C04_Attachment II -SOW_12363N26Q4246.pdf
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- Solicitation number
- 12363N26Q4246
About this file
This is a Statement of Work for eastern oyster single nucleotide polymorphism (SNP) genotyping services required by the USDA Agricultural Research Service. The performance period extends from September 1, 2026 through August 31, 2031, consisting of a base year plus four option years. The contractor must provide SNP genotyping services on DNA samples extracted from eastern oyster tissues delivered in 96-well plates containing aqueous buffer, with samples provided in multiples of 384. Genotyping must be completed using the AXIOM OYSTERCV 384S Axiom array (SKU 551377) in 384-well format on the GeneTitan Instrument or equivalent.
The contractor shall deliver genotyping data in PLINK format and raw data files in .cel format, meeting specified technical requirements including chromosome codes concordant with Axiom annotation (values 1-10), mitochondrial loci coded as MT, genotypes ordered by chromosome with mitochondrial loci last, and identical Family ID and Individual ID reflecting sample names. All PLINK text files must be space-delimited. Required performance benchmarks include SNP call rates ≥97% for passing samples, a minimum sample pass rate of 95%, a fully integrated Laboratory Information Management System (LIMS) for sample tracking, and quality control procedures ensuring sample and data integrity. Data and results must be delivered within 60 days of sample receipt along with a written report. Deliverables will be transmitted digitally to NCWMAC in Kingston, Rhode Island through a secure electronic portal. Line Item 01 covers SNP Array Genotyping per group of 384 samples.
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Other files
| File | Type | Posted |
|---|---|---|
| C04_SF 1449_12363N26Q4246.pdf | ||
| C04_Attachment I - Terms and Conditions_12363N26Q4246.pdf |
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Attachment II
Eastern oyster SNP genotyping
Performance Period
The overall performance period is Sept 1, 2026 – August 31, 2031. This includes a base year plus 4 option years.
Statement of Work:
The USDA Agricultural Research Service requires single nucleotide polymorphism (SNP) genotyping from DNA extracted from eastern oyster tissues. DNA samples for genotyping will be provided in 96-well plates containing an aqueous buffer. Samples will be provided in multiples of 384. SNP genotyping will be completed using the AXIOM OYSTERCV 384S Axiom array (SKU 551377) for SNP genotyping in the 384-well format on the GeneTitan Instrument or equivalent. Deliverables will be the genotyping data for all the samples in PLINK format and the raw data files in .cel format (CEL files). The PLINK files shall meet the following specifications:
• Chromosomes codes concordant with the Axiom annotation for the array (values of 1-10)
• Mitochondrial loci having a chromosome code of MT
• Genotypes in order by chromosome with the mitochondrial loci last
• Family ID and Individual ID being identical and reflecting the sample name
• All PLINK text files being space-delimited
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.
All data and results will be included with a written report and provided along with the raw genotype data within 60 days of sample receipt.
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 in place a series of quality control (QC) steps to ensure samples and data integrity;
5. Completion and return of data is required within 60 days of sample receipt
Schedule of Line Items:
Line Item 01 – SNP Array Genotyping, group of 384 samples
Attachment II
Deliverables:
SNP Array Genotyping: The genotype files (PLINK format genotype calls and .cel files in accordance with the SOW) and QC summary for all samples will be sent digitally to the NCWMAC in Kingston, RI by providing the files for download through a secure electronic portal.
| Eastern oyster SNP genotyping |
| Performance Period |
| Statement of Work: |
| The following performance elements and benchmarks are required: |
| Schedule of Line Items: |
| Deliverables: |
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