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The APTIMA Assay for Chlamydia trachomatis is a target amplification nucleic acid probe test that utilizes target capture for the in vitro qualitative detection of ribosomal RNA (rRNA) from Chlamydia trachomatis (CT) in clinician-collected endocervical, vaginal and male urethral swab specimens, patient-collected vaginal swab specimens, and female and male urine specimens. The assay is also intended for use with the testing of gynecological specimens collected in the PreservCyt® Solution and processed with the Cytyc ThinPrep® 2000 System. The assay may be used to test specimens from symptomatic and asymptomatic individuals to aid in the diagnosis of chlamydial urogenital disease.

Clearance of this premarket notification extends the clinical performance claims of the commercially available GEN-PROBE APTIMA Assay for Chlamydia trachomatis to include PreservCyt liquid Pap specimens (collected and processed by the Cytyc ThinPrep 2000 Processor) as acceptable testing specimens. The ancillary kit formulated for this specific application is the commercially available GEN-PROBE APTIMA Specimen Transfer Kit. The components of the APTIMA Specimen Transfer Kit include: (1) a transport tube containing transport media with a penetrable cap and (2) specific instructions for use regarding decontamination and specimen processing procedures. The APTIMA Specimen Transfer Kit may only be used in conjunction with GEN-PROBE APTIMA Assays for the detection of Chlamydia trachomatis and/or Neisseria gonorrhoeae.

The GEN-PROBE® APTIMA® Assay for Chlamydia trachomatis, specifically for its expanded indication with ThinPrep Specimens, underwent a clinical study to evaluate its performance.

1. Table of Acceptance Criteria and Reported Device Performance:

The document describes the performance in terms of sensitivity and specificity. While explicit acceptance criteria are not called out as "acceptance criteria," the clinical study results are presented, suggesting that these performance metrics were deemed acceptable for the device's expanded use.

2. Sample Size Used for the Test Set and Data Provenance:

• Sample Size: 1,647 female subjects were evaluated in the clinical study.
  • 1,288 asymptomatic subjects
  • 359 symptomatic subjects
• Data Provenance: The study was a prospective multi-center clinical study. The data was collected from OB/GYN, family planning, public health, women’s, and STD clinics. The country of origin is not explicitly stated, but the submission to the FDA and use of brand names like Cytyc ThinPrep 2000 System suggest a US-centric study or at least a study adhering to US regulatory standards.

3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications of Those Experts:

• The document does not mention the use of experts to establish the ground truth in the traditional sense of human readers adjudicating images or cases.
• Instead, the ground truth (patient infected status) was established using a patient infected status algorithm. This algorithm relied on the results of two reference Nucleic Acid Amplification Tests (NAATs) on endocervical swab specimens.

4. Adjudication Method for the Test Set:

• Adjudication Method: The patient infected status was determined by an algorithm that used two reference NAATs (APTIMA Combo 2 Assay and APTIMA CT Assay) on endocervical swab specimens.
  • An infected patient status required both reference NAATs to be positive.
  • A non-infected patient status required at least one reference NAAT to be negative.
  • This can be considered a form of "2-out-of-2" positive for infection, and "1-out-of-2" negative for non-infection, rather than human adjudication.

5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study was done:

• No MRMC comparative effectiveness study was done. This study focuses on the standalone performance of the APTIMA Assay for Chlamydia trachomatis when using PreservCyt liquid Pap specimens, not a comparison involving human readers with and without AI assistance.

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

• Yes, a standalone performance evaluation was done. The clinical study directly assessed the performance of the APTIMA CT Assay on PreservCyt liquid Pap specimens against the defined patient infected status algorithm. This represents the algorithm's performance without direct human interpretation of the assay results, other than performing the lab test.

7. The Type of Ground Truth Used:

• Algorithm Consensus (from reference NAATs): The ground truth for the clinical study was established by a patient infected status algorithm based on the results of two highly sensitive and specific reference Nucleic Acid Amplification Tests (NAATs) – the APTIMA Combo 2 Assay and the APTIMA CT Assay – performed on endocervical swab specimens. This is a common and robust method for establishing ground truth for infectious disease diagnostics.

8. The Sample Size for the Training Set:

• The document does not explicitly state the sample size for a training set. Diagnostic assays like the APTIMA Assay are developed through extensive research and analytical validation (limit of detection, analytical specificity, interference, recovery studies) before large-scale clinical validation. The details provided primarily cover the validation study for the expanded indication. It is typical for the assay to have been developed and optimized using various samples, but a specific "training set" in the machine learning sense is not described.

9. How the Ground Truth for the Training Set was Established:

• As a specific "training set" and its ground truth establishment are not detailed in the provided document, this information cannot be extracted. The document focuses on the validation of an existing assay for an expanded specimen type. The ground truth for the extensive analytical studies would likely have been established using well-characterized culture isolates and spiked samples with known concentrations of C. trachomatis as described in the Limit of Detection, Analytical Specificity, and Recovery sections (e.g., using IFU/assay as a measure for CT organisms).

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