(178 days)
The Verigene Warfarin Metabolism Nucleic Acid Test is an in vitro diagnostic for the detection and genotyping of the *2 and *3 alleles of the CYP2C9 gene and a single-point polymorphism (C to T at position 1173) of the VKORC1 gene, from EDTA-anticoagulated whole blood samples, as an aid in the identification of patients at risk for increased warfarin sensitivity. The test is intended to be used on the Verigene System.
The Verigene System is an in vitro diagnostic device intended for processing and genotyping multiple genes in a DNA sample utilizing gold nanoparticle probe technology. The Verigene System consists of the Verigene Processor and the Verigene Reader, each with its own onboard proprietary software.
The Verigene System is an in vitro diagnostic device for processing and genotyping multiple genes in a DNA sample. The Verigene System consists of two instruments, the Verigene Processor and the Verigene Reader, and utilizes single-use, disposable Test Cartridges to process and genotype multiple genes in a DNA sample in approximately 1½ hours.
The analysis sequence is the same for each of the three tests (i.e., CYP2C9*2 and *3 and VKORC1). After extracted and purified DNA, mixed with hybridization buffer, is loaded into the sample well of the Test Cartridge, it is ready for processing and is inserted into the Verigene Processor. An internal barcode reader reads the cartridge ID and sends the information to the Verigene Reader. From this information, the Verigene Reader establishes the hybridization parameters and starts the hybridization process.
The genotyping process occurs with a hybridization of the target analyte to a synthetic gene-specific oligonucleotide capture strand on the Test Cartridge's substrate. A synthetic mediator target-specific oligonucleotide is included with the test-specific sample buffer to form a hybridization "sandwich" with the gene sequence of interest. Washing steps following the target hybridization remove the unbound DNA from the hybridization chamber. A probe, composed of a gold nanoparticle with covalently bound oligonucleotides complementary to a sequence on the intermediate oligonucleotide, is introduced after the target wash. After the probe hybridization is completed, a series of washing steps remove the unbound probe from the hybridization chamber. A two-part signal enhancement reagent is added to the hybridization chamber and reacts with the gold nanoparticle to amplify the signal for the Verigene Reader scanning and analysis.
Upon completion of the genotyping process, the user removes the Test Cartridge from the Verigene Processor which is now ready for the next test.
Once the reagent portion of the Test Cartridge is removed by the user, the substrate is inserted into the Verigene Reader. The Verigene Reader illuminates the signal-enhanced nanoparticles specifically bound to either the wild type or mutant captures for the gene. A photosensor reads the relative brightness of each spot and the Verigene Reader outputs a result based on relative levels of brightness of the wild type to mutant signals.
Here's a breakdown of the acceptance criteria and the study that proves the device meets them, based on the provided text:
Acceptance Criteria and Device Performance
The document doesn't explicitly state "acceptance criteria" in a separate section with pass/fail metrics. Instead, it presents performance characteristics (reproducibility and accuracy) as evidence of the device's suitability. Based on the data provided, the implied acceptance criteria would be high percent agreement (call rate) for genotyping across different sites and conditions, and no incorrect calls (mis-calls).
Here's a table summarizing the reported device performance, interpreted as meeting implied acceptance for accuracy and call rate:
| Category | Locus | Acceptance Criteria (Implied) | Reported Device Performance (Worst Case) | Reported Device Performance (Best Case) |
|---|---|---|---|---|
| Accuracy (Agreement vs. Bi-directional Sequencing) | CYP2C9*2 | High correct call rate (>90%) with 0% mis-calls | Correct Call Rate: 67% (Mutant) | Correct Call Rate: 92% (Wild-type) |
| CYP2C9*3 | High correct call rate (>90%) with 0% mis-calls | Correct Call Rate: 88% (Heterozygous) | Correct Call Rate: 100% (Mutant) | |
| VKORC1 | High correct call rate (>90%) with 0% mis-calls | Correct Call Rate: 89% (Heterozygous) | Correct Call Rate: 97% (Mutant) | |
| All Loci | Overall Panel | Total panel read rate consistently high | Total panel read rate: 91.1% | Total panel read rate: 91.1% |
| Reproducibility (Initial Study) | CYP2C9*2 | High call rate (>90%) with 0% mis-calls | Call Rate: 89% (Site 2) | Call Rate: 94% (Site 1) |
| CYP2C9*3 | High call rate (>90%) with 0% mis-calls | Call Rate: 89% (Site 2) | Call Rate: 94% (Site 1) | |
| VKORC1 | High call rate (>90%) with 0% mis-calls | Call Rate: 89% (Site 2) | Call Rate: 94% (Site 1) | |
| Reproducibility (Extraction Method Study) | All Loci (After run 2) | High call rate (>95%) with 0% mis-calls | Call Rate: 100% (All Sites) | Call Rate: 100% (All Sites) |
| All Loci (After run 1) | High call rate (>90%) with 0% mis-calls | Call Rate: 91% (Site 1, 2) | Call Rate: 96% (Site 3) | |
| Limit of Detection (Call Rate above 40 ng/µL) | All Loci | Call rate of 95-100% with no mis-calls | Call Rate: 92% (40 ng/µL, 500 ng/µL) | Call Rate: 100% (200, 400 ng/µL) |
Note on "Acceptance Criteria": The document focuses on demonstrating performance rather than explicitly stating pre-defined thresholds the device must meet. However, the data presented, especially the 0% incorrect calls and generally high correct call rates, suggests these were the implicit criteria for acceptable performance. The "No Calls" indicate samples where a definitive genotype could not be assigned, which is different from an incorrect call.
Study Details:
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Sample size used for the test set and the data provenance:
- Accuracy Study (Test Set): 238 samples.
- Reproducibility (Initial Study): 5 genomic DNA samples, tested in triplicate daily for 3 days at each of 3 sites (total 90 test runs per locus at site 1, 45 test runs per locus at sites 2 & 3).
- Reproducibility (Extraction Method Study): Panel of 23 blood specimens. At each of the 3 sites, each specimen was extracted and run once, with a re-test if there was a "no call."
- Limit of Detection Study: 12 cartridges per DNA concentration level.
- Data Provenance: The document does not explicitly state the country of origin for the samples or specify if the studies were retrospective or prospective. It states "All purified DNA samples were from whole blood collected using EDTA as the anticoagulant" for the accuracy study, and "aliquots of a panel of 23 blood specimens were utilized" for the extraction method reproducibility. This suggests they were clinical samples, but further detail is not provided.
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Number of experts used to establish the ground truth for the test set and the qualifications of those experts:
- The ground truth for the accuracy study was established by bi-directional sequencing analysis at an independent reference laboratory. The document does not specify the number of experts or their qualifications, but the method itself (bi-directional sequencing) is a gold standard for genetic genotyping.
- For the second reproducibility study (extraction method), the "genotypes of the DNA samples were confirmed by bidirectional sequencing." Again, the number and qualifications of experts are not specified, but the ground truth method is clear.
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Adjudication method (e.g., 2+1, 3+1, none) for the test set:
- The document does not describe any human adjudication method for the test set results. The comparison is made directly between the device's genotype calls and the results from bi-directional sequencing.
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If a multi reader multi case (MRMC) comparative effectiveness study was done, If so, what was the effect size of how much human readers improve with AI vs without AI assistance:
- No, a multi-reader multi-case (MRMC) comparative effectiveness study was not done. This device is a molecular diagnostic test for genotyping, not an imaging device that requires human interpretation or assistance from AI. The output of the device is a genotype call.
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If a standalone (i.e., algorithm only without human-in-the-loop performance) was done:
- Yes, the performance studies described (reproducibility, accuracy, limit of detection) represent standalone performance of the Verigene System and Verigene Warfarin Metabolism Nucleic Acid Test. The device provides a direct genotype output, and its performance is evaluated against a ground truth without human intervention in the interpretation of the primary result. The summary states, "The Verigene Reader outputs a result based on relative levels of brightness of the wild type to mutant signals."
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The type of ground truth used (expert consensus, pathology, outcomes data, etc.):
- The primary ground truth used was bi-directional DNA sequencing, which is a highly accurate molecular method for determining DNA sequences and identifying genetic variants.
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The sample size for the training set:
- The document does not provide details on a separate "training set" or its sample size. The studies described are performance validation studies (accuracy, reproducibility, LOD) rather than studies focused on the development and training of a machine learning algorithm. The Verigene System utilizes "gold nanoparticle probe technology" and "onboard proprietary software" but does not explicitly mention a machine learning or AI component requiring a traditional training set in the context of this 510(k) summary.
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How the ground truth for the training set was established:
- As no explicit "training set" or description of its characterization is provided in the document, there's no information on how its ground truth was established.
§ 862.3360 Drug metabolizing enzyme genotyping system.
(a)
Identification. A drug metabolizing enzyme genotyping system is a device intended for use in testing deoxyribonucleic acid (DNA) extracted from clinical samples to identify the presence or absence of human genotypic markers encoding a drug metabolizing enzyme. This device is used as an aid in determining treatment choice and individualizing treatment dose for therapeutics that are metabolized primarily by the specific enzyme about which the system provides genotypic information.(b)
Classification. Class II (special controls). The special control is FDA's guidance document entitled “Class II Special Controls Guidance Document: Drug Metabolizing Enzyme Genotyping Test System.” See § 862.1(d) for the availability of this guidance document.