SOW_Low-coverage_Whole_Genome_Sequencing_v2.pdf

STATEMENT OF WORK

for

Next-Generation Sequencing of prepared library for low coverage Whole Genome Sequencing

Requisition#143021-25-0184 / Requirements-25-3258 2 June 2025

1.0 Background. The National Oceanic and Atmospheric Administration (NOAA), National Marine Fisheries Service (NMFS), Northeast Fisheries Science Center (NEFSC) is the research arm of NOAA Fisheries in the region. The Center plans, develops, and manages a multidisciplinary program of basic and applied research. Wild harvest of Atlantic sea scallops Placopecten magellanicus is the most lucrative commercial bivalve fishery in the US ($488 million USD annually), however sea scallop landings are projected to decline by 50% at the end of the century in part from ocean acidification (OA; elevated ρCO2). Adaptive genetic change can occur rapidly and offset consequences of environmental change yet depend on variation maintained within an existing population. Thus, population genetics are essential to improve accuracy of risk assessment models by examining the capacity for sensitive species to evolve and counteract long-term ecosystem-scale change. To date, few existing studies postulate that there is high genetic differentiation between sea scallops in the Mid-Atlantic bight (MAB) and the Gulf of Maine (GOM). Expansion of this thread is key, as warming will press populations poleward and shift wild harvesters to cooler, more-acidified systems such as the GOM. Further, observed premature die-offs in southern MAB (as ‘juveniles’, ~2-3 years in age) threaten fishery collapse in this region (D. Hart, pers. commun., 8/1/2023; D. Rudders, pers.

commun., 8/5/2023). Building upon previous work, we will use the newly built and annotated reference genome for the sea scallop P. magellanicus to compare differences in population genetics between two distinct populations each experiencing different rates of OA and ocean warming. Using low coverage Whole Genome Sequencing (lcWGS) we will quantify genetic changes in scallops between populations, and map those changes to phenotypic responses where possible. To this end, we will contract services to extract DNA from tissue samples, complete library preparation and sequence targeting 150 base pair paired-end reads at a coverage depth of 4x for individually indexed and pooled libraries. The NovaSeq S4 platform will accommodate the required read depth of N > 120 pooled individuals with a 1.7 gigabase genome. Ultimately, this project will fill important gaps in knowledge about adaptive capacity of scallops to impending challenges and provide important information for predictive models that are used to monitor and regulate important scallop fisheries.

This study will provide much needed information regarding the potential for adaptation in scallops, essential for estimating long-term population responses, identify populations and regions that are most vulnerable, and, where possible, work with resource managers and the fishing community to mitigate population loss caused by OA and warming, and explore possible solutions, such as assisted gene flow, sanctuaries, and rotated fishing grounds.

2.0 General Requirements

2.1 Scope of Work. Non-Personal Service. Contractor shall provide all trained labor, equipment, materials, supervision, transportation, permits, insurance, and quality control necessary to provide molecular extraction of fixed tissue samples, library preparation, and Next-Generation

Sequencing of prepared pooled library for low coverage Whole Genome Sequencing for the NMFS/NEFSC (Milford Lab). Performance under this contract known as “Work”. Contractor shall be fully knowledgeable of all contract requirements and shall ensure Work is accomplished in accordance with the terms and conditions of the contract in a manner that will promote and maintain a safe environment.

We require three tasks in the year, including extraction library preparation, and sequencing services to accommodate a variable number of individuals sent to the vendor.

1. Task 1: We will send the vendor fixed tissues from 120 individual sea scallops. The vendor will complete DNA extraction and library preparation of each sample to build 1 pooled library that includes the 120 indexed sea scallops. The vendor will first extract DNA from each sea scallop tissue sample fixed in DNA/RNA shield and ascertain the quality and quantity of DNA in each extraction. Extractions will be repeated for samples that do not pass quality control. The vendor will employ a library preparation workflow involving the following: fragmentation, adapter ligation, indexing, PCR amplification, clean up and size selection, quantification, and normalization for equimolar pooling. If necessary, and prior to pooling to a single library, repeat extraction(s) and/or library preparation(s) for samples that did not pass QC and quantification.

Low-pass whole genome sequencing will be completed on an Illumina platform (i.e. NovaSeq S4) that offers paired end reads of 150bp and 4x coverage per individual. Given the number of individuals and the number of reads provided by the NovaSeq S4 platform, this task will allow us to achieve the coverage per individual needed given the genome size of the sea scallop (1.7 Gb).

DNA extraction, library preparation, and sequencing on will be conducted according to the following specifications:

● Must complete DNA extractions of tissue samples fixed in DNA/RNA shield

● Must build 1 equimolar-pooled library containing all indexed individuals

● Must provide low pass whole genome sequencing for the pooled library containing N = 120 samples, sequenced as 150bp paired-end reads at 4X coverage for a genome size of ~1.7 Gb.

● Must provide a quality report and FASTQ files in an electronic format

● Must be able to provide a fast turnaround time (~8-12 weeks)

2.1.1 Contractor shall be a fully trained authorized service provider of molecular extractions, library preparation, and Next Generation Sequencing on the Illumina platforms HiSeq and NovaSeq S4. Contractor shall at all times ensure Work is accomplished in accordance with the terms and conditions of the contract in a safe and professional manner.

2.1.2 Special Qualifications and Permits. Contractor shall ensure all required skill sets, and permits are obtained and maintained for performance under this contract.

2.1.3 Quality Control. Quality Control is the responsibility of the Contractor

2.2 Place of Performance. At Vendor's Location.

2.3 Period of Performance/Delivery: Contractor shall deliver sequences to NEFSC within 4 weeks of sample submission and no later than (est) September 18, 2026 for each period of performance (See table below for dates).

CLIN 0001 – Task 1 (est) Sep 19, 2025 - Sep 18, 2026

3.0 Security Requirements. Security Clearances are not required.

3.1 Contractor employees and associated subcontractors performing under this contract MUST be U.S. citizens or MUST have established and maintain legal residence in the U.S., and be authorized by the US Government to work in the United States (i.e. Green card, worker authorization, etc.).

4.0 Safety, Security, Fire Protection, Environmental Controls, Conservation of Utilities, and Compliance with Laws and Regulations.

4.1 Safety Requirements. Contractor shall take all necessary precautions to meet proper safety standards, and regulations of all local, state and federal codes and regulations.

4.2 Security. There are no specific security requirements for performance under this contract.

5.0 Government Roles.

5.1 The Contracting Officer (CO) is the only individual with the authority to authorize changes within this contract that will have an effect on the scope, and monetary values (increase or decrease) of contract.

5.2 The Technical Point of Contact (TPOC) is the individual designated by the CO at contract award to perform administrative functions on the contract. The key role of the TPOC is to monitor the performance of the contract. The TPOC will observe, document, and communicate Contractor performance to the CO. TPOC and alternate TPOC (if applicable) will be responsible for the inspection and acceptance of performance and any deliverables under the contract. The TPOC does NOT have authority to change the terms and conditions of the contract. When in the opinion of the Contractor, the TPOC requests efforts outside the existing scope of the contract, the Contractor shall promptly notify the CO in writing. Contractor under such direction shall take no action until the CO has resolved the issue or has otherwise issued a modification to the contract. TPOC is: Katherine McFarland 440-567-7335, katherine.m.mcfarland@noaa.gov

6.0 Government Responsibilities:

6.1 Government shall inspect the Work performed under this contract. Any corrective action required as a result of the inspection will be accomplished prior to final monthly billing. Government will document instances of deficiencies.

6.2 Contractor may be notified of deficiencies in performance in writing by the CO. Oral deficiency notifications will be confirmed in writing by the CO. Contractor shall take prompt corrective action upon notice of deficiency. Prompt is defined as within 24 hours of notification.

6.3 Government Furnished Property, Materials, Equipment and Services (GFP/M/E/S). N/A

7.0 Contractor Responsibilities.

7.1 Contractor Furnished Property, Materials, Equipment and Services (GFP/M/E/S).

Contractor shall provide all plant, trained labor, equipment, materials, supervision, transportation, permits, insurance, and quality control necessary to achieve the quality performance standards of the Work in this contract.

7.1.1 Contractor shall immediately notify the CO if discrepancies are discovered between the existing property conditions and those noted on the SOW.

7.1.2. Contractor shall notify the CO immediately when it is discovered that the deliverable schedule will not be met to work together to revise the schedule as necessary. Contractor shall communicate with the CO and revise the schedule as necessary. Contractor shall not deviate from schedule without prior approval from the CO.

7.1.3 Contractor shall be fully knowledgeable of all requirements of the contract documents and shall make themselves aware of all job site conditions that will affect their performance.

7.1.4 Contractor shall maintain an adequate workforce trained to safely and satisfactorily perform under this contract.

7.1.5 Contractor shall ensure all employees and subcontractors are fully trained and have a full understanding of the statement of work task requirements; government will not provide instruction or oversight.

7.1.6 Contractor shall ensure all Contractor employees, and all associated subcontractor(s) are experienced in the type of work involved and familiar with the specifications of this contract. Contractor is responsible for damage to any Government equipment and supplies caused by Contractor personnel.

7.1.7 Contractor shall comply with all applicable interstate, local, state, and federal codes and laws.

7.1.8 Contractor shall perform in accordance with professional industry standards.

7.1.9 Contractor shall accomplish all tasks to meet the requirements of the SOW.

8.0 Specific Tasks. Contractor and subcontractors working under this contract shall be fully knowledgeable and skilled in the scientific disciplines required to successfully fulfill this requirement. Contractor shall be fully knowledgeable of all contract requirements. Contractor shall at all times ensure Work is accomplished in accordance with the terms and conditions of the contract in a safe and professional manner. Contractor shall perform the following tasks (as detailed in section 2.1):

CLIN 0001: gDNA extraction, Zyme Quick DNA Miniprep, Low pass whole genome sequencing to a depth of ~550Gb sequenced as 150bp paired end reads and 4x coverage of 1.7 Gb genome, data delivery sFTP

9.0 Deliverables. Contractor shall provide the identified deliverables in the manner and time frame identified.

Deliverable #1: (for CLIN 0001) A quality report and FASTQ files of sequencing output in an electronic format. Required no later than 8-12 weeks from the time of sample submission.

10.0 IT Security. Not applicable. Requirements of 48 CFR 1352.239-73 do not apply and a Security Accreditation Package is not required.

11.0 Section 508. Not applicable.

12.0 Invoicing. Contractor shall provide “proper” invoices in arrears of tasks performed (and expensed) with the last invoice being submitted within 30 days of contract completion. Invoices shall be submitted (via electronic copy) no later than by the 10th day of the billing month.

1. Payments will be based on receipt of a proper invoice and satisfactory contract performance and guidelines in FAR 32.9, Prompt Payment.

2. To constitute a proper invoice, the Contractor’s invoice shall be prepared in accordance with, and contain the elements specified in FAR 52.212-4(g), “Invoices”.

3. The Government will return invoices that do not comply with FAR 52.212-4(g), “Invoices” within 7 days after the date the invoice was received along with a statement as to the reasons why it is not a proper invoice.

4. The Contractor will send invoices in accordance with the terms and conditions of this contract to the following address (electronic submission of invoices is preferred):

Please reference the Contract/Order Number in your email subject line when submitting invoices.