Attachment 1 Rev 1 Seq_Service_Performance Work Statement.doc
DOC document 84 KB Posted
- Attached to
- High-Throughput Sequencing Service Federal contract opportunity
- Solicitation number
- 1232SA25Q0931
About this file
This Performance Work Statement (PWS) details a high-throughput sequencing service for the USDA Agricultural Research Service's Fargo Cereal Crops Improvement Research Unit. The project requires processing 600 RNA samples for mRNA-Seq, 40 DNA samples for Whole Genome Bisulfite Sequencing (WGBS), and 200 metabolite samples for LC-MS analysis. Contractors must prepare libraries, perform sequencing, and deliver quality control reports and data within specific timelines: QC reports within 6 business days, library preparation within 5 business days, sequencing run statistics within 7 business days, and final sequencing data within 10 business days after library quality confirmation.
The solicitation is a small business set-aside (NAICS Code 541714) for a firm fixed-price purchase order, with delivery to the PA Cereal Crops Research unit in Fargo, ND. Performance standards include maintaining sequencing quality and quantity, with financial penalties for not meeting specified sequencing amounts or quality thresholds (e.g., 1% service price reduction for each 1% decrease from requested sequencing amount). The government will retain full data rights, and contractors must have experienced laboratory staff capable of library assay and instrument operation. Offerors must have an active SAM.gov registration and submit quotes valid for at least 60 days.
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Other files for this federal contract opportunity
| File | Type | Posted |
|---|---|---|
| Solicitation_1232SA25Q0931-0002.pdf | ||
| Sol_1232SA25Q0931_Amd_0002.pdf | ||
| Sol_1232SA25Q0931_Amd_0001.pdf | ||
| Solicitation_1232SA25Q0931.pdf | ||
| Attachment 2 - Wage Determination 2015-4969 Rev 29.pdf | ||
| Attachment 1 Seq_Service_Performance Work Statement.doc | DOC document |
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Text version
Performance Work Statement (PWS) Revision 1, (Amendment 0001) Project: Sequencing Service
GENERAL INFORMATION
1.0 Background and Purpose: The Fargo Cereal Crops Improvement Research Unit investigates the genomics of small grains in the US. Our focus is to assist the community by providing genotyping service and performing primary research on the identification of gene regions that influence traits. Once found, this knowledge is used to accelerate breeding of better cultivars with high yield, excellent quality, and innate disease resistance. To do this high-throughput sequencing, along with interrogation of the gene expression capacity is necessary to evaluate the genomes of populations to find these regions.
2.0 Definitions: QC – Quality Control; Gb – Gigabase; POC – Point of Contact; PE – Paired End; DNA - Deoxyribonucleic acid; RNA - Ribonucleic acid
CONTRACTOR REQUIREMENTS
3.0 Technical Requirements/Tasks:
LC-MS: Metabolomics profiling – Preparation of metabolite library from submitted tissue samples. Quality report submitted via email mRNA-seq: Messenger RNA sequencing library generation – Preparation of sequencing library from submitted total RNA. Quality report submitted via email WGBS: Bisulfite Whole Genome Sequencing -Illumina sequencing library generation – Preparation of sequencing library from submitted DNA. Quality report submitted via email
| Quantity |
| Unit of Issue |
| Part Name or Number |
| 600 |
| Sample |
| RNA extract + mRNA-Seq + 6 G data |
| 40 |
| Sample |
| DNA extract + EnzMethyl-Seq + 250 G data (WGBS) |
| 200 |
| Sample |
| Metabolite extract + LC-MS + analysis |
4.0 Deliverable / Schedule:
· Sample tissue will be submitted to the contractors on an as-needed basis via delivery service throughout the performance period for a total of samples as determined in the table below.
| Quantity |
| Unit of Issue |
| Part Name or Number |
| 600 |
| Sample |
| RNA extract + mRNA-Seq + 6 G data |
| 40 |
| Sample |
| DNA extract + EnzMethyl-Seq + 250 G data (WGBS) |
| 200 |
| Sample |
| Metabolite extract + LC-MS + analysis |
· Every sample will be processed to extract either RNA, DNA or metabolites and converted into libraries and sequenced or analyzed to the customers specifications as described in the contractor’s submission documentation.
· Every submitted library will be QC analyzed and pooled for sequencing to the customers specifications as described in the contractor’s submission documentation.
· All reports will be delivered via email to the government POC.
· All final data (raw and assembled) will be provided via a download link.
· Timely submission of deliverables is essential to successful completing this requirement. Schedules for deliverables are specified in below.
Key Deliverables
| Item No. |
| Deliverable |
| Objective |
| Due |
| 1 |
| QC report of submitted sample |
| To identify if sample should be re-submitted |
| No later than three (6) business days after submitted sample is received |
| 2 |
| Library Prep & Sequencing |
| To perform the task |
| Initiated no later than five (5) business days after confirmation of sample QC |
| 3 |
| Sequencer Run Statistic Report |
| To identify if the sequencing run was successful |
| No later than seven (7) business days after confirmation of sample QC |
| 4 |
| Sequencing Data |
| To receive data for analysis |
| No later than ten (10) business days after confirmation of library quality |
5.0 Government Furnished: N/A 6.0 Travel: N/A 7.0 Contractor’s Key Personnel: Contractor must have laboratory staff experienced in assaying the quality of libraries and running the instruments.
8.0 Security Requirements: Data submission portal will be password protected.
9.0 Data Rights: The data will be solely owned by the government and the contractor will have no rights or obligations to the data once it is transferred.
10.0 Performance Requirement Measures: {Indicate how the government will measure the contractor's performance for specific tasks or work critical to the mission essential items).
· Payment deduction is generally a remedy for non-performance, not as an incentive. Non-Monetary incentives may include award term contract arrangement (contractor is awarded periods of performance) or Past Performance for quality level of performance.
| Performance Objective |
| Required Task or Deliverable |
| Performance Standard |
| Method of Surveillance |
| Positive/Negative Incentive |
% for NOT meeting the Task
| Desired Outcome or what must be accomplished as the end result of this contract. |
| Stare the task or deliverable that must be accomplished for the desired result. |
| State error rates, accuracy rates, completion of milestones, cost control, etc. The government must set the standards. |
| (State the method and who performs the surveillance |
| Incentives can be monetary, non-monetary, realist, attainable and built on performance objectives and standards. Use positive or negative incentives when performance exceeds standard or is below standards. |
| Sequencing Library Preparation and Sequencing |
| Sequencing Library ( mRNA, WGBS) and sequencing data |
| Sufficient quality and quantity to meet the requested sequencing amounts |
| Inspection of run statistic report and assessment once data is received |
| 1% of service price every 1% decrease from requested sequencing amount |
-1% of lane price every 1% decrease from 80% Q30 of the requested sequencing amount.
| Metabolite Library Preparation and a measurement |
| Metabolite Library and target measurements |
| Sufficient quality and quantity to meet the requested amounts |
| Inspection of run statistic report and assessment once data is received |
| -1% of price every 1% decrease from expected amounts |
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