B. dna methylation SOW_2025_v1 (2).pdf

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

STATEMENT OF WORK (SOW) (SERVICES)

GENERAL INFORMATION

Title of Project:

DNA methylation microarray processing services for the Baltimore Longitudinal Study of Aging

(BLSA).

Statement of Need and Purpose:

The purpose of this requirement is to obtain laboratory and related analytic services for the continuation of a project assessing aging related change over time in genome-wide methylation through evaluation of archived BLSA DNA samples using DNA methylation microarrays.

Background Information and Objective:

Epigenetic change has been proposed as a ‘hallmark’ of aging and an element of the biological mechanisms underlying the aging process. DNA methylation is one of the most commonly studied epigenetic marks and has been associated with aging phenotypes and age-related diseases in cross-sectional studies however longitudinal characterization of DNA methylation remains rare. Archived samples from the BLSA offer a unique opportunity to fully describe the trajectory of DNA methylation over time and across the life course as well as a chance to relate change in DNA methylation to a broad range of aging phenotypes. To capture potential nonlinear change in DNA methylation this project interrogates genome-wide DNA methylation using serial samples from a large number of BLSA participants collected over several follow-up visits. The current requirement will expand the study sample to include DNA from BLSA participants not previously assayed and extend the longitudinal follow-up of the project by assaying recently collected DNA samples. To assure comparability of data which is essential for characterization of longitudinal trajectories, the microarray processing services need to be identical to those provided by the previous service provider, the UCLA Neuroscience Genomics

Core.

Period of Performance:

The period of performance shall be 12 months from receipt of samples.

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 perform genome-wide DNA methylation microarray assays for 992 archived DNA samples from the BLSA.

1. The Contractor shall provide all necessary microarrays, reagents, consumables and equipment. The investigators and study staff of the BLSA prefer use of the Illumina Infinium

MethylationEPIC v2.0 BeadChip for compatibility with existing DNA methylation data.

2. The Contractor shall implement and document quality assurance and quality control procedures suitable to the specifics of the project.

3. The Contractor shall complete bisulfite conversion and microarray processing for provided

DNA samples and appropriate controls.

4. The Contractor shall repeat assays where assay failure is due to a technical issue other than DNA sample quantity or quality as appropriate.

LEVEL OF EFFORT:

The Contractor shall provide a team comprised of a senior researcher and/or technical researcher and laboratory staff sufficient to complete the assays and appropriate quality control analyses.

GOVERNMENT RESPONSIBILITIES

The Government shall provide adequate quantities of de-identified BLSA DNA samples to the

Contractor and associated data necessary for quality control analyses, such as sex. Project related samples and data will be provided to the Contractor for performance of work efforts only.

All samples and data provided to the Contractor must be treated as confidential and not be shared or disclosed to any third party.

DELIVERY OR DELIVERABLES

The Contractor shall provide the raw files generated by the microarray scanner software with one file per assay and spreadsheets or database files with relevant quality control metrics

(including experimental batches, specimen usage, assay success/failure rates, normalization processes), as well as an electronic copy of a report summarizing the laboratory methods and technical specifications used. All files are to be delivered within 364 calendar days of receipt of the samples by the Contractor.

REPORTING REQUIREMENTS

The Contractor shall submit via e-mail a progress report every six (6) months during the contract period of performance or a final report if the project is completed in a shorter period. The report shall include tasks completed since submission of the last progress report and a list of tasks to be completed, inclusive of timeframe. This report shall also describe any problems that arose and state the resolution or provide an explanation if a solution was not identified.

OTHER CONSIDERATIONS

Travel:

N/A

Key Personnel:

The key personnel requirements for the senior researcher or technical researcher are as follows:

• A Masters or PhD in a laboratory or health science field.

• Extensive experience in high throughput laboratory methods.

• Expertise in quality control, preprocessing, and analytic methods related to genome-wide

DNA methylation microarrays.

Information System Security Plan:

Data Rights:

The National Institute on Aging (NIA) shall have unlimited rights to and ownership of all deliverables provided under this contract including reports, recommendations, briefings, work plans and all other deliverables. 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:

The Contractor is not required to develop, procure, maintain, or use Electronic and Information

Technology (EIT) in the performance of the SOW.

Publications and Publicity:

Contracting Officer’s Representative (COR)

The Contracting Officer's Representative (COR) for this contract will be Dr. Eleanor M.

Simonsick of the Translational Gerontology Branch (simonsicklel@mail.nih.gov). Dr. Simonsick will represent the Government for the purpose of this contract:

The COR is responsible for: (1) monitoring the Contractor's technical progress, including the surveillance and assessment of performance and recommending to the Contracting Officer changes in requirements; (2) interpreting the statement of work and any other technical performance requirements; (3) performing technical evaluation as required; (4) performing technical inspections and acceptances required by this contract; and (5) assisting in the resolution of technical problems encountered during performance.

The Contracting Officer is the only person with authority to act as agent of the Government under this contract. Only the Contracting Officer has authority to: (1) direct or negotiate any changes in the statement of work; (2) modify or extend the period of performance; (3) change the delivery schedule; (4) authorize reimbursement to the Contractor for any costs incurred during the performance of this contract; (5) otherwise change any terms and conditions of this contract; or (6) sign written licensing agreements. Any signed agreement shall be incorporated by reference in Section K of the contract.

The Government may unilaterally change the COR designation for this contract.

Confidentiality of Information:

The Government will not provide to the contractor any information or data of a personal nature about individual(s) or proprietary information or data pertaining to an institution or organization which is confidential.