Statement of Work NIAID CSP Genome.docx

STATEMENT OF WORK (SOW)

TITLE: Genomics services for the NIAID Centralized Sequencing Program

1) BACKGROUND INFORMATION

The National Institute of Allergy and Infectious Disease (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 is comprehensive program that obtains genetic testing, harmonizes phenotypic and genomic data, performs variant interpretation, and provides clinically validated results for patients enrolled in a diverse set of protocols at the NIH Clinical Center. The goal of the NIAID Centralized Sequencing Program 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 Centralized Sequencing Program. The objective is to purchase whole genome sequencing. The Centralized Sequencing Program will have direct implications for the care of NIH patients and for the discovery of disease mechanisms.

Period of Performance: One (1) 12-month period.

3) SCOPE:

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

4) CONTRACTOR REQUIREMENTS:

Whole genome sequencing for 800 samples. 10 rapid turnaround time genomes.

· Clinical Whole Genome Sequencing (N = 800):

· Delivery of FASTQ files

· Data delivery via Globus endpoint

· Meets CLIA/CAP requirements for clinical sequencing

· Ability to accept DNA and blood samples

· SNP trace using Fluidigm for sample identity analysis, assessment of contamination, sex, and relationships with other samples

· Minimum sequencing read depth of at least 95% at 20X coverage

· Provision of QC information regarding data quality. Specifically, measures of read quality, median coverage, contamination screen, and % of genome >=20X

· Accept DNA isolated from multiple tissue types, including blood, saliva, fibroblasts, etc. We are willing to provide samples to validate the process.

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

· Ability to accept small batch sizes, < 60 samples in one batch

· Results returned within 6 weeks

· Rapid turnaround time Clinical Whole Genome Sequencing (N = 10):

· Delivery of FASTQ files

· Data delivery via Globus endpoint

· Meets CLIA/CAP requirements for clinical sequencing

· Ability to accept DNA and blood samples

· SNP trace using Fluidigm for sample identity analysis, assessment of contamination, sex, and relationships with other samples

· Minimum sequencing read depth of at least 95% at 20X coverage

· Provision of QC information regarding data quality. Specifically, measures of read quality, median coverage, contamination screen, and % of genome >=20X

· Accept DNA isolated from multiple tissue types, including blood, saliva, fibroblasts, etc. We are willing to provide samples to validate the process.

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

· Ability to accept small batch sizes, < 2 samples in one batch

· Results returned within 3 weeks

5) CONTRACTOR SUPPLIED MATERIALS

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

6) GOVERNMENT FURNISHED MATERIALS

If genomic DNA samples are used, NIAID will deliver them in 96-well plates with tubes containing 2D barcodes. Exclusionary criteria: NIAID will not be able to affix labels to individual tubes.

7) REPORTING REQUIREMENTS AND DELIVERABLES FOR CLINICAL WHOLE GENOME SEQUENCING:

The required turn-around time for sequencing and receipt of deliverables is 6 weeks, or less, from the time the contractor receives the patient sample.

We also require the vendor to offer a “rapid” option with 3-week turnaround time for receipt of deliverables from WGS from the time the contractor receives the patient sample. This option is expected to be used approximately once a month.

Deliverables:

· FASTQ files for all samples within 6 weeks. Transfer shall occur via cloud-based platform that meets security requirements for transfer to NIH/NIAID servers.

· Reports on quality metrics , including measures of read quality, median coverage, contamination screen, and % of genome >=20X on each sample for use by the NIAID team.

8) 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.