Specifications.pdf
PDF 128 KB Posted
- Attached to
- Parentage Assignments Services for Rainbow Trout Federal contract opportunity
- Solicitation number
- 12305B23Q0160
About this file
This document outlines specifications for parentage assignments services for rainbow trout. The USDA ARS National Center for Cool and Cold Water Aquaculture requires parentage assignments for 160 full-sib families of rainbow trout totaling 3,000 DNA samples, including parents genotyped in duplicates. Services include DNA extractions, genotyping using 96 or more SNPs, and assigning at least 95% of offspring with high confidence. Deliverables are the assignment results and genotyping data in Excel or flat files. Unused samples must be returned.
The specifications define performance requirements for DNA quantity, genotyping call and pass rates, sample tracking system, barcoding, quality control, and 90-day completion. Three line items specify pricing for DNA extraction and genotyping, parentage analysis and assignments, and return shipping. Deliverables are due within 90 days of sample receipt and must be provided via secure download or hard drives delivered to the agency. This relates to the federal contract opportunity for these parentage assignment services issued by the USDA Agricultural Research Service.
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| File | Type | Posted |
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| Terms and Conditions.pdf |
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Specifica ons
The USDA ARS National Center for Cool and Cold Water Aquaculture requires parentage assignments services for rainbow trout from 160 full-sib individual families, including 320 parents genotyped in duplicates (so total of 640 genotype sets for 320 parents) and 2,360 offspring. The service includes DNA extractions and single nucleotide polymorphism (SNP) genotyping of 3,000 rainbow trout DNA samples using low-density (LD) assays of 96 SNPs or more and high confidence assignment of at least 95% of the offspring. Deliverables will include the results of the parentage assignment analysis and the genotyping raw data for all the samples in Excel file or in flat files. Unused tissue samples and 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 or equal to 90%;
3. Minimum offspring sample pass rate of 95% 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 required 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:
Line Item 01 – DNA extractions and SNP genotyping of 3,000 rainbow trout DNA samples All government samples will be provided before October 30, 2023.
Line Item 02 – Parentage analysis results and assignments for each individual sample with high confidence assignment of at least 95% of the offspring
Line Item 03 – Return shipping of all unused tissue samples in ethanol and DNA samples
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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