B50 calculation), Surface Plasmon Resonance (SPR), IP-MS, NCI - 60 RP Array, and NCI-60 IHC. Additionally, Leidos performed quality spot-checking 30 reagents that are currently available through distributors. All affinity reagents posted on the PCRP portal are available through low-cost distributors and have links to order pages. Distributors include the Developmental Studies Hybridoma Bank (DSHB), the DNASU Plasmid Repository at Arizona State University (DNASU), and Custom Designed Immunologics Inc. (CDI). Rutgers-supplied antigens are also available as plasmids through DNASU with links provided on the PCRP portal. CDI, Inc. is a monoclonal production facility in Puerto Rico and is an associated partner with the JHU center. Currently on the portal (July 2015), there are 1059 available reagents to 351 unique hTF proteins, with more mAbs coming on-line in the next year. Because of the well-known difficulties with the reliability of commercially available antibodies, an independent, third party assessment of the reagents is needed to enhance community adoption. Not all available and future reagents should undergo additional assessment via a third party contract. The reagent list should exclude: 1) reagents made against non-Rutgers antigens, 2) rAbs available at DNASU, and 3) mAbs or rAbs that exceed the 4 Abs/per unique protein threshold. Given these criteria, the estimated number of reagents to target for independent validation is 500. All affinity validation SOPs are listed on the PCRP data portal. The information generated by this independent assessment will add objective value to the reagents produced by this consortium. The proposed contract will allow additional validation and follow-up to the reagents, as well as publishable data analyses. II. Purpose and Objectives The purpose of this acquisition is to 1) have a third party validation of the available mAb and rAb affinity reagents meeting the above stated criteria, 2) deposit all data (positive or negative) on PCPR data portal, 3) have the positively validated mAbs and rAbs sequenced with sequence data deposited and stored on the PCRP data portal, and 4) have the results analyzed and published in a scientific journal. Project Design All affinity reagents shall be obtained through the DSHB and CDI distribution centers. Antigens may be obtained as noted in the section below. The mAb and recombinant phage display Fabs will be assessed in the assays noted below. Work to be performed 1. Acquisition/Production of Materials a. Antigens: All source antigens will be obtained from Rutgers via subcontract, if possible. If not possible, antigens obtained/produced from other sources (eg. commercially-available lysates or proteins, or Rutgers plasmids from DNASU) shall be considered and agreed upon by the CO and COR. Purified targets from Rutgers are cost estimated at ~$2,500 per antigen. Some antigens, however, may be available in enough quantities from existing stock without need to re-purify. Since the Rutgers center has experience with the expression of these antigens, there is significant benefit to obtaining antigens through this source. However, a combination of multiple sources may be necessary. Negative results from secondary source antigens, must be re-assessed with originally-produced antigen. Detail plans for antigen production or accruement shall be outlined in the capability statement. b. Affinity reagents: mAb will be produced either from hybridoma clones obtained through DSHB; or supernatant or semi-purified from CDI. RAN reagents will all be procured from DSHB as recombinant Fabs. Fabs can then be expressed as IgG, if preferred. A combination of all of the above may be used. c. Cell lines to be used: Six cell lines predetermined and agreed upon, will be used. Two or more of the cell lines will be from the Encyclopedia Of DNA Elements (ENCODE) Project designated cell type list. The contractor shall be responsible for procuring and verifying cell lines. In the event that a chosen cell line is found not to be suitable, other cell lines approved by the contractor and NIH coordinators will be implemented in the assay. 2. Laboratory work to be performed a. Ab validation assays i. Western blotting at endogenous levels in 6 chosen cells lines ii. ICC (with and without knockdown) in 6 chosen cell lines iii. IP-MS in one chosen cell line The budget will only allow for one attempt in 6 cell lines for WB and ICC. If IP-MS fails, in the first cell line, a second attempt in another designated cell line will be performed. RAN affinity reagents can be tested either as Fab or IgG expression, but only in one format per assay for consistency purposes. Tracking of failed attempts should be performed for determination of statistical relevance. b. Sequencing of monoclonal antibody variable regions. Deposition of sequence data will be to the PCRP data portal. 3. Analyze data in collaboration with a statistician regarding correlation of results and to produce a document for publication in scientific journal. The NIH PCRP coordinators will be co-authors of the manuscript and will assist in the preparation of the manuscript. 4. Maintain the confidentiality of the data received, produced, and distributed and adhere to information technology practices in all aspects of data management to assure that only authorized individuals can gain access to datasets. 5. Provide secure back-up of all data essential to the project, including but not limited to all reagent validation data, maintained by information technology ( IT) professional in a secure server with results (positive or negative) deposited to the PCRP data portal. 6. All remaining samples used for testing shall be retained for future experiments and must be stored for future research purposes for the life of the contract. 7. Changes to reagents or assays must be agreed upon by the contractor and NIH PCRP coordinators. Specific performance requirements are: A. REPORTING ACTIVITIES 1. Quarterly Progress Report The Quarterly Progress Report shall consist of a description of the work performed during the prior 3 months and include a table which details the number of assays and reagents that have been completed. There should also include a table indicating the running queue of reagents and where they are in the assay process. The format of the report shall be determined in consultation with and approval by the Contracting Officer (CO) and Contracting Officer's Representatives (COR). The first reporting period consists of the first full 3 months of performance, including any fractional part of the initial month. Thereafter, the reporting period shall consist of 3 full calendar months. The report shall be submitted within 15 calendar days following the close of the reporting period. A Quarterly Progress Report is not due for the final three month period of the contract. One copy of each Quarterly Progress Report shall be submitted to the CO and primary COR by e-mail in PDF document format with tables additionally in Microsoft excel format. Quarterly data should be deposited in a timely manner to the PCRP data portal. 2. Final Report The format and contents of the Final Report shall be determined in consultation with the CO, COR, and Alternate COR. After approval of the Final Report format by the CO, the Final Report shall be delivered electronically in PDF document format to the CO and COR. The final report will include the third party assessment manuscript submitted for publication (see below), and also shall include recommendations for future research and development and directions in the area of antibody validation. Any copies of published articles supported by the contract, but not copies of the Quarterly Progress Reports, shall be included. One copy of the Final Report shall be submitted to the Contracting Officer and one to the Contracting Officer's Representative, on or before the expiration date of the contract. 3. Publication The work performed and subsequent statistically validated data should be analyzed in collaboration with a statistician regarding correlation of results and to produce a document for publication in a peer-reviewed scientific journal. The manuscript of the third party assessment must be submitted to a peer-reviewed scientific journal by the end of the contract. The NIH PCRP coordinators will be co-authors of the manuscript and will assist in the preparation of the manuscript. It shall summarize the findings of the studies performed under the contract, and should include both positive and negative results. III. Anticipated Period of Performance The anticipated period of performance of any resultant contract from this potential requirement shall begin on or around September 1, 2016 through August 30, 2018, and include an option to exercise up to one (1) additional one year optional period of performance. IV. Capability Statement/Information Sought Interested parties shall review this notice and the requirements of the project. Failure to do so will be at your firm's own risk. The following information shall be included in the capability statement: 1. A general overview of the respondents' opinions about the difficulty and /or feasibility of the potential requirement, and any information regarding innovative ideas or concepts. 2. Information in sufficient details of the respondents' (a) staff expertise, including their availability, experience, and formal and other training; (b) current in-house capability and capacity to perform the work; (c) prior completed projects of similar nature; (d) corporate experience and management capability; and (e) examples of prior completed Government contracts, references, and other related information. 3. The respondents' DUNS number, organization name, address, point of contact, and size and type of business must be listed on their capability statement. 4. Any other information that may be helpful in developing or finalizing the requirements of the potential acquisition. 5. The capability statement shall not exceed 10 single-sided pages (including all attachments, resumes, charts, etc.) presented in single-space and using a 12-point font size minimum, in either Microsoft Word or Adobe Portable Document Format (PDF), with 8-1/2 by 11 inch paper size, and 1 inch top, bottom, left and right margins. 6. All proprietary information should be marked as such. Statements should also include an indication of current certified small business status; this indication should be clearly marked on the first page of your capability statement (preferably placed under the eligible small business concern's name and address). 7. Responses will be reviewed only by NIH personnel and will be held in a confidential manner. V. Information Submission Instructions: The capability statement shall be submitted electronically (via email) to Iris Merscher, Contract Specialist, at iris.merscher@nih.gov, on August 17, 2015, 10:00 A.M., EASTERN TIME and must reference synopsis number HHS-NIH-NHLBI-RDSS-03-IM. All responses must be received by the specified due date and time in order to be considered. This Research and Development (R & D) Sources Sought Notice (RDSS) is for information and planning purposes only and shall not be construed as a solicitation or as an obligation on the part of the National Heart, Lung, and Blood Institute (NHLBI). The NHLBI does not intend to award a contract on the basis of responses nor otherwise pay for the preparation of any information submitted. As a result of this notice, the NHLBI may issue a Request for Proposal (RFP). THERE IS NO SOLICITATION AVAILABLE AT THIS TIME. However, should such a requirement materialize, no basis for claims against NHLBI shall arise as a result of a response to this notice or the NHLBI's use of such information as either part of our evaluation process or in developing specifications for any subsequent requirement. "Disclaimer and Important Notes: This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published in Federal Business Opportunities. However, responses to this notice will not be considered adequate responses to a solicitation. Confidentiality: No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s)."
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