RFQ Attachment 1 - SOW_revised 9-11-24.pdf

STATEMENT OF WORK (SOW)

9/11/2024

TITLE: Genomics Services for the NIAID Centralized Sequencing Program

1) BACKGROUND INFORMATION

National Institutes of Health (NIH), 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 whole genome sequencing and associated deliverables. The CSP will have direct implications for the care of NIH patients and for the discovery of disease mechanisms.

3) PERIOD OF PERFORMANCE

Period of Performance: One (1) 12-month base period with four (4) 12-month option periods.

4) SCOPE:

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

5) CONTRACTOR MANDATORY DELIVERABLES:

Clinical Whole Genome Sequencing – data generation and delivery (N = 1400-1500 base quantity):

1. Includes data delivery via secure transfer such as Google Cloud Platform (GCP), Globus, Aspera.

2. Meets Clinical Laboratory Improvement Amendments (CLIA) and the College of American Pathologists (CAP) requirements for clinical sequencing.

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

4. Compressed Reference-oriented Alignment Map files (CRAMs) and Variant Call Format files (VCFs).

5. Unfiltered Genomics Variant Call Format files (gVCFs).

6. Structural variant (SV) calls.

7. Mitochondrial variant calls.

8. Repeat expansion calls.

9. Fluidigm single nucleotide polymorphism (SNP) trace or comparable assay for sample identity analysis, assessment of contamination, sex, and relationships with other samples.

10. Minimum sequencing read depth of at least 90% at 20X coverage with mean coverage of ≥30X.

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

12. Results returned within 4 weeks.

Clinical genome sequencing with interpretation and clinical report (n = 100 option quantity):

1. Proband-only analysis with option for duo and trio analysis.

2. Phenotype-based analysis + American College of Medical Genetics and Genomics (ACMG) screening panel for secondary findings.

3. Ability to accept various batch sizes ranging from 1-100 samples.

Contractor skills, capacity, and expertise:

1. Contractor displays demonstrated expertise in genetics and genomics and capacity to complete high-throughput genome sequencing.

2. Personnel includes bioinformaticians and clinical molecular geneticists board certified by the

American College of Genetics and Genomics.

3. Strong communication and project management skills.

6) CONTRACTOR DESIRED DELIVERABLES

Deliverables for Clinical Genome Sequencing:

1. Polygenic scores for diseases such as asthma, atrial fibrillation, breast cancer, chronic kidney disease, coronary heart disease, hypercholesterolemia, etc.

2. Pharmacogenomic allele calls

3. Demonstrated consistent recent high-quality data approaching or exceeding 95% at 20X coverage

4. Provision of Quality Control (QC) information regarding data quality. Specifically, measures of read quality, median coverage, contamination screen, and % of genome >=20X

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

6. Ability to accept sample information via Excel manifests.

7. Provide information about data processing and variant calling pipeline used.

7) CONTRACTOR SUPPLIED MATERIALS

The Contractor shall provide plates for shipping and all consumable reagents except those mentioned below.

8) GOVERNMENT FURNISHED MATERIALS

If genomic DNA samples are used, NIAID will deliver them in 96-well deep well plates with tubes containing 2D barcodes. Sample plates must be compatible with QIAgility robotic aliquoting.

9) REPORTING REQUIREMENTS AND DELIVERABLES FOR CLINICAL GENOME

SEQUENCING:

The required turn-around time for sequencing and receipt of deliverables is a maximum of 4 weeks 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 will 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 and receipt of samples. Issues with samples due to quality and/or quantity, identity issues from Fluidigm SNP trace, 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.

Delivery schedule:

Deliverable Delivery schedule Minimum sequencing read depth of at least 90% at 20X coverage with mean coverage of ≥30X 28 days after sample accessioning

CRAMs and VCFs 28 days after sample accessioning

SV calls 28 days after sample accessioning

Mitochondrial variant calls 28 days after sample accessioning

Repeat expansion calls 28 days after sample accessioning Fluidigm SNP trace for sample identity analysis, assessment of contamination, sex, and relationships with other samples

Notify NIH within 48 hours after sample issues are found

10) 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.