Amendment 1 RFP 75N93023R00013.pdf

AMENDMENT #1 RFP No. 75N93023R00013 1

Amendment No. 1 RFP No. 75N93023R00013

“Functional Omics Core Laboratory”

Solicitation Number: 75N93023R00013

Amendment Number: One (1)

Amendment Issue Date: March 15, 2024

Proposal Due Date/Time: May 17, 2024, at 3:00 PM, Local Time (Unchanged)

Issued By: Karen Telphia

Contract Specialist

OA/DEA/NIAID/NIH/DHHS

5601 Fishers Lane, Room 3D10, MSC 9821 Bethesda, Maryland 20892-9821

Points of Contact: PRIMARY karen.telphia@nih.gov Karen Telphia, Contract Specialist Phone: 240.669.2960

Please note that we do NOT intend to extend the due date for submission of proposals as a result of this amendment. The date specified for receipt of proposals remains unchanged.

Offerors must acknowledge receipt of this Amendment by identifying the amendment number and the date of the amendment on each copy of the submitted proposal. Failure to receive your acknowledgement may result in the rejection of your proposal. Except as provided herein, all terms and conditions of the solicitation remain unchanged and in full force and effect.

The purpose of this Amendment is to provide responses to questions from potential offerors, regarding the solicitation.

RESPONSES TO QUESTIONS FROM POTENTIAL OFFERORS:

Question 1 When is the Letter of Intent due?

Response to Question 1 April 16, 2024 mailto:karen.telphia@nih.gov

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Question 2 Is there information on the type and number of proteomics samples that offeror’s should include in their proposal (proteomics is barely mentioned)?

Response to Question 2 The Scope and Technical Requirements sections in the Statement of Work specify that: This contract shall conduct, develop, acquire, improve, implement, validate, analyze and report data from state-of-the-art high-throughput functional omics assays and approaches (e.g., genomics, epigenomics, transcriptomics, proteomics) for comprehensive characterization of immune responses in samples from in vivo or in vitro studies investigating simian immunodeficiency virus (SIV), simian-human immunodeficiency virus (SHIV), HIV and other infectious diseases.

The omics assays may include generating, analyzing, and integrating data generated from genome, epigenome, transcriptome, and proteome. The types of assays and the samples will be defined by individual study protocols designed by the collaborating investigator, the COR, and/or other individuals identified by the COR, in collaboration with the Contractor. The assays will be performed on fresh, cryopreserved, or fixed samples from primarily NHP studies but may include samples from small animal models, in vitro studies or human clinical studies.

Use state-of-the-art functional omics assays and technologies (e.g., genomics, epigenomics, transcriptomics and proteomics) as required by individual study protocols for comprehensive analyses of single-cell genes, methylated DNA and modified histone proteins in chromosomes, RNA, and proteins.

As to proteomics analyses, please note that the type and number of samples for proteomics analyses will be defined by individual study protocols in parallel to the other functional omics assays for genomics, epigenomics, and transcriptomics.

In general, as to the type and number of samples for performing the indicated functional omics assays (including proteomics), and for costing purposes, offerors can propose a mix of these different types of -omics approaches, and how many fresh, cryopreserved, or fixed samples would be assigned for each proposed type of -omics assay.

Question 3 Are Multiple PIs allowed?

Response to Question 3 No, you cannot have multiple PIs.

Question 4 What is the expected funding set aside at NIH for this program (i.e., budget limits/constraints)?

Response to Question 4 The Government is not allowed to provide such information.

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Question 5 The text states that “conformance to GLP procedures for contract laboratory activities will be reviewed by an independent quality control assurance unit”; and then states somewhat contradictory that “the Contractor shall establish an independent QA Program not associated with the Contract to conduct regular quality inspections to ensure conformance to GLP procedures”. Specifically, what do you mean by “independent”? Can you please provide an example of how this is achieved for other similar programs that are funded, and point us to the leaders of that Program for consultation?

Response to Question 5 In the context of this contract, an independent quality control (QA) assurance unit relates to a team of 3-4 scientific experts who are not directly part of the contract team. Following the issuance of the contract, the offeror, in consultation with the CO and COR, is expected to organize a QA program for regular (e.g., yearly) quality inspections to ensure conformance to GLP procedures by reviewing the contract SOPs, protocols, and raw data of interest.

Question 6 On Page 78 the technical proposal page limit is stated to be 200 pages. But on then on page 90 the stated page limit is shown as 150 pages. Which is correct page limit for the technical proposal?

Response to Question 6 150 pages is the page limitation.

Question 7 The text lists of many different seq platforms but does not give details on what type of proteomics analyses are to be provided. Can you please provide these details on proteomics?

Response to Question 7 A few examples of proteomics analyses include CyTOF (Cytometry by Time of Flight) Mass Cytometry, CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes) and LC-MS (Liquid Chromatography–Mass Spectrometry).

Question 8 UW was listed in the solicitation as the Core Lab in the previous Functional Genomics Core Lab contract. We noticed that current funding period for UW Core ends in 2025. I wonder if you expect UW to submit renewal for this cycle.

Response to Question 8 We cannot provide such information.

Question 9 From the solicitation, it seems to me that you expect to fund one Core Lab. My research focus on proteomics and epigenetic regulation through histone modifications. I am curious if you would entertain proposal on the proteomics/histone modifications aspects of the solicitation?

AMENDMENT #1 RFP No. 75N93023R00013 4

Response to Question 9 Your proposal must be responsive to our solicitation in its entirety and all of the technical requirements outlined in the Statement of Work. We cannot direct an offeror on how nor what to propose.

Question 10 I saw an exemplary budget and personnel on SOW in the solicitation. I wonder if the budget and work scope is pretty much set to 2.7 FTEs and ~ 2,790 samples each year. 2,790 samples each year sounds a little high for proteomics and histone modifications analysis with 2.7 FTE in my group. I wonder if you can help provide some clarification?

Response to Question 10 The Government did not provide a budget for this requirement. We leave this up to the offerors to propose. The FTEs are the requirement and cannot be adjusted. In general, please note that the type and number of samples for functional omics assays and analyses will be defined by individual study protocols and the number of samples included in the RFP are for costing purposes only.

END OF AMENDMENT NO. 1, RFP No. 75N93023R00013