USDA Single Nucleotide Polymorphism Array Genotyping in Rainbow Trout - SOW.docx

Single Nucleotide Polymorphism Array Genotyping in Rainbow Trout Statement of Work: The USDA ARS National Center for Cool and Cold Water Aquaculture requires single nucleotide polymorphism (SNP) genotyping of 2,304 rainbow trout DNA samples using Axiom myDesign TG arrays for SNP genotyping in rainbow trout in the 384-well format (O_my_50K; Catalog Number 550571; https://www.thermofisher.com/order/catalog/product/550571?SID=srch-srp-550571) on the GeneTitan Instrument or equal. Deliverable will include the genotyping data for all the samples and the raw data files in .cel format (CEL files). 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 DNA samples (2,000 ng per sample). The following performance elements and benchmarks are required:

1. Passing samples have SNP call rates greater than or equal to 97%.

2. Minimum sample pass rate of 95%.

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 during the SNP genotype processing.

6. Completion and return of required data is required within 45 days of samples receipt.

Schedule of Line Items:

Line Item 01 – SNP genotyping of 2,304 rainbow trout DNA samples Samples will be provided on or before September 30, 2021.

Deliverable will include the genotyping data for all the samples and the raw data files in .cel format (CEL files). 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 45 days after receipt of all Government provided samples. The order number shall be included on all documentation and shipments.