Attachment 2 - Quality Assurance Surveillance Plan.pdf

QUALITY ASSURANCE SURVEILLANCE PLAN (QASP)

FOR

DNA Extraction and Genotyping Services for Cotton

1. PURPOSE

This Quality Assurance Surveillance Plan (QASP) is a Government developed and applied document used to make sure that systematic quality assurance methods are used in the administration of the Performance Based Service Contract (PBSC) standards included in this contract and in subsequent task orders issued there under. The intent is to ensure that the Contractor performs in accordance with performance metrics set forth in the contract documents, that the Government receives the quality of services called for in the contract and that the Government only pays for the acceptable level of services received.

The QASP has been developed by the requiring activity. It is designed to provide direction to personnel performing contract surveillance activities. Personnel surveying the contract terms and conditions and SOW requirements will periodically review the QASP throughout the life of the contract.

The Contracting Officer's Representative (COR) will monitor Contractor in the aspects of receiving the samples, processing timeline, data quality, and data transfer.

2. SCOPE

The QASP is put in place to provide Government surveillance oversight of the Contractor's quality control efforts to ensure the products/results specified in the Purchase Order are delivered on time and meet the requirements of the Purchase Order. The QASP is not intended to duplicate the Contractor's Management Plan.

3. GOVERNMENT RESOURCES

The following definitions for Government resources are applicable to this plan:

Contracting Officer - A person duly appointed with the authority to enter into, administer, or terminate contracts and make related determinations and findings on behalf of the Government.

Contracting Officer's Representative (COR) - An individual designated in writing by the Contracting Officer to act as his authorized representative to assist in administering a contract.

The source and authority for a COR is the Contracting Officer. COR limitations are contained in the written letter of appointment.

4. RESPONSIBILITIES

The Government resources shall have responsibilities for the implementation of this QASP as follows:

Contracting Officer - The Contracting Officer ensures performance of all necessary actions for effective contracting, ensures compliance with the terms of the contract and safeguards the interests of the United States in the contractual relationship. It is the Contracting Officer that ensures the Contractor receives impartial, fair, and equitable treatment under the contract. The Contracting Officer is ultimately responsible for the final determination of the adequacy of the Contractor's performance.

Contracting Officer's Representative (COR) - The COR is responsible for technical administration of the project and ensures proper Government surveillance of the Contractor's performance. The COR is not empowered to make any contractual commitments or to authorize any contractual changes on the Government's behalf. Any changes that the Contractor deems may affect contract, price, terms, or conditions shall be referred to the Contracting Officer for action.

5. METHODS OF QA SURVEILLANCE

The below listed methods of surveillance shall be used in the administration of this QASP.

Customer Feedback - Customer feedback may be obtained from program staff for the USDA- ARS Genomics and Bioinformatics Research Unit (GBRU) at Raleigh, NC. Customer complaints, to be considered valid, must set forth clearly and in writing the detailed nature of the complaint, must be signed and must be forwarded to the COR. The COR shall maintain a summary log of all formally received customer complaints as well as a copy of each complaint in a documentation file.

Periodic Review - The COR will periodically review delivery schedules, data quality reports, and sample processing status to ensure compliance with contract requirements.

Deliverable Inspection - Each deliverable (genotype data, QC reports, metadata) will be inspected upon delivery to ensure compliance with technical specifications outlined in the Statement of Work.

6. LEVELS AND STANDARDS OF SERVICE

The standards of services are held to and comply with the standards specified in the Purchase Order, commercial/industry, and government standards for genomic services.

7. IDENTIFIED QA SURVEILLANCE ITEMS

Performance Requirements

Required Services Performance Objective

Performance Requirement

DNA Extraction from freeze-dried cotton leaf tissue (~85 plates, approximately 8,000 samples)

Extract high-quality DNA suitable for genotyping from freeze-dried leaf tissue of variable quality.

DNA concentration and purity must meet minimum standards for genotyping platform.

DNA QC metrics documented and provided to Government. Samples failing QC identified and reported.

High-Density SNP Genotyping

Genotype cotton samples using fixed SNP panel with minimum 15,000 statically defined markers.

Minimum 15,000 SNP markers with known chromosomal positions. Markers evenly distributed across cotton chromosomes. Array suitable for U.S.-cultivated Gossypium hirsutum. Standards and blanks included for quality control.

Genotyping Quality Control

Ensure high-quality genotyping data with acceptable call rates.

Per-sample call rates documented and reported. Overall genotyping success rate reported. Problematic markers or samples identified. Quality control procedures documented.

Data Delivery Deliver complete genotype data in requested format for all successfully genotyped samples.

Data format: tab-delimited text, CSV, or agreed-upon format compatible with standard bioinformatics software. User-friendly data with descriptive column headers. Complete genotype matrix with sample IDs, marker names, chromosomal positions, and genotype calls. Raw data included.

Quality Control Report

Provide comprehensive QC documentation for DNA extraction and genotyping.

Report includes: DNA extraction statistics (concentration, yield, purity) or agarose gel, per-sample call rates, overall success rates, list of failed samples with reasons, marker performance statistics, documentation of any processing issues.

SNP Marker Metadata

Provide complete marker information and annotations.

Marker IDs, chromosomal positions, reference/alternate alleles, platform specifications, version information, processing dates.

Timeline Compliance

Complete processing within specified timeframe.

Processing completed within 4-6 weeks of sample receipt for each batch. Regular status updates provided to Government.

Sample Handling Maintain sample integrity and chain of custody.

Proper sample tracking and identification throughout processing. Samples retained for minimum one (1) year post-delivery or returned to sender. Documentation of sample handling procedures.

8. PERFORMANCE STANDARDS

The following performance standards shall be used to evaluate contractor performance:

Performance Area Acceptable Performance Unacceptable Performance

DNA Quality ≥90% of samples meet minimum DNA quality standards for genotyping

<90% of samples meet standards (accounting for inherent sample quality issues)

Genotyping Success Rate

≥85% overall sample success rate with acceptable call rates

<85% overall success rate

SNP Call Rate ≥95% call rate per successfully genotyped sample

<95% call rate per sample

Marker Number ≥15,000 markers from a statically defined panel

<15,000 markers from a statically defined panel OR markers from a non-static panel (i.e., genotyping by sequencing or skim sequencing)

Timeline Processing completed within 4-6 weeks per batch

Processing exceeds 6 weeks without justification

Data Delivery Complete, accurate data in specified format, including raw data

Incomplete data, formatting errors, missing information

Communication Timely notification of issues, regular status updates

Failure to communicate problems or status

Documentation Complete QC reports and metadata provided

Incomplete or inadequate documentation

9. DOCUMENTATION

The COR shall, in addition to providing documentation to the Contracting Officer, maintain a complete Quality Assurance file. All such records will be retained for the life of this contract.

Documentation shall include:

● Sample shipment records and receipt confirmations

● Processing status updates from Contractor

● Data delivery records

● Quality control reports

● Customer feedback or complaint logs

● Correspondence with Contractor regarding performance

● Inspection reports for deliverables

● Payment authorization records