75N91024R00001Amend3_FE.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

3. EFFECTIVE DATE 4. REQUISITION/PURCHASE REQUISITION NUMBER 5. PROJECT NUMBER (If applicable)

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

STANDARD FORM 30 (REV. 11/2016)

Prescribed by GSA FAR (48 CFR) 53.243

FACILITY CODE

9A. AMENDMENT OF SOLICITATION NUMBER

9B. DATED (SEE ITEM 11)

10A. MODIFICATION OF CONTRACT/ORDER NUMBER

10B. DATED (SEE ITEM 13)

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.

12. ACCOUNTING AND APPROPRIATION DATA (If required) copies of the amendment; (b) By acknowledging receipt of this amendment on each copy of the offer submitted;

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

CHECK ONE A. THIS CHANGE ORDER IS ISSUED PURSUANT TO: (Specify authority) THE CHANGES SET FORTH IN ITEM 14 ARE MADE IN THE CONTRACT ORDER

NUMBER IN ITEM 10A.

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C. THIS SUPPLEMENTAL AGREEMENT IS ENTERED INTO PURSUANT TO AUTHORITY OF:

D. OTHER (Specify type of modification and authority)

15C. DATE SIGNED

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PAGE OF PAGES

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Previous edition unusable

2. AMENDMENT/MODIFICATION NUMBER

Alexis Hudak

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

The purpose of Amendment 3 is to answer offerors' questions related to RFP # 75N91024R00001 which were not previously addressed in Amendments 1 and 2.

The hour and date specified for receipt of offers remains unchanged: 2/26/2024 at 3:00 PM Eastern prevailing time.

Except as provided herein, all terms and conditions of the document referenced in Item 9A or 10A, as heretofore changed, remains unchanged and in full force and effect.

National Cancer Institute Office of Acquisitions 8490 Progress Drive, Suite 400, Frederick, MD 21701-4998

TO ALL POTENTIAL OFFERORS

75N91024R00001

1 8

02/15/2024

2/15/2024

OFFICE OF ACQUISITIONS

NATIONAL CANCER INSTITUTE

REQUEST FOR PROPOSAL NUMBER: 75N91024R00001

Amendment No.: 3

Date of Issuance: 02/15/2024

The above numbered Request For Proposal (RFP) is amended as set forth below. The hour and date specified for receipt of offers remains unchanged: 2/26/2024 at 3:00 PM Eastern prevailing time.

Offerors MUST acknowledge receipt of the amendment prior to the hour and the date specified in the solicitation or as amended, by separate letter, telegram, or email which includes a reference to the RFP and Amendment number. For your convenience, the Proposal Intent Response Form is provided in SECTION J - List of Attachments of this RFP, for this purpose.

FAILURE OF YOUR ACKNOWLEDGMENT TO BE RECEIVED AT THE PLACE DESIGNATED

FOR THE RECEIPT OF OFFERORS PRIOR TO THE HOUR AND DATE SPECIFIED MAY

RESULT IN REJECTION OF YOUR OFFER.

This Amendment provides responses to questions received under RFP 75N91024R00001:

Question 1:

For large businesses, what percentage or amount of the work done needs to be subcontracted?

Answer 1: Please reference the most recent Subcontracting Goals listed at the bottom of the page on SBCX’s website at https://osdbu.hhs.gov/

Section 12.6 Business Proposal Instructions, #5, Small Business Subcontracting Plan has been amended to remove the following language:

HHS expects each procuring activity to establish minimum subcontracting goals for all procurements. The anticipated minimum goals for this RFP are as follows:

32% for Small Business; 5% for Small Disadvantaged Business; 5% for Women-Owned Small Business; 3% for HUBZone Small Business; and 3% for Veteran-Owned Small Business and Service-Disabled Veteran-Owned Small Business.

The above-referenced language on page 87 of the RFP has been superseded and replaced by the following language (changes highlighted in yellow below):

Please reference the most recent Subcontracting Goals listed at the bottom of the page on SBCX’s website at https://osdbu.hhs.gov/

Question 2:

In the previous 2018 RFP N02CO87001-94 (that this RFP replaces) Paragraph 4 pg. 57 indicates that for an award to be made, an offeror must negotiate an acceptable small business subcontractor plan (no specification as to Individual or Commercial). On page 47 #17 of this RFP, more restrictive language is used and indicates that a pre-negotiated Small Business https://osdbu.hhs.gov/ https://osdbu.hhs.gov/

Commercial Plan must already be in place: “*Since this is a commercial requirement, please complete page 1 and check commercial on 1. Type of Plan on Page 2. In addition, please provide a copy of your commercial plan.”

Does this new requirement specifically exclude a proposal based on an acceptable Individual Subcontractor Plan if “individual” is checked on Page 2?

Answer 2: No, an offeror may submit an individual, master, OR commercial subcontracting plan, whichever applies to the particular business. The instructions for submitting a Small Business Subcontracting Plan in section 8.10, Subcontracting Provisions of the RFP have been amended as follows (changes highlighted in yellow below):

8.10 Subcontracting Provisions

If the proposed contract exceeds a total estimated cost of $750,000 for the entire period of performance, the offeror shall be required to submit an acceptable subcontracting plan in accordance with the terms of the clause entitled "Small Business Subcontracting Plan," FAR Clause No. 52.219-9, incorporated herein by reference in the Solicitation, See SECTION 10 - LIST OF ATTACHMENTS, BUSINESS PROPOSAL ATTACHMENTS of this RFP for an example of such a plan. OFFEROR TO SUBMIT SUBCONTRACTING PLAN VIA SBCX WEBSITE: https://osdbu.hhs.gov/subcontracting/9872d396-4a64-494c-a2e4-e77c5fdb16ab

The Business Proposal Attachments section in Section 10 of the RFP, is amended as follows:

17 Small Business Subcontracting Plan

Shall be submitted via:

https://osdbu.hhs.gov/subcontracting/9872d396-4a64- 494c-a2e4-e77c5fdb16ab

An example of the plan/form can be referenced at:

https://oamp.od.nih.gov/sites/default/files/DGS/contracting-forms/HHS%20SubK%20Plan%20Template%20- %20updated%20March%202022.pdf

Question 3:

Page 47 #17 indicates that a Commercial Plan must be in place. Further, it is stated on the subcontracting plan template (link at #17, pg. 47) that: “ …this plan applies to the entire production of commercial service or items or a portion thereof. The contractor sells commercial products and services customarily used for non-government purposes...”

Is the language “entire production of commercial service or items...” meant to indicate that the Plan covers all products and services that a vendor offers (e.g. catalog and custom items), or does it mean that the Plan must also show that the vendor similarly subcontracts non-government business?

Answer 3: Please see the answer to question 2 above for the amended language; a commercial subcontracting plan is not necessarily required; the offeror should submit the type of small business subcontracting plan that they have in place and is applicable to the offeror’s business.

Question 4:

Is Long Read technology such as PacBio or ONT needed for any SOW?

https://osdbu.hhs.gov/subcontracting/9872d396-4a64-494c-a2e4-e77c5fdb16ab https://osdbu.hhs.gov/subcontracting/9872d396-4a64-494c-a2e4-e77c5fdb16ab https://osdbu.hhs.gov/subcontracting/9872d396-4a64-494c-a2e4-e77c5fdb16ab https://oamp.od.nih.gov/sites/default/files/DGS/contracting-forms/HHS%20SubK%20Plan%20Template%20-%20updated%20March%202022.pdf https://oamp.od.nih.gov/sites/default/files/DGS/contracting-forms/HHS%20SubK%20Plan%20Template%20-%20updated%20March%202022.pdf https://oamp.od.nih.gov/sites/default/files/DGS/contracting-forms/HHS%20SubK%20Plan%20Template%20-%20updated%20March%202022.pdf

Answer 4: No, the sample SOWs do not cover the long read technology due to cost considerations.

Question 5:

How much detail related to the pools should be described in the base?

Answer 5: The proposal to the base IDIQ and the proposal to a pool will be reviewed together.

There is no need to repeat the information.

Question 6:

Page 70 of the base RFP states: “Each proposal must be prepared in two parts: a “Technical Proposal” and a “Business Proposal” for each pool in which an offeror proposes and clearly identified.”

Can you please clarify if we need to submit a separate business proposal for each pool (4 separate business proposals) AND a business proposal for the base ID/IQ (total 5 business proposals); or is one overall business proposal required?

Answer 6: Separate business and technical proposals are required for the IDIQ and each pool an offeror is proposing to and for the kick-off task order. Offerors do not need to propose a budget (excel workbook, Attachment 18) for the entire IDIQ; only for the individual pools proposed against and for the kick-off task order. Please see Additional Business Proposal Instructions, Attachment 10, and Attachment 14, Additional Technical Proposal Instructions for further details.

Question 7:

Is Attachment 18, Breakdown of Proposed Estimated Costs, (Excel file) required for each pool separately? Also, this spreadsheet requires calculation of annual totals for each cost element.

Please clarify how many samples should be assumed for this calculation, for each contract period/year, for each pool?

Answer 7: Yes, Attachment 18, Breakdown of Proposed Costs is required for each pool separately, per Section 12.1 General Instructions, #4, Separation of Technical and Business Proposals (page 70) of the RFP. Please see the minimum operational capacity requirements in each of the respective four sample task order SOWs. These requirements are also indicated on page 1 and page 2 of the Att10AdditionalBusinessProposalInstruc.pdf, where sample numbers are listed to calculate the total cost.

Question 8:

Attachment 10 – Additional Business Proposal Instructions; pricing tables. As this is potentially a multi-year contract, and prices change, should the pricing tables reflect current pricing, and if so, how are follow on contract years pricing to be included?

Answer 8: Current pricing should be reflected in the estimate, along with projected costs for all periods in the respective sample task order/SOW for each pool your firm is proposing against.

Question 9:

Attachment 5 - DNA What is the maximum number of samples anticipated per year?

Answer 9: The sample volume depends on the accruals of future projects. The information is not available right now. Past volumes of DNA sequencing were from hundreds to thousands per year.

Question 10:

Attachment 5 – DNA For samples where material is limited, can you give a minimum amount of analyte provided for WES and WGS?

Answer 10: The limited material some projects used was as low as 200ng.

Question 11:

Attachment 5 – DNA Are long-read technologies that support detection of CNVs and structural differences typically missed by short read technologies required or desired for WGS?

Answer 11: No, the long-read technology is not listed in the sample task orders.

Question 12:

Attachment 5 – DNA Can you provide examples of the off-the-shelf capture products desired?

Answer 12: The SOW does not specify the commercial products. The offerors can propose one or multiple products that meet the requirement. The program office can request a specific commercial capture system for proposals in future tasks.

Question 13:

Attachment 5 – DNA For whole exome, are high accuracy methods for detecting low frequency variants in heterogeneous tumors (such as duplex sequencing, template tagging) desired or required?

Answer 13: The SOW does not specify the technical methods. The offerors can propose any technical approaches that meet the deliverable requirement.

Question 14:

Attachment 6 – Bulk RNA What is the maximum number of samples anticipated in a month?

Answer 14: The sample volume depends on the accruals of future projects. The information is not available right now. Past volumes of RNA sequencing were from hundreds to thousands per year.

Question 15:

Attachment 6 – Bulk RNA Is RNA capture, which does not target the entire transcriptome, an option for low quality samples?

Answer 15: The sample RNAseq SOW asks for the total RNAseq of the whole transcriptome after ribosomal RNA depletion.

Question 16:

Attachment 6 – Bulk RNA In the solicitation (Section 2.1), there is discussion of mRNA-seq, but no mention of it in the Attachment 6, are we to understand that this is not a desired assay?

Answer 16: The IDIQ contract solicitation covers a general scope that could be in future tasks.

The Sample RNAseq task order SOW lists typical tasks which allows the offerors to propose detailed approaches. And the listing is not comprehensive.

Question 17:

Attachment 7 Is a case the same as a sample?

Answer 17: A sample is a unit for molecular characterization. A case can be defined as a patient case. In the SOW for DNAseq (Attachment 5), a case is usually a normal sample and a tumor sample pair. In the other task order SOWs (Attachments 6, 7, and 8), a case is the same as a tumor sample for counting purposes.

Question 18:

Attachment 7 Is there an estimated total sample number for the duration of the five-year contract?

Answer 18: The sample volume depends on the accruals of future projects. The information is not available right now.

Question 19:

Attachment 7 Is there an average range of how many samples will be received per month?

Answer 19: The sample volume varies based on the accruals of active projects. The information is not available right now.

Question 20:

Attachment 7 Will the GCC be responsible for completing the bisulfite conversion for methylation EPIC arrays?

Answer 20: For methylation arrays, BPC will send DNA aliquots extracted from tumor tissues.

GCC is required to perform the bisulfite conversion to run the methylation microarrays.

Question 21:

Attachment 7 Will they be able to supply 15-20ul aliquots at concentrations between 50-100 ng/ul? If not, what is the expected volumes and concentrations of the aliquots?

Answer 21: Currently, the BPC ships 25ul at concentrations of about 20 ng/ul for methylation arrays.

Question 22:

Attachment 7 Are samples that fail quality metrics going to be replaced? If not, do we proceed with the expectation that the data for these samples may have lower quality results?

Answer 22: The offeror shall work with BPC to request a sample replacement that failed quality metrics. If a replacement is not available, the offeror will work with the Program Office to move forward. The decision is usually project-specific.

Question 23:

Attachment 7 The proposal mentions that failed samples will not be billed for twice, should we price our quotes to reflect a price that includes a fail rate based on historical experience? Specifically, bisulfite conversion methods do not always yield enough converted DNA to move forward, repeating the protocol on the failing samples may be necessary to either combine both aliquots or use the better yielding sample.

Answer 23: This contract uses a fixed unit price. The offeror shall provide a pricing that covers all the costs.

Question 24:

Attachment 7 Will the GCC be responsible for completing the FFPE Restore protocol on the samples for the methylation EPIC arrays?

Answer 24: GCC is responsible for needed procedures to produce quality deliverables.

Question 25:

Attachment 8 For single cell, is there a preferred platform?

Answer 25: The SOW does not specify a platform. The document states that “the proposed platforms shall use widely adopted commercial off-the-shelf products.” The program office will determine the suitability of the proposed platforms for future tasks.

Question 26:

Attachment 8 What is the anticipated max number of cases per month?

Answer 26: The sample volume depends on the accruals of future projects. The information is not available right now.

Question 27:

Attachment 8 For single cell ATAC, is the expectation for multi-omics (both scRNA and scATAC) or just ATACseq alone? If yes to multi-omics, are you differentiating between single nuclei snRNAseq and single cell (scRNAseq) or is “single cell” meant to be inclusive of both?

Answer 27: Performing scRNAseq and scATACseq together is the preferred option.

The offerors can propose either single-nuclei sequencing or single-cell sequencing depending on the tissue type and the technical approach.

Question 28:

Attachment 8 Do you anticipate scRNA immune profiling?

Answer 28: The sample SOW does not list scRNAseq immune profiling.

Question 29:

Attachment 8 For spatial RNAseq #4 it appears that you are primarily interested in platforms such CosMx, which has an oncology panel. Are other less targeted platforms desired, especially if higher resolution? Are there additional constraints that preclude the use of broad target, higher resolution platforms to meet the need of #4?

Answer 29: #4, The “targeted in situ spatial gene expression with cellular/subcellular resolution” does not specify a commercial platform or a panel selection. Targeted oncology panels are available from multiple companies for spatial gene expression.

The text in the SOW “a commercially available Cancer Gene Panel” should be all lowercase letters. Offerors can propose any commercial platforms that meet the requirements.

The number of probes in the sample SOW is used to make the cost comparable. There are no constraints that preclude the use of a broad target, or higher resolution platforms to meet the need of #4.

Question 30:

Attachment 8 Are spatial multi-omics capabilities desired?

Answer 30: The SOW allows offerors to combine the characterization platforms in a multi-omics fashion.

Question 31:

Attachment 8 Do we have any information on tissue quality and what type of tissues?

Answer 31: The tissue can be either fresh frozen or FFPE. The quality of the tissues will be project-dependent. The tissue will be tumor specimens.

Question 32:

Attachment 8 Will the GCC be performing the sectioning?

Answer 32: The GCC will not perform the tissue sectioning.

Question 33:

Attachment 8 Recognizing that a minimum capacity is 32, what is the expected average demand for scRNA and spatial?

Answer 33: The sample volumes will be based on the project's needs. The information is not available now.

Question 34:

Attachment 8 For spatial, it is also important to know how regions of interest will be selected in a slide if needed. Will the projects be using a morphology marker on the same slide with the tissue that receives the probe or an overlay with IHC or IF marker or an H&E or other stain? For example, morphology markers of PanCK +CD45 is one of the most standard kits for cancer research.

Some platforms require H&E stain. Details are needed to properly estimate the cost.

Answer 34: The SOW does not specify the usage of the Region Of Interest (ROI). Offerors can propose the ROI method if the platform requires the approach. The offerors need to include all costs necessary for processing with the platform proposed.

END OF AMENDMENT 3