Genotyping and Associated Molecular Services IDIQ 2023-2027.docx

Genotyping and Associated Molecular Services

Performance Period The overall performance period is January 1, 2023 – December 31, 2028. This includes a base year plus 4 option years.

Statement of Work:

The USDA Agricultural Research Service requires single nucleotide polymorphism (SNP) genotyping, microsatellite testing, and DNA extraction from Atlantic salmon tissues. Atlantic salmon tissue samples will consist of either fin clips or muscle tissue that has been preserved in ethanol or freeze dried. Some DNA samples may require the extracted DNA to be aliquoted out into 3 lots. One lot will be used for the required genotyping, and the remaining two lots from each sample will be placed in uniquely identified, human readable, sealed 96 or 384 well plates and returned to the USDA along with a key linking the unique sample ID to plate and well locations.

Atlantic salmon DNA genotyping will be completed using the N.A. Atlantic Salmon50K Axiom myDesign TG array for single nucleotide polymorphism (SNP) genotyping in the 384-well format (Thermo-Fisher SKU number 551260 or Neogen SKU number 478) on the GeneTitan Instrument or equal. Deliverables will include the genotyping data for all the samples and the raw data files in .cel format (CEL 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.

Microsatellite Genotyping and Continent of Origin (COO) Analysis Service will include standard DNA isolations and microsatellite genotyping across a panel of established markers as described in Appendix 3 of the State of Maine General Permit for Atlantic Salmon Aquaculture [Ssa197DU, Ssal71DU, Ssa202DU, SSOSL438, Ssa289, SSOSL311]. Resulting microsatellite PCR products will be separated on a genetic analyzer and the alleles for each locus will be scored and binned into an allele-calling template designed by the US fish and Wildlife Service (USFWS). Resulting genotype data will be analyzed for continent of origin (COO) in accordance with guidelines as per USWFS, and the State of Maine General Permit for Atlantic Salmon Aquaculture. All data and results will be included in a written report and provided along with the raw genotype data within 30 days of testing. Raw genotype data and summary information from each fish will be complied in an Excel file. Compare the summary genotype information to the USFWS database to determine continent of origin for each fish. This information (genetic information and ancestry classification) will be included in a written report and provided along with the raw genotype data within 30 days of testing. All samples sent to the vendor should be returned to the USDA or destroyed after they have been tested.

The following performance elements and benchmarks are required:

1. Amount of DNA per sample required is at least 1,500 ng of total salmon genome DNA per aliquot;

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

3. Minimum sample pass rate of 95%;

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. Plates returned to the USDA must also have unique human readable tags along with a key linking the unique sample ID from each submission to plate and well locations;

6. Vendor must have in place a series of quality control (QC) steps to ensure samples and data integrity;

7. Completion and return of raw/original genotyping data is required within 60 days of delivery for samples where tissue samples are submitted.

8. Completion and return of the DNA aliquots is required within 30 days of delivery of tissue samples.

9. Completion and return of raw/original genotyping data is required within 30 days of delivery for samples where DNA samples are submitted.

10. Completion and return of COO testing results to USDA within 35 days

11. Submission of COO testing results to USFWS within 35 days

Schedule of Line Items:

Line Item 01 – DNA extractions from Atlantic salmon tissue, fin clips or muscle either stored individual tubes in ethanol or freeze dried. DNA to be used for either Line Item 04 Genotyping or Line Item 05 COO genotyping.

Line Item 02 – DNA extractions from Atlantic salmon tissue, fin clips or muscle either stored in individual tubes in ethanol or freeze dried. DNA to be placed in 96 well plates with unique human readable tags and barcodes, along with a key linking the unique sample ID from each submission to plate and well locations. Extracted DNA will be sent to the USDA in Franklin, ME.

Line Item 03 – DNA extractions from Atlantic salmon tissue, fin clips or muscle either stored in individual tubes in ethanol or freeze dried. DNA to be aliquoted out into 3 lots in 96 well plates with unique human readable tags and bar codes, along with a key linking the unique sample ID from each submission to plate and well locations. One lot of DNA to be used for either Line Item 04 Genotyping or Line Item 05 COO genotyping. Two lots of DNA to be returned to the USDA in Franklin, ME.

Line Item 04 – Genotyping Atlantic salmon DNA on N.A. Atlantic Salmon50K Axiom myDesign TG array for single nucleotide polymorphism (SNP) genotyping in the 384-well format (Thermo-Fisher SKU number 551260 or Neogen SKU number 478) on the GeneTitan Instrument or equal, vendor supplies the genotyping array/chip.

Line Item 05 – Microsatellite Genotyping and COO Analysis Service Microsatellite genotyping across a panel of established markers as described in Appendix 3 of the State of Maine General Permit for Atlantic Salmon Aquaculture [Ssa197DU, Ssal71DU, Ssa202DU, SSOSL438, Ssa289, SSOSL311]. Resulting microsatellite PCR products will be separated on a genetic analyzer and the alleles for each locus will be scored and binned into an allele-calling template designed by the US fish and Wildlife Service (USFWS). Resulting genotype data will be analyzed for continent of origin (COO) in accordance with guidelines as per USWFS, and the State of Maine General Permit for Atlantic Salmon Aquaculture. All data and results will be included in a written report and provided along with the raw genotype data within 30 days of testing. Raw genotype data and summary information from each fish will be complied in an Excel file. Extracted DNA and/or unused fin clips will be returned to the USDA following analysis.

Deliverables:

DNA Extractions: DNA extracted from line item 04 will have two lots shipped to the NCWMAC in Franklin, ME at the shipping address listed below. DNA will be shipped in sealed 96 well plates with human readable tags along with a key linking the unique sample ID from each submission to plate and well locations.

SNP Array Genotyping: The genotyping data for all samples run on the salmon array will be sent to the NCWMAC in Franklin and the NCCCWA in Leetown. The raw data files in .cel format (CEL files) will be sent secure electronic portal. All data must be provided via secure portal download. The order number shall be included on all documentation and shipment.

Microsatellite and COO testing: Upon request, the summary genotype information and copies of raw genotype data will be sent to USFWS via email for analysis and official determination of continent of origin, provide communications with USFWS to maintain updated procedures and fish analyses for North American classification. The Raw data and report should be emailed to brian.peterson@usda.gov.

Criteria for selection in order of priority:

1. Demonstrated experience with both legislation requirements and scientific procedures required for Continent of Origin genotyping as described in the State of Maine General Permit for Atlantic Salmon Aquaculture;

2. Protocol for conducting, analyzing, and interpreting Continent of Origin Testing

3. Continuity of Continent of Origin testing reports for comparison with previous reports provided over the past 3 years.

4. Price