DNA methylation patterns and renal cell carcinoma

Contracting Office Address

The Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 9609 Medical Center Drive, Rockville, MD 20850, UNITED STATES

1.0    DESCRIPTION

The Division of Cancer Epidemiology and Genetics (DCEG), plans to procure services, on a sole source basis, from Epigenetic Clock Development Foundation, 1124 West Carson Street, MRL Building, 3rd Floor, Torrance, CA 90502.

The response close date of the notice for this requirement is in accordance with FAR 5.203(b). This acquisition will be processed under FAR Part 12 - Acquisition for Commercial Items and will be made pursuant to the authority in FAR Part 13.106-1(b)(1)(i); and is exempt from the requirements of FAR Part 6. The North American Industry Classification System code is 541715 and the small business size standard is 1,000 employees.

It has been determined there are no opportunities to acquire green products or services for this procurement.

2.0    BACKGROUND

The Department of Health and Human Services (DHHS), National Institutes of Health (NIH), National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics (DCEG) is conducting research on per- and polyfluoroalkyl substances (PFAS), which are a group of organofluorine chemical contaminants that have been manufactured and used in a variety of industries since the 1940s. PFAS bioaccumulate in humans, and studies have reported associations with different adverse health effects. In 2016, the International Agency for Research on Cancer (IARC) classified one of the most commonly detected PFAS in human serum, PFOA, as a possible human carcinogen (Group 2B) on the basis of limited evidence of carcinogenicity in laboratory animals and limited findings of associations with testicular and renal cancers in humans from small studies of exposed individuals working at or living near a PFAS-producing plant. 

The biological mechanisms by which PFOA may increase the risk of kidney cancer are unknown. Some hypothesized biological mechanisms include oxidative stress, cytotoxicity, inflammation, altered hormone pathways and epigenetic alterations. PFOA may act in part via peroxisome proliferator-activated receptor (PPAR)-alpha activation, which modulates lipid and glucose homeostasis, inflammation, and cell differentiation and proliferation. More recent studies suggest that the adverse health effects associated with PFOA exposure may be meditated through DNA methylation. Alterations in DNA methylation following PFOA exposure have been reported in epidemiologic studies and experimental models. However, no studies have examined the association between PFOA exposure and DNA methylation in human or mouse kidney tissue.

We will conduct a trans-species analysis evaluating epigenetic alterations associated with PFOA exposure in human kidney tumors and compare the results with those observed in kidney tissue from controlled PFOA-exposed mice. 

2.1    OBJECTIVE

The objective of this procurement is to obtain and analyze DNA methylation profiles for a multi-species epigenome-wide association study of renal cell carcinoma. 
3.0    SCOPE

The Contractor shall analyze DNA methylation in 888 DNA samples. NIH will aliquot and ship the DNA specimens to the Contractor for analysis. 

4.0    CONTRACT REQUIREMENTS/ AND PERSONNEL QUALIFICATIONS

The Contractor shall analyze DNA methylation using the Illumina Mammalian array for 888 samples for inclusion in a epigenome-wide association study.
4.1    The Contractor shall perform the following tasks:

4.1.1    The Contractor shall analyze 888 samples with DNA specimens amenable for DNA methylation analysis.

4.1.2    NIH shall aliquot and ship DNA specimens for the above referenced samples. 

4.1.3    The Contractor shall provide both raw and normalized DNA methylation results after experimental and computational processing of Illumina Mammalian array data. No residual samples will remain after analysis as the number of samples has been precisely estimated.

4.2    PROHIBITION AGAINST PERSONAL SERVICES

5.0    TYPE OF ORDER

This is a firm fixed price purchase order. 

6.0    NON-SEVERABLE SERVICES

The services specified in each contract line item (CLIN) have been determined to be non-severable services - a specific undertaking or entire job with a defined end product of value to the Government.

7.0    PERIOD OF PERFORMANCE

Period of performance shall be 12 months from the date of award.
8.0    PLACE OF PERFORMANCE

All work shall be performed at the Contractor’s facility.

9.0    REPORT(S)/DELIVERABLES AND DELIVERY SCHEDULE

All written deliverables shall be sent electronically to the NCI Technical Point of Contact (TPOC), TBD at award, in a Microsoft-compatible format, such as Microsoft Excel or text file unless approved by the TPOC in accordance with the deliverable schedule below. The TPOC shall review the contents of all draft deliverables. If no comments or requests for revisions are provided to the Contractor within 30 business days, the deliverables shall be considered acceptable. If revisions are required, NCI shall respond to the Contractor within five (5) business days of receiving the deliverable, specifying the required changes/revisions. Final copies of approved drafts shall be delivered to the NCI TPOC within five (5) business days after receipt of the Government’s comments. 

All DNA specimens shall be sent directly to the Clock Foundation for sample handling and processing. In conjunction with the laboratory, the POC shall review the quality and quantity of the samples received. If no comments or requests are provided within 30 days, the specimens shall be considered acceptable.

All deliverables shall be provided to the NCI per the following deliverable schedule:

DELIVERABLE     DELIVERABLE DESCRIPTION / FORMAT REQUIREMENTS    DUE DATE
Task 4.1.1    Emails or phone calls with the Contractor to discuss DNA methylation analysis.    30 days prior to final analysis. As needed.
Task 4.1.2    Emails or phone calls to confirm arrival of the samples at the laboratory and that the samples are in good condition.     Within 3 days of shipment of samples.
Task 4.1.3    Beta matrix and .idat files from DNA methylation analysis    Within 3 months of receiving the samples.

10.0    INSPECTION AND ACCEPTANCE CRITERIA

Pursuant to FAR clause 52.212-4, all work described in the SOW to be delivered under this contract is subject to final inspection and acceptance by an authorized representative of the Government. The authorized representative of the Government is the NCI TPOC, TBD, who is responsible for inspection and acceptance of all services, materials, or supplies to be provided by the Contractor.

Section 508 of the Rehabilitation Act, as amended by the Workforce Investment Act of 1998 (P.L. 105-220) requires that when Federal agencies develop, procure, maintain, or use information and communication technology (ICT), it shall be accessible to people with disabilities. Federal employees and members of the public who have disabilities must have access to, and use of, information and data that is comparable to people without disabilities. Remediation of any materials that do not comply with the applicable Section 508 requirements as set forth below, shall be the responsibility of the Contractor.

Products, platforms and services delivered as part of this work statement that are ICT, or contain ICT, must conform to the Revised 508 Standards, which are located at 36 C.F.R. § 1194.1 & Apps. A, C & D, and available at https://www.access-board.gov/guidelines-and- standards/communications-and-it/about-the-ict-refresh/final-rule/text-of-the-standards- and- guidelines.

Per Section 508 and as mandated under HHS Policy for Section 508 Compliance and Accessibility of Information and Communications Technology (ICT) (07/2020) all documents or electronic files provided to the NIH NCI under contract must be conformant with Section 508 standards and accessible to persons with disabilities. Conformance shall be confirmed by use of material provided at HHS OS Factsheets & Reference Guides and verified through the use of the HHS Checklist Documents (WCAG 2.0 Refresh); in addition, contractors and vendors are encouraged to make use of the instructional materials and checklists at GSA Section 508.gov’s Create Accessible Digital Products.

11.0    UNIQUE QUALIFICATIONS OF THE CONTRACTOR

The Epigenetic Clock Development Foundation (“Clock Foundation”) is a non-profit specializing in DNA methylation analyses and is currently the only institution which has a robust and scalable pipeline for the Infinium Mammalian Methylation array, with both the pipeline and the array being designed by Clock Foundation members. The degree of expertise needed
and the infrastructure are not currently available elsewhere. This is the only institution able to provide large-scale analysis of Infinium Mammalian Methylation arrays. The Epigenetic Clock Development Foundation is well-qualified concerning all aspects required for the completion of this contract, having run thousands of assays of this kind. It has the experience necessary to carry out the terms of this procurement. The center has staff that are dedicated to handling the biospecimens in an orderly and efficient manner. NCI has had extensive discussions with
researchers in the U.S., and the Epigenetic Clock Development Foundation was identified as the only contractor with a proven pipeline capable of providing analysis for hundreds of Infinium Mammalian Methylation arrays.

12.0    SUBMISSION INSTRUCTIONS

This notice is not a request for competitive quotations. However, if any interested party believes it can meet the above requirements, it may submit a proposal or quote for the Government to consider. The response and any other information furnished must be in writing and must contain material in sufficient detail to allow NCI to determine if the party can perform the requirement.  All responses and questions must be sent via email to the Contract Specialist, Dana Summons, at dana.summons@nih.gov by no later than 3:00 PM EST on August 1, 2023, (8/1/23). A determination by the Government not to compete this proposed requirement based upon responses to this notice is solely within the discretion of the Government. Information received will be considered solely for the purpose of determining whether to conduct a competitive procurement. In order to receive an award, Contractors must be registered and have valid certification through SAM.gov. Reference: 75N91023Q00126 on all correspondence.