D_WGS_cohort2_SOW.pdf

Version 11-30-2016-1 FAR Part 11—Describing Agency Needs

STATEMENT OF WORK (SERVICES)

(SOW)

GENERAL INFORMATION

Title of Project:

Whole genome sequencing for HANDLS participants: Cohort 2

Statement of Need and Purpose:

Investigators in the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) study require whole genome sequencing data to expand the Nationa Institute on Aging (NIA) current research examining whether rare genetic variants present in racial minority populations contribute to observed health disparities in obesity and chronic kidney disease. Samples from HANDLS participants have been obtained over the longitudinal study, starting in 2004, and thus some samples are over 15 years old and many are over 10 years old.

Background Information and Objective:

Health disparities in age-related chronic conditions such as obesity and chronic kidney disease (CKD) are well documented. Importantly, obesity and CKD have been linked to accelerated aging, the risk for age-associated conditions at younger ages than usual. Although genetics may contribute to observed health disparities, there are only limited studies in the racial and ethnic minority populations most affected by obesity and CKD. The objective of this work is a follow-up of the National Institute on Aging (NIA) current research to examine health disparities associated with obesity and CKD through whole genome sequencing to investigate the contributions of genomics to the disproportionate burden of disease incidence, prevalence, morbidity, and mortality in minority groups within the United States. The long-term goal is to create a consistent dataset of whole genome sequencing to complement the NIA’s longitudinal HANDLS behavior and health data.

Period of Performance:

August 15, 2022 to August 14, 2023

SCOPE OF WORK

General Requirements:

Independently, and not as an agent of the Government, the Contractor shall furnish all the necessary services, qualified personnel, material, equipment, and facilities, not otherwise provided by the Government as needed to perform the Statement of Work below:

Specific Requirements:

The contractor shall deliver plates to the Government sufficient to run 70 samples, some of which have been stored for ten or more years. The contractor shall perform whole genome sequencing, and specifically shall:

• confirm genomic DNA quantity and quality by performing DNA concentration measurements and volume checks

• examine agarose gels on all samples as an industry-standard method for screening DNA marker quality prepare PCR-free sequence libraries for all samples

• sequence the libraries at a minimum of 30x coverage with 2×150 base pair runs

• provide the Government the opportunity to replace any sample that fails to pass these quality checks at no extra charge

• perform primary and secondary analysis of the sequencing data including but not limited to read alignment, variant calling, and quality control analyses

• provide written summaries and documentation of the methods used to perform the whole genome sequencing pipeline

• supply the whole genome sequencing data in a mutually acceptable electronic format that preserves study participants’ confidentiality.

Following data delivery and upon request by the Government, the contractor shall provide attendance at Government laboratory staff meetings and the contractor shall provide technical consultations as needed.

GOVERNMENT RESPONSIBILITIES

The Government will provide genomic DNA samples with a minimum concentration of 500 nanograms (ng; per sample) to the contractor for quality control metrics, library preparation, and sequencing. The Government will load the genomic DNA samples on contractor-provided plates.

DELIVERY OR DELIVERABLES

The contractor shall provide the following deliverables:

• Analytic plates delivered to the Government at the Biomedical Research Center in Baltimore, MD

• A report on the concentration of all genomic DNA samples

• A report on the genomic DNA sample integrity and purity

• A summary report outlining any problems from sample quality control metrics

• PCR-free sequencing libraries for all samples

• Electronic sequencing data in a mutually agreed upon device that shall contain the analysis-ready, aligned reads in the electronic compressed version of binary alignment map (CRAM) file format, along with the reference genome version used for alignment, and joint multi-sample called variants in the electronic variant call format (VCF) file format. These electronic data files shall be securely transferred to a portable disk drive and delivered to the Government at the Biomedical Research Center.

• Return any leftover DNA on dry ice by overnight shipping to the Government at the Biomedical Research Center.

• Upon the Government’s request, written summaries and documentation of all methods and parameters used to perform the whole genome sequencing pipeline

• Upon the Government’s request, attend staff meetings and provide technical consultations as needed.

REPORTING REQUIREMENTS

N/A

OTHER CONSIDERATIONS

Travel:

Travel is not required.

Key Personnel:

N/A

Information System Security Plan:

N/A

Data Rights:

The National Institute on Aging shall have unlimited rights to and ownership of all deliverables provided under this contract, including reports, data updates and statistical results. This includes the deliverables provided under the basic contract and any optional task deliverables exercised by the contracting officer.

In addition, it includes any additional deliverables required by contract change. The definition of “unlimited rights” is contained in Federal Acquisition Regulation (FAR) 27.401, “Definitions.” FAR clause 52.227-14, “Rights in Data-General, is hereby incorporated by reference and made a part of this contract/order.

Section 508—Electronic and Information Technology Standards:

N/A

Publications and Publicity:

N/A

Confidentiality of Information:

N/A