D1 SOW.doc

STATEMENT OF WORK (SERVICES)

(SOW)

GENERAL INFORMATION

Title of Project:

Whole genome sequencing for HANDLS participants Statement of Need and Purpose:

Investigators in the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) study require whole genome sequencing (WGS) data to expand our current research examining whether rare genetic variants present in racial minority populations contribute to observed health disparities in age-related diseases. 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. A contract is required because the Government does not have available facilities or resources to perform this work consistent with other WGS performed on HANDLS samples.

Background Information and Objective:

Health disparities in age-related chronic conditions such as obesity and chronic kidney disease (CKD) are well documented. Importantly, diseases such as 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. The objective of this work is expanding our current research to examine health disparities associated with age-related diseases 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 longterm goal is to create a consistent dataset of whole genome sequencing to complement the longitudinal HANDLS behavior and health data.

Period of Performance:

August 15, 2024 to August 14, 2025

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 will deliver plates to the Government sufficient to run 95 samples, some of which have been stored for ten or more years. The contractor will perform whole genome sequencing, and specifically shall:

· Sequence libraries on the NovaSeq 6000 platform using 150 bp paired end runs and NovaSeq 6000 S4 v1.0 Reagent Kit with NovaSeq Xp v1.0 4-Lane kit or standard workflow

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

· Re-attempt sequencing in the case that DNA quality and quantity is sufficient, but sample fails sequencing-based QC

· 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

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

· Quality control checks will include: confirming sex, identifying unexpected duplicates and relatedness, confirming relatedness, providing sample performance information and sample identity confirmation against the sequencing data, in addition to confirming coverage, contamination, mapped reads, and other general quality metrics.

· Alignment and variant calling will be performed with the DRAGEN Germline v4.0.3 pipeline. After quality is confirmed, joint variant calling should be performed producing a multi-sample VCF file.

· 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. Data delivered will include:

· per sample CRAMs

· per sample gVCFs

· per sample VCFs

· joint-called multi-sample VCF

· per sample structural variant and CNV calls

· QC report and data dictionary

· Sample manifest with flagged problems

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 will provide the following deliverables:

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

· Written summaries and documentation of the methods used to perform the whole genome sequencing pipeline

· Whole genome sequencing data in a mutually acceptable electronic format that preserves study participants’ confidentiality. Data delivered will include:

· per sample CRAMs

· per sample gVCFs

· per sample VCFs

· joint-called multi-sample VCF

· per sample structural variant and CNV calls

· QC report and data dictionary

· Sample manifest with flagged problems

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

· 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:

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:

Publications and Publicity:

Confidentiality of Information:

Version 11-30-2016-1

FAR Part 11—Describing Agency Needs