SOW NIAID CSP Long Read Genome 20250702.pdf

STATEMENT OF WORK (SOW)

TITLE: Genomics services for the NIAID Centralized Sequencing Program

1) BACKGROUND INFORMATION

The National Institute of Allergy and Infectious Diseases (NIAID) Division of Intramural Research (DIR) scientists study all aspects of infectious diseases, including the causative agent, vectors, and pathogenesis in human and animal hosts. Clinical research is an integral part of this mission, enabling key lab discoveries to be rapidly translated into methods to prevent, diagnose, or treat disease. DIR researchers annually conduct more than 200 clinical trials at the NIH Clinical Center on the Bethesda, Maryland, campus and at collaborating U.S.

and international sites.

In support of clinical research, the NIAID Centralized Sequencing Program (CSP) is comprehensive program that obtains genetic testing, harmonizes phenotypic and genomic data, performs variant interpretation, and provides clinically validated results for participants enrolled in a diverse set of protocols at the NIH Clinical Center. The goal of the NIAID CSP is both to contribute to the understanding of underlying genetic etiology of disease and to address the clinical need for genomic evaluations.

2) PURPOSE AND OBJECTIVES OF THE ACQUISITION

The purpose of this acquisition is to support the mission of DIR to obtain genetic testing for the NIAID CSP.

The objective is to purchase long read genome sequencing and associated deliverables. The CSP will have direct implications for the care of NIH patients and for the discovery of disease mechanisms.

Period of Performance: One 12-month period

3) SCOPE:

The scope of this effort includes the services and industry knowledge necessary to provide long read genome sequencing as specified in this SOW.

4) CONTRACTOR REQUIREMENTS:

Long Read Genome Sequencing at 20X depth of coverage – data generation and delivery (N = 75):

1. Long read genome sequencing on PacBio Revio platform

2. Includes data delivery via secure transfer such as AWS, GCP, Globus, Aspera

3. Accept DNA isolated from multiple tissue types, including whole blood, saliva, fibroblast, peripheral blood mononuclear cell (PBMC), and other tissues

4. Delivery of raw unmapped readds, including the following:

a. Raw Data - HiFi Read (.bam/.pbi)

b. QC data

5. Minimum sequencing read depth of 20X coverage

6. SNP trace for sample identity analysis, assessment of contamination, sex, and relationships with other samples

7. Provide methylation and acetylation data

8. Ability to accept small batch sizes, < 50 samples in one batch as well as larger batches of 50-

100 samples per batch

9. Results returned within 60 days upon sample receipt

10. Must be able to accept genomic DNA from standard automated extraction (not only high molecular weight DNA)

Attachment 1 - SOW

Long Read Genome Sequencing at 30X depth of coverage– data generation and delivery (N = 75):

1. Long read genome sequencing on PacBio Revio platform

2. Includes data delivery via secure transfer such as AWS, GCP, Globus, Aspera

3. Accept DNA isolated from multiple tissue types, including whole blood, saliva, fibroblast, peripheral blood mononuclear cell (PBMC), and other tissues

4. Delivery of raw unmapped reads, including the following:

a. Raw data BAM files - HiFi Read (.bam/.pbi)

b. QC data

5. Minimum sequencing read depth of 30X coverage

6. SNP trace for sample identity analysis, assessment of contamination, sex, and relationships with other samples

7. Provide methylation and acetylation data

8. Ability to accept small batch sizes, < 50 samples in one batch as well as larger batches of 50-100 samples per batch

9. Results returned within 60 days upon sample receipt

10. Must be able to accept genomic DNA from standard automated extraction (not only high molecular weight DNA)

Contractor skills, capacity, and expertise:

1. Contractor displays demonstrated expertise in genetics and genomics and capacity to complete long read genome sequencing.

2. Strong communication and project management skills

5) CONTRACTOR DESIRED DELIVERABLES

Desired Deliverables for Long Read Genome Sequencing:

1. Demonstrated consistent recent high-quality data

2. Provision of QC information regarding data quality. Specifically, measures of read quality, median coverage, etc.

3. Provision of sample data upon request, e.g., NA12878, to aid in assessment of control data quality

4. Ability to accept sample information via Excel manifests

6) CONTRACTOR SUPPLIED MATERIALS

The Contractor shall provide all consumable reagents necessary for sequencing except those mentioned below.

7) GOVERNMENT FURNISHED MATERIALS

If genomic DNA samples are used, NIAID will deliver them in 96-well plates with tubes containing 2D barcodes.

8) REPORTING REQUIREMENTS AND DELIVERABLES FOR CLINICAL GENOME

SEQUENCING:

The required turn-around time for sequencing and receipt of deliverables is 60 days from the time the contractor receives and accessions the samples.

Upon start of award, contractor and government team will be required to hold an orientation briefing/kick-off meeting during which specific workflows for sample quantity, volume, concentration range, and quality be reviewed. All controlled vocabulary regarding sample and individual information be covered, as well as processes for submitting orders, tracking order progress, communication about samples, and downloading data.

Timely follow up for questions related to contract is to be completed via targeted meetings and/or email communication.

Contractor reviews and confirms manifests sent with samples and receipt of samples. Issues with samples due to quality and/or quantity, identity issues, mismatch with manifests, and other issues preventing samples from moving forward in sequencing pipeline be communicated to NIH within 48 hours. Known process issues within contractor lab can be resolved without prior approval from NIH.

9) INSPECTION AND ACCEPTANCE

All deliverables will be inspected by the project manager, a Government employee of the Division of Intramural Research. Acceptance will occur when results are successfully transferred to NIH per the specifications and format outline in the requirements above.