Statement of Work v2.docx
DOCX document 342 KB Posted
- Attached to
- Intent to Sole Source Geotyping by Sequencing (tGBS) Federal contract opportunity
- Solicitation number
- 1240BG24Q0002
- Issued by
- Department of Agriculture Forest Service
About this file
This document outlines a statement of work for a federal contract to conduct genomic analysis on moose samples. The USDA Forest Service is seeking a commercial laboratory to perform tunable genotyping by sequencing on DNA extracts from moose specimens to generate single nucleotide polymorphism data for determining fine-scale population structure. Key deliverables include notification of sample quality within three weeks, a final summary report within 10-16 weeks, and data files containing all SNP data and sequencing files within 10-16 weeks. There are no security requirements or government furnished property other than funding. Data generated will be owned by the USDA Forest Service. A related special notice references intent to sole source the work under solicitation number 1240BG24Q0002.
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US Department of Agriculture (USDA)
Statement of Work
Project tGBS genotyping-by-sequencing of DNA Samples of Moose General Information
1.0 Scope of Work
The goal of this project is to generate large-scale genome data (SNP data—Single Nucleotide Polymorphism) for DNA extracts of moose for the purpose of conducting population genetic structure analysis.
2.0 Background
We are conducting DNA analysis on moose (Alces alces) for the State of Montana where we need genomic data and thousands of SNPs in order to determine fine-scale population structure for management.
We therefore need the technical capabilities of a commercial lab that can accomplish tunable genotyping by sequencing (tGBS) approach to process samples from these taxa us. The tGBS method has superior accuracy for determining variable SNP sites with less missing data than traditional SNP discovery and has the ability to detect rare alleles even in small or inbred populations. We have used this approach successfully in the past for other animals, including those that are non-model systems including our published work on stoneflies:
Young, Michael K.; Smith, Rebecca J.; Pilgrim, Kristine L.; Fairchild, Matthew P.; Schwartz, Michael K. 2019. Integrative taxonomy refutes a species hypothesis: The asymmetric hybrid origin of Arsapnia arapahoe (Plecoptera, Capniidae). Ecology and Evolution. 9: 1364-1377.
Contractor Requirements
3.0 Technical Requirements / Tasks
The technical methodologies to be used to generate genomic data from these taxa are as follows; all work will be performed by a commercial laboratory, Iowa without government supervision.
· DNA extracts from specimens provided by Kristy Pilgrim will be evaluated for Quality (DNA concentration)
· DNA samples are then prepared, and DNA sequencing libraries will be constructed from each sample
· Raw DNA sequence data will be generated using Next Generation Sequencing for each sample
· Barcode sorting to demultiplex samples is performed
· Polymorphic DNA sites (SNPs) will be identified
· DNA reads from each sample will be aligned and trimmed
· Samples will then be genotyped using the identified SNPs
· Data and summary report will be provided to Kristy Pilgrim USFS RMRS 10-14 weeks from sample submission
A generalized workflow for sample processing for SNP makers:
4.0 Government Furnished
There is no government furnished support other than funding to the company to perform DNA sample processing.
5.0 Deliverables / Schedule
The deliverables/schedule are as follows:
1) Notification of DNA sample quality 3 weeks after samples are received.
2) A final, summary report will be provided 10-16 weeks after samples are received.
3) Data files containing all SNP data and accompanying DNA sequencing files will be provided 10-16 weeks after samples are received.
Example 1 Key Deliverables
| Item No. |
| Deliverable |
| Objective |
| Due |
| 1 |
| Notification of DNA Sample Quality |
| Confirms the number of DNA samples that pass QC and will be processed for SNP analysis using tGBS |
| 3 weeks after samples are received |
| 2 |
| Final Summary Report |
| Report documenting findings and summary of SNP markers |
| 10-16 weeks after samples are received |
| 3 |
| Final DNA Data Files |
| Provides raw SNP data and accompanying DNA sequencing files |
| 10-16 weeks after samples are received |
6.0 Travel
There is no travel associated with this PO
7.0 Contractor’s Key Personnel
Will be identified once contract is awarded
8.0 Security Requirements
There are no Security Requirements
9.0 Data Rights
Data generated is the property of USDA-USFS
10.0 Section 508 – Electronic and Information Technology Standards There is no Information Technology to be Acquired image1.png image2.png image3.png image4.png image5.png image6.png image7.png image8.png image9.png image10.png image11.png image12.png image13.png image14.png image15.png image16.png image17.png image18.png image19.png image20.png image21.png image22.png image23.png image24.png image25.png image26.png image27.png image28.png image29.png image30.png image31.png image32.png image33.png image34.png image35.png image36.png image37.png image38.png image39.png image40.png image41.png image42.png image43.png image44.png image45.png image46.png image47.png image48.png image49.png image50.png image51.png image52.png image53.png image54.png image55.png image56.png image57.png image58.png image59.png image60.png image61.png image62.png image63.png image64.png image65.png image66.png image67.png image68.png image69.png image70.png image71.png image72.png image73.png image74.png image75.png
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