Oyster SNP Genotyping SOW 8.7.2025.docx
DOCX document 25 KB Posted
- Solicitation number
- 1232SA25Q0812
About this file
This document is a Statement of Work (SOW) for SNP genotyping services for eastern oysters, issued by the USDA Agricultural Research Service. The project requires genotyping 3,072 DNA samples from phenotyped eastern oysters using Applied Biosystems Axiom Oyster CV 384HT-format genotyping arrays, with a performance period from September 15, 2025 to September 14, 2026. The contract, valued at $36,864.00, specifies strict technical requirements including a 95% SNP call rate, 90% sample pass rate, and use of a Laboratory Information Management System for sample tracking.
Key deliverables include genotype data in PLINK format, raw .cel files, preliminary quality control, and a QC report, to be submitted within 60 days of sample delivery. The related federal contract opportunity (Solicitation Number 1232SA25Q0812) indicates this will be a Firm Fixed Price contract awarded using a Lowest Price Technically Acceptable (LPTA) evaluation method. The procurement is classified under NAICS code 541714 for Biotechnology Research and Development, with a small business size standard of 1,000 employees, and will be awarded by the USDA Agricultural Research Service's National Center for Watershed Agricultural and Climate Research in Kingston, Rhode Island.
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Eastern Oyster SNP Genotyping
Performance Period:
September 15, 2025 – September 14, 2026 Statement of Work:
The USDA Agricultural Research Service requires single nucleotide polymorphism (SNP) genotyping of 3072 samples of extracted DNA from phenotyped eastern oysters that are part of a genetic improvement program. Genotype data will be combined with phenotype and pedigree information to increase the accuracy of breeding values and accelerate the achievement of genetic gains. Without this service, the integrity of the ARS eastern oyster breeding program will be compromised, the continuity of selective breeding interrupted, and delivery of improved germplasm to stakeholders will be delayed.
ARS will provide the contractor with one microgram of high-quality DNA extracts in 20 ul volumes. The contractor will complete the genotyping using the Applied Biosystems Axiom Oyster CV 384HT-format genotyping arrays (Thermo-Fisher SKU 551377) with Axiom 2.0 reagent kit and GeneTitan MC instrument. SNP arrays, reagents, and consumables to run the samples were purchased by ARS in FY24 for a related project and are already in custody of the contractor. The contractor will provide all services, equipment and facilities necessary to perform the service. Deliverables include genotype data for all the samples in PLINK format and the raw data files in .cel format (CEL files), preliminary QC of the data, and a QC report.
The following performance elements and benchmarks are required:
1. Passing samples have SNP call rates greater than or equal to 95%;
2. Minimum sample pass rate of 90%;
3. Vendor must have a fully integrated LIMS (Laboratory Information Management System) for sample tracking to ensure that there are no errors in matching the genotypes to the samples;
4. Vendor must have barcodes or barcoded plates for the DNA samples.
5. Vendor must have in place a series of quality control (QC) steps to ensure samples and data integrity;
6. Completion and return of raw/formatted genotype data and QC report is required within 60 days of delivery from when samples are submitted.
Deliverables:
The genotyping data for all samples run on the oyster array will be returned to PI Proestou and Bio Sci Technician Keegan Hart (NCWMAC, Kingston, RI) in raw and PLINK formats through a secure electronic portal. All data must be provided via secure portal download. The order number must be included on all data and documentation provided.
Cost of Service Contract:
The anticipated cost of this contract is $36,864.00
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