Epigenetic Age Analysis of Large Whales

Synopsis: Notice of Intent to Award a Sole-Source Contract

Announcement Number: 143015-25-Q0033

The US Department of Commerce (DOC), National Oceanic and Atmospheric Administration (NOAA), National Marine Fisheries Service (NMFS), Office of Protected Resources (OPR) intends to negotiate on a sole source basis with the Epigenetic Clock Development Foundation, using the procedures in FAR Part 13, to provide Epigenetic Age Analysis services for Large Whales. Services will provide for the epigenetic analyses and age estimation for up to 96 North Atlantic right whale or other whales from skin biopsies of whales. Biopsy samples are in a frozen archive and skin samples will be provided for extraction, or DNA extraction will take place in the NOAA, Southeast Fisheries Science Center and provided to the Clock Foundation. Once the samples are received, the Clock Foundation will perform the methylation array assay and provide the data and report to NOAA.

The ability to use epigenetic age estimation of living mammals have revolutionized studies of long-lived species, particularly for free-swimming wild cetaceans where age estimation is particularly challenging. DNA methylation (DNAm) can affect gene expression and strong correlations between DNAm patterns and age have been observed in humans and many nonhuman vertebrates including in cetaceans such as killer whales, bowhead whales and bottlenose dolphins. These analyses are used to construct "epigenetic clocks" which could be used to estimate chronological age. In addition, studies are now evaluating age acceleration due to environmental stressors? in mammalian species using these same techniques.

This analysis will focus primarily on interrogating DNA methylation in the context of CpG dinucleotides as a key epigenetic mechanism mediating between the environment and the genome using skin samples from North Atlantic right whales and other whale species. The epigenetic clocks developed in mammals, particularly some cetacean species, have demonstrated the validity of using cytosine methylation data to estimate the age of long- lived cetaceans and have broad applications supporting their conservation and management. This study will use genomic DNA from remote skin biopsies collected under a scientific research permit from free- swimming whales that are identified through photo-identification.

The methylation analysis approaches described here is fully operational in laboratories and the work will be overseen and managed by the Epigenetic Clock Development Foundation (Clock Foundation). The Clock Foundation laboratory that performs raw methylation analysis has dedicated infrastructure in place to facilitate quantitative high-throughput and genome-wide measurements of epigenetic markers. The analysis will focus primarily on interrogating DNA methylation in the context of CpG dinucleotides as a key epigenetic mechanism mediating between environment and genome, as it currently represents the most accessible and reliable markers for quantitative epigenetic measurements. DNA methylation studies take advantage of bisulfite treatment of genomic DNA that selectively deaminates cytosine residues that are not methylated, while leaving methylated cytosines intact. Thus, this approach converts epigenetic information to sequence-based information that will be measured in an unbiased genome-wide assay.

This project will use the Illumina Horvath Mammalian Methylation Chip. This enables the quantitative interrogation of more than 37,000 CpG methylation conserved mammalian loci per sample. The technology allows one to evaluate whether an intervention that affects DNA methylation levels in one species (e.g. mouse) also affects the corresponding DNA methylation levels in another species (e.g. human), and it is tailor-made for cross-species comparisons. The statutory authority for other than full and open competition is FAR 13.106-1(b)(1)(i), Only one responsible source.

The North American Industry Classification Code (NAICS) for this acquisition is 541715, Research and Development in the Physical, Engineering, and Life Sciences (except Nanotechnology and Biotechnology) with a Small Business Size Standard of 1,000 Employees.

This is not a solicitation for competitive quotes, nor will one be posted on the SAM.gov Contract Opportunities website.

The determination by the Government not to compete this proposed requirement based upon responses to this notice is solely within the discretion of the Government. However, if any interested party believes that it is capable of meeting the requirements, and in an effort to comply with the requirements outlined in FAR 5.102, a firm may request an electronic copy of the solicitation from the Contracting Officer, Natasha Thieman, Natasha.Thieman@noaa.gov.

All electronic correspondence shall have the subject line read: Announcement Number: 143015-25-Q0033

All responsible sources may submit a Capability Statement and/or a quote in accordance with the solicitation, which shall be considered by the agency if received on or before 11:00 AM (EDT) on September 9, 2025. The Capability Statement must contain material in sufficient detail to allow NOAA to determine if the party can meet all of the requirements.

The solicitation will remain open from August 26, 2025 to September 9, 2025.