Statement of Work PO CSI 2020 SNP arrays.pdf

STATEMENT OF WORK (SOW)

TITLE: Genomics services for the NIAID Centralized Sequencing Initiative

In support of clinical research, the NIAID Centralized Sequencing Initiative 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 Initiative is both to contribute to the understanding of underlying genetic etiology of disease and to address the clinical need for genomic evaluations.

1) PURPOSE AND OBJECTIVES OF THE ACQUISITION

The purpose of this acquisition is to support the mission DIR to obtain genetic testing for the NIAID Centralized Sequencing Initiative. The centralized sequencing initiative will have direct implications for the care of NIH patients and for the discovery of disease mechanisms. The types of sequencing required for the initiative are; custom microarrays for Comparative Genomic Hybridization (CGH), SNP microarrays, whole Genome Sequencing (WGS) and RNAseq. Genome sequencing allows for discovery of monogenic and polygenic contributions to disease. Clinical microarrays will provide clinical analysis of copy number variants contributing to those diseases. This particular acquisition focuses on research genome-wide SNP arrays to enable the study of common variants.

2) CONTRACTOR REQUIREMENTS:

Research SNP array with genome-wide coverage of common variants (N = 350) o Sample processing and microarray scanning o Feature extraction: processing of raw image files o QC of data including sample identity analysis, assessment of contamination, sex, and relationships with other samples o Delivery of batch-specific and cumulative PLINK binary files and raw data files, e.g.

GenomeStudio files

3) CONTRACTOR SUPPLIED MATERIALS

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

4) GOVERNMENT FURNISHED MATERIALS

NIAID will supply patient samples. 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.

5) REPORTING REQUIREMENTS AND DELIVERABLES

Deliverable format:

Delivery of batch-specific and cumulative PLINK binary files and raw data files, e.g. GenomeStudio files within 6 weeks. Inclusion of QC metrics for data including sample identity analysis, assessment of contamination, sex, and relationships with other samples. Transfer to occur via cloud-based platform that meets security requirements for transfer to NIH/NIAID servers.

6) INSPECTION AND ACCEPTANCE

All deliverables will be inspected by the project manager, an 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.