Epigenetics Sequencing Request

        Epigenetics Sequencing Request                    
                            
NOTICE OF INTENT TO NEGOTIATE A SINGLE-SOURCE CONTRACT                            
Special Notice: FD-2026-362                            
NOAA/NMFS/SEFSC                            
                            
                            
The U.S. Department of Commerce (DOC), National Oceanic and Atmospheric Administration (NOAA), National Marine Fisheries Service (NMFS), Office of Management and Budget (OMB) intends to negotiate and award a purchase order, on a sole source basis, under the authority of FAR 12.102(a) and 41 USC 1901,  with Seqmatic.

                           
The anticipated award date is 8/21/2026                    

The requirement is to procure the following: This requirement is for: Services, non-personal, to provide all labor, equipment and materials (unless otherwise provided herein) necessary to provide whole-genome DNA (30 samples) and epigenetic (60 samples) sequencing services for the provided samples for the Southeast Fisheries Science Center Marine Mammal and Turtle Division in accordance with the statement of work.

NO SET ASIDE IS TO BE USED FOR THIS SOLE SOURCE REQUIREMENT. THE APPLICABLE SIZE STANDARD IS NORTH AMERICAN INDUSTRY CLASSIFICATION SYSTEM (NAICS) CODE 541380 with a Small business size standard of $19M. The applicable Product service code (PSC) is B529 Special Studies/analysis- Scientific Data.

                        
This Sole Source Determination is based on NOAAA's requirement that Seqmatic is the only Vendor that provides the required Services.                            
"A well established issue in next-generation sequencing, including both whole genome
DNA sequencing and methylation sequencing, is the presence of batch effects. These
batch effects are “a pattern of variation due to the merging of data sets produced
separately that can confound or mask biological patterns. While usually mitigated by
randomization or consistency in methods (e.g., library preparation and sequencing
procedure), batch effect represents a major concern for studies carried over several
years or across multiple laboratories, as well as for reanalysis of public data sets.”
(Dallaire and Mérot 2022).
Previous sequencing of Rice’s whale samples for whole genomes have been conducted
with Seqmatic. It is essential to minimize the potential batch effects by keeping
consistent the facility, methods, and equipment upon which this species has been
sequenced. This is critical to achieve robust data that are not biased by the sequencing
facility and library preparation and therefore to draw accurate biological conclusions from
these data. Switching to a new provider for this contract would likely introduce a
confounding factor in our analysis that we would not be able to disentangle from a true
biological signal, thus jeopardizing the accuracy of conclusions from these analyses.
Further, Seqmatic has low input DNA requirements for genomic sequencing where they
recommend 20uL but accepts a minimum of 10uL. Because samples are extremely
challenging to obtain, it is important to retain DNA for future use. Seqmatic will also
return unused DNA.
Dallaire, Xavier, and Claire Mérot. ""A setback into a success: What can batch effects tell
us about best practices in genomics?."" Molecular Ecology Resources (2022):
1675-1677.

                        
The requested service is for sequencing of Rice’s whale samples for whole-genome DNA (30 samples)
and whole genome enzymatic-converted methylation (60 samples). We will integrate these data with
individual health status to understand and develop biomarkers for the health, age structure, and overall
resilience of this species. We will leverage whole genome DNA sequencing to quantify species-wide
genetic diversity and inbreeding, infer relatedness across the species, and explore health-related
genomic markers. Next we will integrate whole genome epigenetic data with age and health metrics to
understand the epigenetic contribution to phenotypic variation and to develop health and aging
biomarkers. Finally, we will use these epigenomic data to develop robust epigenetic clocks that will be
used to age future individuals. This information is critical to inform stock assessments of this
endangered species. The expected delivery date is within 30 days of sample receipt, including the
return of critical samples within 90 days of sequencing completion and retention of sequencing libraries
for potential additional sequencing for 120 days following sequencing completion.                           
                            
***THIS PRESOLICITATION NOTICE IS NOT A REQUEST FOR COMPETITIVE PROPOSALS AND NO SOLICITATION PACKAGE IS AVAILABLE. HOWEVER, FIRMS THAT BELIEVE THEY CAN FULLY MEET THE GOVERNMENT'S REQUIREMENTS MAY SUBMIT SUBSTANTIATING DOCUMENTATION OR A REQUEST FOR ADDITIONAL INFORMATION IN WRITING TO THE IDENTIFIED POINT OF CONTACT WITHIN 15 DAYS AFTER PUBLICATION OF THIS PRE-SOLICITATION NOTICE. SUCH REQUESTS AND DOCUMENTATION WILL BE EVALUATED SOLELY FOR THE PURPOSE OF DETERMINING WHETHER OR NOT TO CONDUCT THIS PROCUREMENT ON A COMPETITIVE BASIS. A DETERMINATION BY THE GOVERNMENT NOT TO CONDUCT A COMPETITIVE PROCUREMENT, BASED UPON RESPONSES TO THIS NOTICE, IS SOLELY WITHIN THE DISCRETION OF THE GOVERNMENT. ORAL COMMUNICATIONS ARE NOT ACCEPTABLE IN RESPONSE TO THIS NOTICE.