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The ProAdeno™+ Assay is a multiplex Real Time PCR in vitro diagnostic test for the qualitative detection of human Adenovirus (HAdV) DNA isolated and purified from nasopharyngeal (NP) swab specimens obtained from individuals exhibiting signs and symptoms of acute respiratory infection. This test is intended for use to aid in the diagnosis of HAdV infections in humans in conjunction with other clinical and laboratory findings. The test detects, but does not differentiate, serotypes 1-51.

Negative results do not preclude HAdV infection and should not be used as the sole basis for treatment or other patient management decisions.

The ProAdeno+ Assay enables detection of human adenovirus and an Universal Internal Control.

An overview of the procedure is as follows:

1. Collect nasopharyngeal swab specimens from symptomatic patients using a polyester, rayon or nylon tipped swab and place into viral transport medium.
2. Add Universal Internal Control (UIC) to every sample to monitor for inhibitors present in the specimens.
3. Perform isolation and purification of nucleic acids using a MagNA Pure LC System (Roche) and the MagNA Pure Total Nucleic Acid Isolation Kit (Roche) or a NucliSENS® easyMAG™ System (bioMérieux) and the Automated Magnetic Extraction Reagents (bioMérieux).
4. Add purified nucleic acids to ProAdeno+ Supermix included in the ProAdeno+ Assay Kit. The ProAdeno+ Mix contains oligonucleotide primers, target-specific oligonucleotide probes, and a Taq DNA polymerase. The primers are complementary to a highly conserved region of human adenovirus. The probes are dual-labeled with a reporter dye attached to the 5'-end and a quencher dye attached to the 3'-end (see table below).
5. Perform amplification of DNA in a Cepheid SmartCycler® II instrument. In this process, the probe anneals specifically to the template followed by primer extension and amplification. The ProAdeno+ Assay is based on Tagman reagent chemistry, which utilizes the 5' - 3' exonuclease activity of the Taq polymerase to cleave the probe thus separating the reporter dye from the quencher. This generates an increase in fluorescent signal upon excitation from a light source. With each cycle, additional reporter dye molecules are cleaved from their respective probes, further increasing fluorescent signal. The amount of fluorescence at any given cycle is dependent on the amount of amplification products present at that time. Fluorescent intensity is monitored during each PCR cycle by the real-time instrument.

The provided text describes the clinical performance and reproducibility testing for the ProAdeno™+ Assay. Here's a breakdown of the requested information:

Acceptance Criteria and Reported Device Performance

The document does not explicitly state pre-defined acceptance criteria values for sensitivity and specificity. However, the reported performance is presented in a table. For reproducibility, the overall percent agreement is stated.

Note: The 95% CI for Sensitivity and Specificity appear to have a typo in the provided text (87.1% - 94.3% combined for both). Assuming the first value is for sensitivity and the second for specificity, the corrected representation would be:

• Sensitivity: 97.5% (95% CI: 87.1% - 94.3%)
• Specificity: 95.6% (95% CI: 94.3% - 96.7%)

However, the CI values are given as a range, which makes this interpretation potentially problematic. Without further clarification from the original document, the exact intended 95% CI for sensitivity and specificity remains ambiguous as presented. For the purpose of this analysis, I will retain the values as they appear in the source text, acknowledging the potential discrepancy in the CI range.

Study Details

2. Sample size used for the test set and the data provenance

• Sample Size: 1167 nasopharyngeal (NP) swab samples were initially tested. One sample was excluded due to unresolved results, leading to a final test set of 1166 samples for the clinical performance analysis.
• Data Provenance: The study was a prospective study conducted at 4 U.S. clinical laboratories from October 2009 to August 2010. Samples were NP swab specimens collected for routine respiratory viral testing by each site.

3. Number of experts used to establish the ground truth for the test set and the qualifications of those experts

The document does not specify the number or qualifications of experts used for establishing the ground truth. It states that the reference method was "rapid culture (shell vial) followed by direct fluorescent antibody (DFA) screening and identification." Discrepant analysis for samples in disagreement was performed using "PCR primers obtained from literature followed by sequencing." This implies laboratory-based methods for ground truth, rather than expert human interpretation of images or other subjective data.

4. Adjudication method for the test set

The document describes a form of discrepant analysis. For samples where the ProAdeno+ Assay and the initial reference method (culture/DFA) disagreed, further testing was performed using PCR primers obtained from literature followed by sequencing. This served as the adjudicating method to establish the true status of discrepant samples.

5. If a multi reader multi case (MRMC) comparative effectiveness study was done

No, a multi-reader multi-case (MRMC) comparative effectiveness study was not done. The study evaluates the performance of a diagnostic assay (ProAdeno+ Assay) against a reference laboratory method, not human readers with or without AI assistance.

6. If a standalone (i.e. algorithm only without human-in-the-loop performance) was done

Yes, this was a standalone performance study. The ProAdeno+ Assay is an in vitro diagnostic test, and its performance was evaluated directly against a reference method without human interpretation as part of the primary outcome.

7. The type of ground truth used

The ground truth was established using a combination of laboratory methods:

• Primary reference method: Rapid culture (shell vial) followed by direct fluorescent antibody (DFA) screening and identification.
• Discrepant analysis ground truth: PCR primers obtained from literature followed by sequencing.

8. The sample size for the training set

The document does not specify a separate training set. The descriptions provided are for the clinical performance evaluation and reproducibility assessment. This is typical for a diagnostic test validation, where the focus is on evaluating the device's performance characteristics in a clinical setting rather than training a machine learning model.

9. How the ground truth for the training set was established

As no separate training set is mentioned or described, the method for establishing its ground truth is not applicable from the provided text.

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