75N95024R00040 Amendment 00002.pdf

Offers must acknowledge receipt of this amendment prior to the hour and date specified in the solicitation or as amended, by one of the following methods:

(a) By completing items 8 and 15, and returning or (c) By separate letter or electronic communication which includes a reference to the solicitation and amendment numbers. FAILURE OF YOUR ACKNOWLEDGMENT TO BE RECEIVED AT THE PLACE DESIGNATED FOR THE RECEIPT OF OFFERS PRIOR TO THE HOUR AND DATE SPECIFIED MAY RESULT IN REJECTION OF YOUR OFFER. If by virtue of this amendment you desire to change an offer already submitted, such change may be made by letter or electronic communication, provided each letter or electronic communication makes reference to the solicitation and this amendment, and is received prior to the opening hour and date specified.

E. IMPORTANT: Contractor is not is required to sign this document and return copies to the issuing office.

AMENDMENT OF SOLICITATION/MODIFICATION OF CONTRACT 1. CONTRACT ID CODE

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7. ADMINISTERED BY (If other than Item 6) CODE

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Prescribed by GSA FAR (48 CFR) 53.243

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11. THIS ITEM ONLY APPLIES TO AMENDMENTS OF SOLICITATIONS

The above numbered solicitation is amended as set forth in Item 14. The hour and date specified for receipt of Offers is extended. is not extended.

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IT MODIFIES THE CONTRACT/ORDER NUMBER AS DESCRIBED IN ITEM 14.

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14. DESCRIPTION OF AMENDMENT/MODIFICATION (Organized by UCF section headings, including solicitation/contract subject matter where feasible.)

PAGE OF PAGES

6. ISSUED BY CODE

8. NAME AND ADDRESS OF CONTRACTOR (Number, street, county, State and ZIP Code) (X)

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16B. UNITED STATES OF AMERICA

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Previous edition unusable

00002

Valerie Whipple

The purpose of this amendment is to:

1) Extend the proposal due date to November 21, 2024; 3:00pm local time;

2) Provide answers to questions received; and,

3) Provide the following clarification: If applicable, the Small Business Subcontracting Plan must be submitted by the proposal due date through the U.S. Department of Health and Human Services (HHS) Small Business Customer Experience (SBCX) system via the following link: https://osdbu.hhs.gov/subcontracting/d12562a3-41f8-470a-9516-012142eff4a4

National Institutes of Health National Institute on Drug Abuse Office of Acquisitions Bethesda, MD 20892-7511

75N95024R00040

1 9

11/07/2024

11/07/2024

RFP 75N95024R00040

Questions and Answers:

Q1: We are not clear how we would implement the procedures outlined in Article H.7 of the Solicitation. If a subcontractor ships or transfers “research substances and/or living organisms” to recipients (presumably researchers at other Universities with research funds), are the recipients required to submit payment to the Prime Contractor, within 15 days (bullet d.) and also inform the recipient that “failure to pay an invoice may result in future purchase requests being denied” (bullet e.)?

a. Would the Prime Contractor be responsible for all the invoice and collection for subcontractors, instead of the subcontractors invoicing directly?

b. If the above is the case, then why in, bullet h., does it mention the processing of payments to us, the Contractor, via Pay.gov, if we are already getting payment from the recipients?

c. What happens if the recipients do not pay the invoice?. What is our recourse for collection?

A1: a. The Prime Contractor is responsible for meeting the requirements outlined in Section

H.7 REMITTANCE PROCEDURES FOR SALE OF RESEARCH SUBSTANCES AND LIVING

ORGANISMS. The Contractor can assign duties (e.g., shipping the substances; informing the recipients that “failure to pay an invoice may result in future purchase request being denied) to the subcontractor. However, the Contractor must be the entity submitting payment to the Government through Pay.gov for the research substances and/or living organisms associated with the invoice number received from the Government, in accordance with Paragraph h.

b. The Contractor is not receiving payment via Pay.gov. “The Contractor shall submit payment to the Government through Pay.gov for the research substances and/or living organisms associated with the invoice number received from the Government.”

c. It is incumbent upon the Contractor to demonstrate in its proposal how they will meet the requirements outlined in the SOW.

Q2. In the Solicitation, on page 77, section C. TYPE OF CONTRACT AND NUMBER OF AWARDS, it states "1. It is anticipated that one award will be made from this solicitation and that the award will be made on/about May 1, 2025." Om the other hand, in most other sections, it states March 1, 2025. For instance, Solicitation Pg 15 Article F.1. PERIOD OF PERFORMANCE - OPTIONS, "The base period of performance of this contract shall be from March 1, 2025 through February 28, 2026." or Cover Letter pg. 2 "Base Period March 1, 2025 through February 28, 2026"

The current U24 end date is 02/28/25. What is the anticipated start date?

A2: The correct anticipated start date is on or about March 1, 2025.

Q3. Are the references for the technical proposal to be included in the 30-page limit, or in the appendix or a separate reference section?

A3: The references do not need to be included in the 30-page limit.

Q4: Can you please confirm that if two organizations are partnering on this application, a multi (two)-PI application is acceptable?

“The multiple PI option is based on the proposed project, not on the number of performance sites or the number of participating institutions.

Multiple PIs under research contracts shall use the Subcontract Model. In this approach, offerors submit a single proposal, and a single award is made to the prime contractor. The prime contractor, when appropriate, will award subcontracts to fund the components of the project at the other institutions. The relationship between the Contractor and subcontractors must be designed to support all components of the project.”

A4: Per page 92 in the Solicitation, a multiple PI application is acceptable for this RFP.

Proposals submitting with multiple PIs must include a leadership plan and use the Subcontract Model (as applicable).

Q5: Tube level accessioning will be a substantial budgetary ask for the current 3.5 million collection transfer in. Is this mandatory at the tube level?

A5: The current collection is accessioned at the tube level, with minor exceptions. For proposal development purposes, offerors should describe their recommended approach to biospecimen accessioning, the rationale, and any pros and cons.

Q6: How much QC data is available for the current 3.5M collection?

A6: QC data for DNA samples includes DNA purity and concentration, and limited use of a SNP identity panel which provides data on gender, sample uniqueness, ethnicity, and utility for PCR-based or other downstream analyses. Total RNA concentration and purity are available for a subset of samples.

Quality control measures for iPSC line generation include identity validation of source cells and iPSCs, mycoplasma screening, and assays to assess stemness markers and pluripotency. The genomic integrity of iPSC lines is assayed. Lymphoblast cell lines are tested for cell viability and freedom from contamination. Edited iPSC cell lines are assessed for unintended off-target modifications and contamination with unedited cells.

Offerors should propose their recommended approach for biospecimen QC under this contract.

Q7: How is the current collection tube labeling? Is it matrix or not, allowing for bulk scanning?

A7: Tubes are 2-D barcode labeled. DNA but not cells are labeled in a way allowing for bulk scanning (i.e., in barcoded boxes).

Q8: The RFP requires clinical expertise:

”Psychiatric clinical data curation, standardization, and harmonization, with a comprehensive knowledge of cross-disorder phenotypic dimension”

For budgeting purposes can the NIMH please provide more details re the SCOPE of the clinical data curation, standardization, and harmonization required? Will the clinical subject matter experts (SMS’s) be manually curating data from approx. 16K donor/patient cases each year? We would like to know more details about what this side of the SOW would entail.

A8: The scope of clinical data curation, standardization, and harmonization includes review of diagnosis-related data submitted by studies, including diagnostic definitions, and generation of a harmonized diagnosis for each subject (the “NIMH Diagnosis”). The NIMH Diagnosis is a consensus diagnosis assigned as an index to facilitate querying the collection across the studies within NRGR.

Q9: Do you know what exact QC is happening for the DNA and cell samples (e.g. nanodrop and/or Qubit?, etc.)

A9: QC data for DNA samples includes DNA purity and concentration, and limited use of a SNP identity panel which provides data on gender, sample uniqueness, ethnicity, and utility for PCR-based or other downstream analyses. Total RNA concentration and purity are available for a subset of samples.

Quality control measures for iPSC line generation include identity validation of source cells and iPSCs, mycoplasma screening, and assays to assess stemness markers and pluripotency. The genomic integrity of iPSC lines is assayed. Lymphoblast cell lines are tested for cell viability and freedom from contamination. Edited iPSC cell lines are assessed for unintended off-target modifications and contamination with unedited cells.

Offerors should propose their recommended approach for biospecimen QC under this contract.

Q10: For whole blood extraction, are PBMC sufficient or must it be isolated CPLs? Also, in the SOW section 3.1, the blood pipeline states 10% LCL and 70% CPL generation. Are the LCLs derived from the 70% CPLs? Or are they derived from PBMCs? Is the remaining blood 20% and for DNA/RNA extraction?

“[3.1] Processing received blood or tissue samples to extract high-quality, well characterized whole blood-derived DNA, plasma, whole blood-derived RNA/cDNA, and primary cell cultures (e.g., fibroblasts). This includes capabilities for processing, generating, and storing renewable resources, including generating LCLs via Epstein- Barr virus transformation from approximately 10% and cryopreserved lymphocytes (CPLs) from approximately 70% of received blood collections that are consented for cell lines, respectively; expansion of fibroblasts from skin punches; and expansion of olfactory cells from nasal biopsies.”

A10: For whole blood extraction, PBMCs are sufficient (it is not required to use CPLs). For section 3.1, the LCLs may be derived from the PBMC. Yes, the remaining blood is for DNA/RNA extraction.

Q11: How many aliquots are created for the different product types? The iPSC inventory looks like >100 aliquots per line.

A11: The following number of aliquots are generated per product type: 1) 8 aliquots of LCLs;

2) 12 aliquots of iPSCs; 3) 2 vials of PBMCs; 4) 1 aliquot of DNA from saliva or whole blood;

5) 4 aliquots of DNA from LCLs.

Q12: Are all new cell culture inventory stored in vapor LN2 tanks?

A12: The current NRGR new cell culture inventory is usually stored in vapor LN2 tanks.

Q13: Whilst gene editing of iPSC’s is mentioned, no edit types or volumes were provided.

Is this known?

A13: Offerors should propose their recommended approach to cell line gene editing and discuss the range of approaches they could make available for use by NRGR.

Q14: What is the sample metadata from the incumbent ‘Sampled’ biorepository? Please provide information about the current database (MySQL, SQL Server, Oracle, etc.) and their respective database sizes.

A14: Sample metadata includes demographic information, ID numbers, and study-defined diagnoses. Submission requirements for the incumbent biorepository can be found on the website, https://www.nimhgenetics.org/submit-your-data/submission-requirements.

NRGR data are stored in two databases: A MySQL 8 Commercial database (50 GB in size) and Microso_ SQL Server LIMS database (2.6 TB in size). For proposal development purposes, describe your recommended approach to database organization. Discuss any assumptions made regarding the status and format of the repository databases that impact the proposed approach and budget.

Q15: What is the size of non-database files (imaging, genotyping, sequencing, etc.) and their respective file types and sizes?

A15: NRGR includes roughly 17 TB of non-database files of various types and sizes. The “Genomic Datasets at NRGR” table on https://www.nimhgenetics.org/resources/genomic-data describes available genomic datasets. Some genomic data are stored on external hard drives. The total size of the website (i.e., html and all data) is 153 GB.

Q16: Please provide additional information regarding the https://www.nimhgenetics.org/ website if available. Is this website proprietary to the incumbent, or is it a government-funded website, and will it be transferred to the new contractor?

A16: The website domain is proprietary to the incumbent and will not be transferred to a new contractor.

Q17: The base period performance start date in the RFP pg 15 states March 1, 2025 start date, however, in later docs an award date of May 1, 2025 is referenced. Which is accurate?

A17: The correct anticipated start date is on or about March 1, 2025.

Q18: Does the current collection have identity confirmation data (i.e., confirm original submission and final product identify uniformity)?

A18: A portion of the NRGR collection has identity confirmation data.

Q19: Can the Government specify how long after award will the incumbent team be available to provide transition-in support and knowledge transfer? (Attachment 3, page 5 of 25)

A19: Per page 5 of Attachment 3, the incumbent team shall be available for the first six months of the Base Year for Transition-In support and activities.

Q20: Can the Government provide either a blank consent form or an NRGR Institutional Certificate for each legacy study? (Attachment 3, page 5 of 25)

A20: A blank consent form or Institutional Certificate cannot be provided for each study.

Q21: Will the Government provide Institutional Review Board (IRB) consent? (Attachment 3, page 5 of 25)

A21: While the project does utilize human specimens, it is not anticipated that the contract will include human subjects research. The determination was based on several factors including that NRGR is not involved in the primary or initial specimen collection and does not have access to or retain any of the codes/identifiers to human subjects. As such, IRB consent is not anticipated to be required for transfer-in of samples.

Q22: Can the Government provide estimates of (1) how many studies may need reconsent, (2) how many studies have RUCDR-specific consent language, (3) how many studies have opted-out of re-contacting participants and (4) the number of legacy studies for which it has (a) a copy of the blank consent form, and (b) the number of studies that the Government has a copy of the NRGR Institutional Certificate, but not a blank consent form?

(Attachment 3, page 5 of 25)

A22: The Government estimates that the majority of NRGR studies will have either a blank consent form or Institutional Certificate on file. The number of studies with RUCDR-specific consent language or studies that have opted out of re-contacting participants cannot be provided at this time.

Q23: Can the Government provide an estimate of how many helpdesk inquiries are expected to be supported per week (Attachment 3, page 11 of 25)

A23: NRGR receives on average 14 helpdesk inquiries per week. Offerors should discuss Helpdesk capabilities and capacity available and their approach to handling variable workload.

Q24: Can the Government confirm the new Contractor will have access to the software code base, database, data files, physical and logical data models, documentation, security infrastructure, etc.? (Attachment 3, page 10 of 25)

A24: The incumbent is required to facilitate the orderly transfer of repository materials and data to a new repository operator in the event that the incumbent does not successfully compete for a subsequent project period.

Q25: Can the Government specifiy [sic] if the existing software/hardware infrastructure is owned by NIMH or is it proprietary?

A25: The existing software/hardware infrastructure is proprietary to the incumbent.

Q26: Can the Government confirm that the Monthly Progress Report can be due on the 10th day of the month? (SECTION C.2.a, Page 7)

A26: Yes, the Monthly Progress Report can be due on the 10th day of the month.

Q27: Please note there is a conflict between the ATO and tranistion [sic] period. Can the Government redefine the requirements for ATO completion until after the transition period is over? (SECTION B, Page 8)

A27: In the RFP, deliverables required to complete the ATO should be submitted within three

(3) months after contract award. Since there may be a transition period if a new contractor is awarded, the ATO timeline will shift to include the transition period.

Q28: There is conflicting information on Page 15 and Page 77, where the anticipated award date (May 1, 2025) is after the anticipated contract start date (March 1, 2025. Can the Government clarify the contract award date?

A28: The correct anticipated start date is on or about March 1, 2025.

Q29: Can the Government confirm if subcontractors can submit Other than Certified Cost Price Data? (Section L, Page 95 Att. 13)

A29: Yes, subcontractors can submit Other than Certified Cost or Pricing Data under certain conditions. See FAR 15.403-1 and FAR 15.403-3.

Q30: Can the Government confirm that subcontractors should submit a sealed bid directly to the government? (Section L, Page 95 Att. 13)

A30: All proposals must be submitted via the Electronic Contract Proposal Submission (eCPS) and not directly to the Contracting Officer. Subcontractors may submit via eCPS and indicate that their submission is part of the subcontract to the Prime Contractor and the Prime Contractor proposal needs to state the same.

Q31: We expect to complete the vast majority of the technical and documentation work for FISMA compliance during the current grant period, which ends in Feb 2025. However, external certification is planned to occur during the next contract period. We would like to obtain clarification on the timeline for FISMA compliance, as there are different deadlines described in the RFP. Specifically, the Plan of Actions and Milestones (POA&M), pages 9 and 36 of the RFP, allows for remediation of medium and low weakness up to 1 year after contract award. However, page 109 of the RFP requires "Demonstrated capacity to reach FISMA-moderate compliance within the first 6 months of award."

Does this mean that the capacity for compliance will be assessed by NIH within 6 months (likely based on the System Security Plan, which is due 30 days after award, and the external evaluation, due 3 months after contract), but remediation of medium and low weakness, if any found after evaluation, can still be completed within 1 year? Thus, full FISMA compliance is to be achieved within 1 year after contract award?

A31: Capacity for FISMA-Moderate Compliance within 6 Months: As stated on page 109, the requirement for “demonstrated capacity to reach FISMA-moderate compliance within the first 6 months” indicates that NIMH will assess progress toward compliance within the initial 6 months after the award. This assessment involves a review of the System Security Plan (SSP), due within 30 days of the award, and the associated security control assessment results, due within 3 months of the award.

Remediation Timeline for Medium and Low Weaknesses: The Plan of Actions and Milestones (POA&M) requirements on pages 9 and 36 specify that medium and low-risk weaknesses identified during the evaluation or later assessments may be remediated within up to 1 year after the contract award.

Summary: The initial 6-month period is intended to confirm vendor capacity and progress toward FISMA-moderate compliance, while the complete remediation of identified medium and low-risk weaknesses may extend up to 1 year. Therefore, full FISMA compliance, including any necessary remediation, would be expected within 1 year following the contract award.

Q32: The link to the Section 508 compliance template in the SOW is broken. Can it be repaired?

A32: The link is:

https://www.hhs.gov/sites/default/files/web/508/contracting/technology/section_508_annual_r eport.doc. (The link downloads a Word document.)

Q33: The font size is stipulated to be 10 to 12 points for the text. In IH grant proposals, the text in tables and figure legends is unspecified. Is there a specification for the text size for the tables and figure legends?

A33: No, there is no required text size for tables and figure legends.

Q34: I am aiding in the submission of the contract proposal for which requires the submission of Protection of Human Subjects Assurance Identification/IRB Certification/Declaration of Exemption form I have found the form on grants.gov however this expired on 6/30/2024 as shown in the screen shot. I want to confirm if this form will be allowed for the submission of our proposal to NIMH or should this form be sourced elsewhere? I did not see it along with the additional attachments in the RFP.

A34: Offerors may use the same form (OMB No. 0990-0263). As of this writing, the form has not yet been updated.

Q35: Is it acceptable to propose a higher number of hours if an offeror feels that additional labor hours are necessary to complete the requirement effectively?

A35: Offerors should propose their budget based on what they determine is reasonable to achieve the scope of work outlined in the RFP. Budget proposals should be based on the type and volume of work described in the Statement of Work for base activities and options for additional quantities.

Q36: Section 3.1 of the SOW is as follows: “[3.1] Processing received blood or tissue samples to extract high-quality, well-characterized whole blood-derived DNA, plasma, whole blood-https://www.hhs.gov/sites/default/files/web/508/contracting/technology/section_508_annual_report.doc https://www.hhs.gov/sites/default/files/web/508/contracting/technology/section_508_annual_report.doc derived RNA/cDNA, and primary cell cultures (e.g., fibroblasts). This includes capabilities for processing, generating, and storing renewable resources, including generating LCLs via Epstein-Barr virus transformation from approximately 10% and cryopreserved lymphocytes (CPLs) from approximately 70% of received blood collections that are consented for cell lines, respectively.”

To assist us in pricing this task: Is there an estimate of the number of blood samples to be received that are consented for cell lines?

A36: As noted in the Statement of Work for Task Area 2, the Contractor shall expect to receive 16,000 samples per year, including: 13,000 blood samples. For the purposes of proposal development, Offerors should assume that CPLs will be generated from 15% of those blood samples and LCLs from 2% of the samples. Actual percentages may vary, based on the needs of the program.

Q37: Which attachments are required to be completed by sub-contractors?

If a subcontractor submits proprietary information directly to the NIH, then which attachments must be submitted directly to the NIH and which ones to the Prime?

A37: Please refer to the instructions/text included in each attachment. Ideally, the Prime Contractor will submit all required documentation. If the Subcontractor prefers to submit directly to the Government, it should submit documents via the Electronic Contract Proposal Submission (eCPS) and not directly to the Contracting Officer. Refer to Q30.