1913881_Statement_of_Work_2018_CNV_Analysis.docx

STATEMENT OF WORK

1) BACKGROUND INFORMATION

DIR scientists study all aspects of infectious diseases, including the causative agent, vectors, and pathogenesis in human and animal hosts. Clinical research also is integral to the DIR mission, enabling key lab discoveries to be rapidly translated into methods to prevent, diagnose, or treat disease. DIR researchers conduct more than 100 clinical trials at the NIH Clinical Center on the Bethesda, Maryland, campus and at collaborating U.S. and international sites.

Custom microarrays for comparative genomic hybridization are needed to support a DIR initiative involving genetic testing of all NIAID patients enrolled in clinical trials located at the NIH clinical center. These tests will allow copy number variation analysis of over 2000 target genes selected by NIAID that cause, or are suspected to cause, immunological diseases in this patient population. This technique will allow identification of chromosomal abnormalities that may be missed by whole exome sequencing. Approximately 10% of patients undergoing whole exome sequencing may require CNV analysis.

2) PURPOSE AND OBJECTIVES OF THE ACQUISITION

The purpose of this acquisition is to provide processing and analysis of comparative genomic hybridization microarrays purchased by NIAID in support of copy number variation analysis of patients admitted to the NIH Clinical Center under NIAID clinical protocols.

3) CONTRACTOR REQUIREMENTS:

· Chromosomal Microarray Analysis: Sample processing and microarray scanning.

· Feature extraction: Processing of raw image files.

· BCM CNV calls: Use of the Baylor Genetics pipeline for making copy-number calls from the microarray data.

· Report: Data review by the Baylor Genetics team for determination of which copy-number calls should be reported clinically. Generation of a report for use by the NIAID team.

· Web-based access to cases and database: Online access for members of the NIAID team to the Baylor Genetics database of prior results. This is useful for interpretation and clinical reporting.

· Data release of raw image files and any intermediate files upon request.

4) CONTRACTOR SUPPLIED MATERIALS

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

5) GOVERNMENT FURNISHED MATERIALS

NIAID will supply CHG microarrays and patient samples

6) REPORTING REQUIREMENTS AND DELIVERABLES

Technical support, remedial repair as needed, and one annual planned maintenance.

7) INSPECTION AND ACCEPTANCE

a) All deliverables will be inspected by a member of the Division of Intramural Research.