Sol_1305M326Q0354_Amd_0001.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: is not is required copies to the issuing office.

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

2. AMENDMENT/MODIFICATION NUMBER 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. 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)

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

PAGE

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

PAGESOF

Contractor

The hour and date specified for receipt of Offers to sign this document and return

RACHEL STONE

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WAD-SAP

7600 Sand Point Way NE

SEATTLE WA 98115

WAD-SAP-S

1305M326Q0354

08/21/2026

08/21/2026

1 4

CONTINUATION SHEET

REFERENCE NO. OF DOCUMENT BEING CONTINUED PAGES

NAME OF OFFEROR OR CONTRACTOR

SUPPLIES/SERVICES

(B)

UNIT

(D)

UNIT PRICE

(E)

AMOUNT

(F)

OPTIONAL FORM 336 (4-86)

Sponsored by GSA FAR (48 CFR) 53.110

ITEM NO.

(A)

QUANTITY

(C)

NSN 7540-01-152-8067

1305M326Q0354/0001

THE DESIGNATED GOVERNMENT OFFICIAL RESPONSIBLE

FOR ACCEPTANCE AND APPROVING INVOICES SHALL BE:

Stephanie Fisher

Stephanie.Fisher@noaa.gov

Period of Performance: 09/30/2026 to

09/29/2027

1305M326Q0354 0001

The purpose of Amendment 0001 to the solicitation is to provide answers in response to questions received:

Question 1. Are you willing to accept PacBio platform as an alternative platform to Illumina?

Answer 1. The Government will consider other platforms but has a preference for the Illumina platform for consistency with all our existing data.

Question 2. Could you please confirm whether the bioinformatic pipeline in Task 7 is required within the base scope, or optional. Task 7 of the SOW (page 10) states: "Samples can be run by Contractor's standard bioinformatic pipeline including quality filtering, noise/chimera removal, ASV/ESV clustering, and taxonomic assignment." The deliverables table on page 12 lists "taxonomic assignment tables" as a required deliverable, but the ambiguous phrasing in Task 7 ("can be run") leaves it unclear whether this pipeline is required under the base scope of work or offered as an optional service.

Answer 2. The bioinformatic pipeline in Task 7 is a preferred service, while it is not strictly required, we prefer that contractors run samples through their bioinformatic pipeline to produce taxonomic assignment tables as deliverables (as quality control) in addition to raw (demultiplexed) sequencing data that we can run through our own pipeline. Contractors that only provide raw data do not have the information needed to maintain quality control across samples, therefore, we strongly prefer that contractors process data to a point where they can assess sample quality and taxonomic assignment products.

Question 3. The SOW notes that downstream taxonomic assignment is outside the scope of the contract, but Task 7 includes taxonomic assignment as part of the Contractor’s standard bioinformatics pipeline, and the Deliverables Schedule lists taxonomic assignment tables. Please clarify whether taxonomic assignment and taxonomic assignment tables are required contract deliverables. If required, please identify the expected taxonomic assignment methodology, reference database, and deliverable format.

Answer 3. Taxonomic assignment is a preferred deliverable, and bioinformatic tools are flexible. The assignment methodology is flexible and can follow available metabarcoding assignment pipelines, such as MMARINeDNA, DADA2, or custom pipelines. The NCBI nt nucleotide database or a curated MIDORI version are acceptable reference databases for the broad range of taxa and markers required. The deliverable format should consist of two tables: (1) one with read counts per amplicon sequence variant (ASV) per sample along with taxonomic assignment, and (2) one with a list of blast hits for each ASV and the taxonomic assignment.

Question 4. The solicitation appears to include two different requirements for sequencing read depth.

Please confirm whether the required read-depth target is 100,000 sequencing reads per sample per assay/marker or 100,000 sequencing reads per sample summed across all assays.

Answer 4. We require a target sequencing read-depth of 100,000 reads per sample per assay/marker.

We understand that some samples with trace amounts of DNA will fall under this target read depth due to inherently low template in samples.

Question 5. Task 2 references a Project Plan for specialized filter processing, and later requirements reference deviations from an approved Project Plan. Please confirm the required contents and due date of the Project Plan and whether it is a post-award deliverable or should be included with the Technical Proposal.

Answer 5. The Project Plan is a post-award deliverable and is not required with the Proposal. The Project

1305M326Q0354 0001

Plan establishes the baseline methods used and can be sent to the Government Technical POC via email.

PIFSC will transmit a Sample Submission Form (in the preferred Contractor format or portal) with each shipment identifying the samples and requested assays, along with any sample-specific handling instructions. If a batch requires handling not addressed in the routine Project Plan, PIFSC and the Contractor will agree on the approach in writing (email is sufficient) before processing begins. At a minimum, the Project Plan shall document:

- The Contractor's technical point of contact and laboratory lead;

- Standard extraction protocols;

- The assay/marker table for markers for a given project, including thermocycling conditions and polymerase; PCR replicates;

- QC acceptance thresholds and the control scheme (extraction blanks, PCR negative controls, positive controls);

- Bioinformatic pipeline description and the format of data deliverables; and

- Batch turnaround times.

Routine batch-level processing does not require a revision of the Project Plan. References in the SoW to a "deviation from the approved Project Plan" mean any departure from the above, resulting from Contractor or Government needs to adapt to troublesome samples. Email is acceptable.

Question 6. The combined synopsis lists a completion date of September 20, 2027, while Section IX lists the Base Period through September 29, 2027. Please confirm the intended final contract performance and deliverable completion date.

Answer 6. Base Period through September 29, 2027.

Question 7. Please confirm whether the completed SF 1449, copies of Sections I and II of the Past Performance Questionnaires, and the title/cover page and cover letter are excluded from the 10-page Technical Proposal page limit and may be submitted separately as front matter or attachments. If PPQ Sections I and II are included within the 10-page limit, may offerors reformat those sections into a condensed format, provided all required information is retained and is identical to the information provided to the assessors, or must the Government-provided Attachment 1 format be reproduced as provided? Please also clarify the preferred placement of the completed SF 1449 and any representations and certifications.

Answer 7. The completed SF 1449, copies of Sections I and II of the Past Performance Questionnaires, and the title/cover page and cover letter are excluded from the 10-page Technical Proposal page limit.

Please submit in accordance with the Standard Language Addendum to 52.212-1 beginning on Page 28.

The completed SF 1449 and any representations and certifications can be included in Volume 1.

Sponsored by GSA FAR (48 CFR) 53.110