Attachment 1_SOW.pdf

Attachment 1

STATEMENT OF WORK (SERVICES)

(SOW)

GENERAL INFORMATION

Title of Project:

Whole genome sequencing for investigation of age-related chronic disease in HANDLS participants

Statement of Need and Purpose:

Investigators in the HANDLS study require whole genome sequencing (WGS) data to expand our current research examining whether rare genetic variants present in White and African American individuals contribute to age-related chronic 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:

Chronic diseases and conditions have been linked to accelerated aging, the risk for age-associated conditions at younger ages than usual. Although genetics may contribute to observed differences in health outcomes, there are only limited studies in both White and African American populations. The objective of this work is expanding our current research to examine health differences associated with age-related chronic diseases through whole genome sequencing to investigate the contributions of genomics to the burden of disease incidence, prevalence, morbidity, and mortality in populations 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:

Twelve (12) month period of performance from date of award.

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 325 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 X-Plus platform with 25B-300 flow cells using 150 bp paired end runs and NovaSeq workflow-series 10B sequencing run 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 v4.3.6 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:

o per sample CRAMs o per sample gVCFs o per sample VCFs o joint-called multi-sample VCF o per sample structural variant and CNV calls o QC report and data dictionary o 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:

o per sample CRAMs o per sample gVCFs o per sample VCFs o joint-called multi-sample VCF o per sample structural variant and CNV calls o QC report and data dictionary o 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:

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: