(168 days)
The ipsogen JAK2 RGQ PCR Kit is a qualitative in vitro diagnostic test for the JAK2 V617F/G1849T allele in genomic DNA extracted from EDTA whole blood. The ipsogen JAK2 RGQ PCR Kit is a real time PCR test performed on the QIAGEN Rotor-Gene Q MDx instrument. The test is intended for use as an adjunct to evaluation of suspected Myeloproliferative Neoplasm in conjunction with other clinicopathological factors.
This test does not detect less common JAK2 mutations associated with Myeloproliferative Neoplasm including mutations in exon 12 and is not intended for stand-alone diagnosis of Myeloproliferative Neoplasm.
The ipsogen® JAK2 RGQ PCR Kit is a qualitative in vitro diagnostic test for the detection of the JAK2 V617F/G1849T allele in genomic DNA extracted from whole blood. The ipsogen JAK2 RGQ PCR Kit uses polymerase chain reaction (PCR), and ARMS (amplification refractory mutation system) technology on the Rotor-Gene O MDx instrument.
Samples are extracted and prepared using the QIAsymphony SP instrument (QSSP) with the QIAsymphony® DSP DNA Mini Kit, followed by assay setup amplification and detection are carried out using the ipsogen JAK2 RGQ PCR Kit with the Rotor-Gene Q MDx and Rotor-Gene AssayManager software version 2.1.x**. Rotor-Gene AssayManager Gamma MDx plug-in installed, version 1.0.x** and an associated JAK2 Assay profile (from file AP ipsogen JAK2 blood US Vx x x**.iap).
The extraction step on the OIAsymphony instrument (OSSP) ensures that enough gDNA (of adequate quality) is purified during each run (no repeated extraction for the same sample is expected unless the instrument states that the step failed).
The ipsogen JAK2 RGQ PCR Kit is designed to be used with the Rotor-Gene Q MDx (RGO) instrument which is a real-time PCR analyzer designed for rapid thermal cvcling and real-time detection of PCR assays. The Rotor-Gene AssayManager (RGAM) controls and monitors PCR reactions and allows the determination of the mutation status based upon PCR results.
The presence of the JAK2 mutation is indicated by the fluorescent signal generated through the use of fluorescently labeled oligonucleotide probes. The probes do not generate a signal unless they are specifically bound to the amplified product. The amplification cycle at which fluorescent signal is detected by the RGO MDx is inversely proportional to the DNA target concentration present in the original specimen.
The ipsogen JAK2 RGQ PCR Kit contains reagents for two separate PCR reactions: one mutation-specific reaction and one wild-type specific reaction mix uses a mutant-specific or wild-type specific primer (Reverse primer), together with a common Forward primer and a labeled probe, to amplify and detect the G1849T mutation or the wild-type sequence in the JAK2 gene.
In addition, each Reaction Mix contains reagents (unlabeled primers, probe and oligonucleotide template) for an internal control reaction. The internal control is designed to be a reaction that does not compete significantly with the mutation-specific or wildtype specific, reaction mixes. and serve to demonstrate that the entire assay process has proceeded correctly for each specimen.
Note: ** x≥ 0, x corresponds to the latest version available on OIAGEN Website
The provided text describes the performance characteristics of the ipsogen® JAK2 RGQ PCR Kit, a qualitative in vitro diagnostic test for the detection of the JAK2 V617F/G1849T allele. This is a molecular diagnostic test, not an AI/imaging device, therefore, many of the requested criteria such as expert adjudication, MRMC studies, and AI-specific ground truth methodologies are not applicable.
Here's an attempt to extract and present the information as per your request, adapting to the nature of the device:
Acceptance Criteria and Device Performance Study for ipsogen® JAK2 RGQ PCR Kit
Note: This device is a molecular diagnostic PCR kit, not an AI-based imaging device. Therefore, criteria related to image analysis, expert readers, MRMC studies, and AI-specific ground truth establishment (like pathology or outcomes data for imaging) are not directly applicable. The "acceptance criteria" here relate to the analytical accuracy of the test in detecting a specific genetic mutation compared to a reference method.
1. Table of Acceptance Criteria and Reported Device Performance
The document does not explicitly state pre-defined quantitative acceptance criteria in a table format. However, the "Performance Characteristics - Non-Clinical Studies" section describes the study's objective and results, implying that the observed accuracy demonstrates the device's acceptable performance. The primary metric presented is concordance with a reference method (Sanger Bi-directional Sequencing, BDS, and subsequently Next Generation Sequencing, NGS).
Based on the study results, we can infer the performance:
| Metric | Acceptance Criteria (Implied) | Reported Device Performance (vs. BDS) | Reported Device Performance (vs. NGS for discordant samples) |
|---|---|---|---|
| Overall Agreement | High concordance with reference method | 96.8% (458/473 subjects) | All 15 discordant samples from BDS agree with ipsogen JAK2 RGQ PCR Kit. |
| Positive Agreement (Sensitivity) | High concordance for positive samples | 100% (165/165 subjects) | Not explicitly stated as a separate metric for NGS, but implying high sensitivity given agreement with NGS. |
| Negative Agreement (Specificity) | High concordance for negative samples | 95.1% (293/308 subjects) | Not explicitly stated as a separate metric for NGS. |
| Accuracy at ≥1% JAK2 V617F | 100% accuracy for samples with ≥1% JAK2 V617F mutation levels (implied acceptance) | 100% accuracy | 100% accuracy |
2. Sample Size and Data Provenance
- Test Set Sample Size: 473 specimens.
- 276 with suspected Polycythemia Vera (PV)
- 98 with Myelofibrosis (ET)
- 99 with Primary Myelofibrosis (PMF)
- Data Provenance: Not explicitly stated, but clinical samples from subjects suspected of having myeloproliferative neoplasms. It is likely retrospective as the samples appear to be collected and then tested. No country of origin is specified.
- Training Set Sample Size: Not applicable for this type of analytical validation study. The kit is a diagnostic reagent system, not a machine learning model that undergoes training.
3. Number of Experts and Qualifications for Ground Truth
- Number of Experts: Not applicable. Ground truth was established using standard molecular diagnostic methods (Sanger Bi-directional Sequencing and Next Generation Sequencing), not by human expert consensus as would be typical for image interpretation.
- Qualifications of Experts: N/A as per above. These are laboratory-based reference methods.
4. Adjudication Method for the Test Set
- Adjudication Method: Not applicable. The ground truth was established by laboratory-based objective methods (BDS and NGS). Discordances were investigated by using a more sensitive reference method (NGS).
5. Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study
- MRMC Study: No. This is a molecular diagnostic kit, not an AI/imaging device requiring human reader interpretation. Therefore, an MRMC study and
assessment of human reader improvement with AI assistance are not relevant.
6. Standalone Performance (Algorithm Only)
- Standalone Performance: Yes, in a way. The "algorithm" here is the chemical and enzymatic process of the PCR kit and the associated instrument's detection capabilities. The study assesses the performance of the kit itself (the "device") in detecting the mutation, independent of human interpretation beyond typical lab procedures and result reporting. The kit's results are compared directly to the reference methods.
7. Type of Ground Truth Used
- Type of Ground Truth:
- Primary Ground Truth: Sanger Bi-directional Sequencing (BDS).
- Confirmatory/Higher Sensitivity Ground Truth for discordant samples: Validated Next Generation Sequencing (NGS).
- The document notes that BDS is "not as sensitive as the JAK2 assay" (which reportedly detects down to 1%), and NGS was used to confirm the 15 discordant samples. This suggests that the ground truth evolved or was refined, with NGS serving as a more robust ground truth for low-level mutations.
8. Sample Size for the Training Set
- Training Set Sample Size: Not applicable. As stated before, this is a diagnostic kit, not an AI model requiring a training set. The "design" of the kit is based on established molecular biology principles, not data-driven learning.
9. How the Ground Truth for the Training Set Was Established
- Ground Truth for Training Set Establishment: Not applicable, as there is no training set for this type of device. The kit's design and validation rely on its analytical performance against known samples or samples characterized by established, robust reference methods.
§ 866.6070 Mutation detection test for myeloproliferative neoplasms.
(a)
Identification. A mutation detection test for myeloproliferative neoplasms is an in vitro diagnostic device intended for the detection of the JAK2 V617F/G1849T allele in genomic DNA extracted from whole blood. The test is intended for use as an adjunct to evaluation of suspected polycythemia vera in conjunction with other clinicopathological factors.(b)
Classification. Class II (special controls). The special controls for this device are:(1) Design verification and validation must include:
(i) A detailed description of all components in the test, including the following:
(A) A detailed description, including illustrations or photographs of non-standard equipment or methods, of the test components, including all required reagents, instrumentation, and equipment.
(B) Detailed documentation of the device software, including standalone software applications and hardware-based devices that incorporate software.
(C) A detailed description of methodology and assay procedures including appropriate internal and external quality controls that are recommended or provided. The description must identify those control elements that are incorporated into the testing procedure.
(D) A detailed specification for sample collection, processing, and storage.
(E) A description of the criteria for test result interpretation and reporting including result outputs, analytical sensitivity of the assay, and the values that will be reported.
(ii) Information that demonstrates the performance characteristics of the test, including:
(A) For indications for use based on a threshold established in a predicate device of this generic type, device performance data from either a method comparison study to the predicate device or through a clinical study demonstrating clinical validity using well-characterized prospectively or retrospectively obtained clinical specimens, as appropriate, representative of the intended use population.
(B) For indications for use based on a threshold not established in a predicate device of this generic type, device performance data from a clinical study demonstrating clinical validity using well-characterized prospectively or retrospectively obtained clinical specimens, as appropriate, representative of the intended use population.
(C) Device reproducibility data generated, using a minimum of three sites, of which at least two sites must be external sites, with two operators at each site. Each site must conduct a study that includes at least two operators per site, two runs per operator per day over a minimum of three non-consecutive days evaluating a sample panel that contains allelic frequencies that span the claimed measuring range, and include the clinical threshold allelic frequency. Pre-specified acceptance criteria must be provided and followed.
(D) Information on device traceability and a description of the value assignment process for calibrators and controls.
(E) Device precision data using clinical samples and controls to evaluate the within-lot, between-lot, within-run, between-run, and total variation.
(F) Device linearity data generated from samples covering the device measuring range and for any standards used in the quantitation of allelic frequencies.
(G) Device analytic sensitivity data, including limit of blank and limit of detection.
(H) Device specificity data, including interference and cross-contamination.
(I) Device and clinical specimen stability data, including real-time stability (long-term storage and in-use stability) and stability evaluating various storage times, temperatures, and freeze-thaw conditions, as appropriate.
(iii) Identification of risk mitigation elements used by the device, including a detailed description of all additional procedures, methods, and practices incorporated into the instructions for use that mitigate risks associated with testing using the device.
(2) The labeling required under § 809.10(b) of this chapter must include:
(i) An intended use statement, including an indication for use that includes the variant(s) for which the assay was designed and validated, for example, JAK2 G1849T.
(ii) A detailed description of the performance studies conducted to comply with paragraph (b)(1)(ii) of this section and a summary of the results.