IDIQ SNP Genotyping and Parentage Assignments in Rainbow Trout - SOW - FY20.pdf
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- Single Nucleotide Polymorphism Genotyping and Parentage Assignment Services in Rainbow Trout
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- 1144243
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This document is a Statement of Work (SOW) for an Indefinite Delivery Indefinite Quantity (IDIQ) contract for Single Nucleotide Polymorphism (SNP) Genotyping and Parentage Assignment Services in Rainbow Trout. The USDA Agricultural Research Service's National Center for Cool and Cold Water Aquaculture requires comprehensive genetic services for rainbow trout, with a base year and four optional extension years. The primary services include DNA extractions, SNP genotyping using low-density assays of at least 180 SNPs, and high-confidence parentage assignments with at least 95% accuracy for offspring.
Key performance requirements include delivering DNA samples with at least 200 ng of total genome DNA, maintaining SNP call rates above 90%, achieving a 95% sample pass rate for offspring and 100% for parents, and utilizing a fully integrated Laboratory Information Management System (LIMS) for sample tracking. The contractor must provide barcoded samples, implement quality control steps, and complete all work within 90 days of sample receipt. Deliverables will include genotyping data in Excel or flat files, parentage analysis results, and the return of unused tissue and DNA samples. The contract periods span from July 2025 to June 2030, with specific line items for DNA extraction, parentage analysis, and sample return for each year.
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Indefinite Delivery Indefinite Quantity (IDIQ) for Single Nucleotide Polymorphism Genotyping and Parentage Assignment Services in Rainbow Trout
Statement of Work: The USDA ARS National Center for Cool and Cold Water Aquaculture requires parentage assignments services for rainbow trout, for a period of performance of a base year, plus four (4) option years. The service includes DNA extractions and single nucleotide polymorphism (SNP) genotyping of rainbow trout DNA samples using low-density (LD) assays of at least 180 SNPs and high confidence assignment of at least 95% of the offspring to parental pairs. Deliverables will include the results of the parentage assignment analysis and the genotyping data for all the samples in Excel file or in a flat files. Unused tissue samples and remaining DNA samples will be sent back to the government. Contractor shall provide all services, supplies, equipment and facilities necessary to provide the deliverable specified in accordance with the terms, conditions, and specifications contained in this document.
The government will provide the tissue samples (fin clips in ethanol) for DNA extractions and genotyping, including samples from the parents of the fish and pedigree information of the specific crosses made. The following performance elements and benchmarks are required:
1. Amount of DNA per sample required is at least 200 ng of total rainbow trout genome DNA;
2. Passing samples have SNP call rates greater than 90%;
3. Minimum required sample pass rate is 95% for offsprings and 100% for the parents;
4. 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;
5. Vendor must have barcodes or barcoded plates for the DNA samples;
6. Vendor must have in place a series of quality control (QC) steps during the SNP genotype processing;
7. Completion and return of data is required within 90 days of samples receipt.
8. Sending back of remaining tissue samples in ethanol and unused DNA samples upon completion of the project.
Schedule of Line Items:
0001 DNA extractions and SNP genotyping of the rainbow trout DNA samples 07/01/2025 – 06/30/2026
0002 Parentage analysis results and high confidence assignments of at least 95% of the offsprings.
07/01/2025 – 06/30/2026
0003 Return shipping of all unused tissue samples in ethanol and all extracted DNA samples
07/01/2025 – 06/30/2026
1001 Option Year I: DNA extractions and SNP genotyping of the rainbow trout DNA samples
07/01/2026 – 06/30/2027
1002 Option Year I: Parentage analysis results and high confidence assignments of at least 95% of the offsprings.
07/01/2026 – 06/30/2027
1003 Option Year I: Return shipping of all 07/01/2026 – 06/30/2027 unused tissue samples in ethanol and all extracted DNA samples
2001 Option Year II: DNA extractions and SNP genotyping of the rainbow trout DNA samples
07/01/2027 – 06/30/2028
2002 Option Year II: Parentage analysis results and high confidence assignments of at least 95% of the offsprings.
07/01/2027 – 06/30/2028
2003 Option Year II: Return shipping of all unused tissue samples in ethanol and all extracted DNA samples
07/01/2027 – 06/30/2028
3001 Option Year III: DNA extractions and SNP genotyping of the rainbow trout DNA samples
07/01/2028 – 06/30/2029
3002 Option Year III: Parentage analysis results and high confidence assignments of at least 95% of the offsprings.
07/01/2028 – 06/30/2029
3003 Option Year III: Return shipping of all unused tissue samples in ethanol and all extracted DNA samples
07/01/2028 – 06/30/2029
4001 Option Year IV: DNA extractions and SNP genotyping of the rainbow trout DNA samples
07/01/2029 – 06/30/2030
4002 Option Year IV: Parentage analysis results and high confidence assignments of at least 95% of the offsprings.
07/01/2029 – 06/30/2030
4003 Option Year IV: Return shipping of all unused tissue samples in ethanol and all extracted DNA samples
07/01/2029 – 06/30/2030
TOTAL
Deliverable will include the genotyping data for all the samples, and the parentage analysis results, and shipping back of all unused tissue samples in ethanol and DNA samples. All data must be provided via secure portal download or in external hard drives delivered FOB Destination to the USDA-NCCCWA, 11861 Leetown Road, Kearneysville, WV 25430. The order number shall be included on all documentation and shipment. Completion and return of deliverable is required within 90 days after receipt of all Government provided samples. The order number shall be included on all documentation and shipments.
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