75N91024R00001 Amend 2_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;

13. THIS ITEM APPLIES ONLY TO MODIFICATIONS OF CONTRACTS/ORDERS.

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.

B. THE ABOVE NUMBERED CONTRACT/ORDER IS MODIFIED TO REFLECT THE ADMINISTRATIVE CHANGES (such as changes in paying office, appropriation data, etc.) SET FORTH IN ITEM 14, PURSUANT TO THE AUTHORITY OF FAR 43.103(b).

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

D. OTHER (Specify type of modification and authority)

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.

15C. DATE SIGNED

15A. NAME AND TITLE OF SIGNER (Type or print)

16C. DATE SIGNED

16A. NAME AND TITLE OF CONTRACTING OFFICER (Type or print)

PAGE OF PAGES

6. ISSUED BY CODE

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

CODE

15B. CONTRACTOR/OFFEROR

(Signature of person authorized to sign)

16B. UNITED STATES OF AMERICA

(Signature of Contracting Officer)

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 2 is to answer offerors' questions related to RFP # 75N91024R00001 which were received after the posting of Amendment 1 on January 19, 2024 through February 1, 2024 at 3:00 PM ET, when the question period ended.

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

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

TO ALL POTENTIAL OFFERORS

75N91024R00001

1 5

02/08/2024

2/8/2024

OFFICE OF ACQUISITIONS

NATIONAL CANCER INSTITUTE

REQUEST FOR PROPOSAL NUMBER: 75N91024R00001

Amendment No.: 2

Date of Issuance: 02/08/2024

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:

What is the required turnaround time?

Answer: The turnaround time for each platform is specified in the sample task order Statement of Work (SOW).

Question 2:

Will the FFPE/fresh frozen samples come in slides/whole block/curls? (RNA seq) Answer: In the case of RNA sequencing, the input material for the GCC contract is RNA aliquots produced and shipped from the Biospecimen Processing Core (BPC). The original tissues processed at BPC can be either FFPE or Fresh Frozen samples in a variety of forms, but that is beyond this contract.

Question 3:

Is it expected that total RNAseq and miRNASeq will be performed on all or a subset of samples?

Answer: This depends on the specific projects where the samples come from. Most projects are expected to perform both total RNAseq and miRNAseq.

Question 4:

Can you give us an idea of volumes and how those will be broken out (i.e., weekly/monthly/ annually)?

Answer: The volumes will depend on the case accrual rate of active projects. We don’t have an estimate until a specific task order for each platform is issued, and each project will have its own defined requirements (when the need arises).

Question 5:

Section 2, Subsection 2.3 Severable and Nonseverable Services states that "Unused funds from one period (line item) may not rollover for use in other periods."

I understand that to mean that funds allocated for use during a certain period of performance may not be used or rolled over for use in other time-periods. It does not clarify whether the money can be used for other services. Can you clarify if unused funds can be used for other services within the same period of performance?

Answer: It is not possible to answer this question in a general fashion since it is unclear which services the potential offeror is referring to. In addition, severable and nonseverable services will be determined at the task order level, not at the IDIQ level, as funds are not committed on the IDIQ base contract.

Question 6:

What are the regulatory requirements of this RFP if any for each task area?

Answer: Please carefully review the RFP and each attachment for specified requirements.

Regulatory requirements are described throughout the original solicitation document/RFP.

Question 7:

Will the service provider be receiving patient identifying information?

Answer:. All samples provided to the contractors shall be de-identified. The GCC contractors should not receive any patient identifying information from BPC.

Question 8:

How long is analysis data required to be stored at the service provider?

Answer: The contractor is required to upload the sequence data to the NCI repository. The local data should be retained until the submitted data is received, processed, and passes the data QC validation at the GDC. The contractor can communicate with the GDC on the data validation schedules of individual projects.

Permanent data retention and archival by the provider is not required.

Question 9:

For Task Area Two, Assuming work performed over multiple years (i.e. 5-year IDIQ/period of performance), would updated versions of panels be accepted (if available) or would the panels need to be consistent year-to-year, project-to-project? What about in the case of panels being discontinued by 3rd party manufacturers?

Answer: The contractor shall inform the program in advance when an updated panel or an alternative panel shall be considered. The program will work with the contractor to determine whether or not to update the panel version or to change a panel selection.

Question 10:

For Task Area One, Section 8: The requirements specify that "Contractor can deliver CLIA certified results for specific services". Please clarify if this refers to the services outlined in this task orders OR if it refers to CLIA certified services in general.

Answer: This contract does not require CLIA-certified services.

Question 11:

Will the individual samples arriving have data matrix codes or other type of barcode for each sample?

Answer: Yes, samples are shipped from BPC with the standard barcodes to be used by GCC.

Question 12:

Please clarify what is meant by "validated" in this RFP. A couple examples below.

A. What does "validated" mean in the section "Example Characterization Platforms" here:

"...using a validated, documented SOP methodology as approved by the program office."

B. Or in Section "C. Description of Work":

"These pipelines shall be conducted with validated methods using high-throughput and quality-controlled protocols."

Answer: The validated method can be a method used in comparable peer-reviewed studies or validated by a peer-reviewed paper with an orthogonal scientific approach.

Question 13:

For total RNA sequencing, what methodology will be needed, whole transcriptome or targeted approach?

Answer: For total RNA sequencing, whole-transcriptome detection of coding and non-coding RNA is expected.

Question 14:

For spatial transcriptome profiling, how will the region of interest (ROI) be defined? What type of profiling (geometric, segment, contour) will be needed? Will there be needed for path consultation?

Answer: The offeror can propose the ROI definition method to be used in the pipeline, but no specific method delineation is specified in the SOW. Pathology consultation is not part of the GCC contract.

Question 15:

Will they publish Q&A from all vendors publicly?

Answer: Yes, answers to questions received by offerors (up until the questions deadline of 02/02/2024 at 3:00 E.T.) are shared publicly on SAM.gov via amendments to the solicitation.

This ensures all potential offerors receive the same information and are given equal/fair opportunity under this solicitation.

Question 16:

For each task area below, can you offer more detail regarding the starting material or sample input type? (i.e. fresh frozen tissue, FFPE, blood, DNA, RNA, etc. and the amount of material).

Are there any input material types that are not listed in the RFI that you foresee vendors may be sent (such as other biological fluids (plasma, serum, saliva) or biosamples (e.g. stool))?

1. High throughput DNA Sequencing (NGS)

2. High throughput RNA Sequencing (NGS)

3. epigenome characterization with NGS

4. single cell/spatial characterization with NGS Answer: For DNA sequencing, standard DNA aliquots will be 750ng. For methylation arrays, standard DNA aliquots will be 500ng. For RNA sequencing, RNA aliquots (2 ug) will be provided. If studies give a lower amount of input material, it will be specified in the task orders.

For pool 3 and pool 4, the sample input can be isolated cells, tissues, or slides depending on the platforms.

There is no information currently available about the input material types mentioned in the last sentence.

Question 17:

Will extracted be needed for any of the pools or task areas? If so, which ones?

Answer: Extraction may be needed for pool 3 such as ATACseq, and pool 4 single cell/spatial characterization. No extraction is expected at GCC for DNAseq, RNAseq or Methylation arrays.

Question 18:

Section 2 - Services states that "multiple awards, up to 16 across all four IDIQ Pools" will be made on or around 9/15/2024. Within these 16, how many vendors do you plan to award to each of the 4 pools? Additionally, can one vendor be awarded in more than one pool?

Answer: There are no specific numbers of awards assigned for each pool. Vendors can propose to one or more pools. A vendor can be awarded in one or more than one pool.

Question 19:

When evaluating vendor proposals, will each pool be evaluated separately, or will the vendor's entire proposal (all 4 pools) be evaluated together?

Our understanding is that technical evaluation factors rank significantly higher than cost/price factors for decision criteria. Is this true when evaluating all 4 pools?

Answer: Each pool will be evaluated separately. Please reference Section 12, General Instructions and Section 13, Evaluation Factors for Award of the Solicitation for details.

Question 20:

Sequencing metrics and deliverables as mentioned in SOWs are based on Short Read Illumina technology and not from any other short read sequencing technology?

Answer: The IDIQ contract SOW does not specify the type of commercial sequencers or technologies.

Question 21:

The final Data deliverable includes FastQ and associated metadata files. Is any further downstream analysis needed such as mapping, alignments, bam file generation, differential expression analysis, Methylation calling etc.?

Answer: The deliverables are platform-dependent and file formats are specified by the NCI repository. Please review the details at https://gdc.cancer.gov/submit-data/gdc-data-submission-portal.

The deliverables for sequencing experiments will be BAM or FastQ as specified by the NCI repository. Alignment for BAM generation may need the pipeline and parameters specified by the NCI repository. The deliverables for microarray experiments are microarray intensities. Most downstream analyses such as methylation calls and differential expression analysis will not be required.

END OF AMENDMENT 2

https://gdc.cancer.gov/submit-data/gdc-data-submission-portal https://gdc.cancer.gov/submit-data/gdc-data-submission-portal