(789 days)
The Vysis EGR1 FISH Probe Kit is intended to detect deletion of the LSI EGR1 probe target on chromosome 5q in bone marrow specimens and to be used, in addition to cytogenetics, other biomarkers, morphology and other clinical information, at the time of acute myeloid leukemia (AML) diagnosis as an aid in determining prognosis. Deletion of chromosome 5q has been associated with an unfavorable prognosis in AML patients.
The Vysis EGR1 FISH Probe Kit uses fluorescence in situ hybridization (FISH) DNA probe technology to determine deletion status of the LSI EGR1 (containing early growth response 1 gene; location chromosome 5q31) probe target in AML specimens. The Vysis EGR1 FISH Probe Kit also contains the LSI D5S23, D5S721 probe (location chromosome 5p15.2) and serves as a control. The kit consists of one vial containing two DNA FISH probes and four general purpose reagents sufficient to process 20 specimens.
Here's a summary of the acceptance criteria and the study details for the Vysis EGR1 FISH Probe Kit, based on the provided text:
Vysis EGR1 FISH Probe Kit: Acceptance Criteria and Study Details
1. Table of Acceptance Criteria and Reported Device Performance
| Acceptance Criteria | Reported Device Performance |
|---|---|
| Analytical Specificity: | |
| LSI D5S23, D5S721 Probe | 100% (95% CI: 98, 100) |
| EGR1 Probe | 100% (95% CI: 98, 100) |
| Analytical Sensitivity: | |
| LSI EGR1/D5S23, D5S721 | 99.6% (95% CI: 99.4, 99.7) for 2R2G signal pattern |
| Normal Cut-off: | |
| Max. 1R2G patterns | Specimens exceeding 6% or 12 1R2G patterns per 200 nuclei considered abnormal. No normal specimens produced 1R2G signals at or above 6%. |
| Reproducibility (Site-to-Site): | |
| Overall Agreement (High Positive) | 100% |
| Overall Agreement (Low Positive) | 100% |
| Overall Agreement (Normal) | 98% (one discordant result out of 60 observations) |
| Reproducibility (Lot-to-Lot): | |
| Overall Agreement (High Positive) | 100% |
| Overall Agreement (Low Positive) | 100% |
| Overall Agreement (Normal) | 100% |
| Clinical Utility (Agreement with Karyotype): | |
| Overall Agreement | 98.90% (179/181) (95% CI: 96.06%-99.70%) |
| Negative Percent Agreement | 100% (171/171) (95% CI: 97.80%-100.00%) |
| Positive Percent Agreement | 80% (8/10) (95% CI: 49.02%-94.33%) |
2. Sample Size Used for the Test Set and Data Provenance
- Analytical Specificity: Metaphase chromosomes from 5 karyotypically normal males.
- Analytical Sensitivity: Interphase nuclei from 25 bone marrow specimens (karyotypically normal or 5p15 and 5q31 deletion-free).
- Verification of Normal Cut-off: Interphase nuclei from 25 bone marrow specimens (karyotypically normal or 5p15.2 and 5q31 deletion-free).
- Reproducibility (Site-to-Site): 2 high-positive, 2 low-positive, and 2 normal specimens (bone marrow cells mixed to create positive controls).
- Reproducibility (Lot-to-Lot): Same 2 high-positive, 2 low-positive, and 2 normal specimens.
- Clinical Utility (Agreement with Karyotype): 181 bone marrow specimens from an Eastern Cooperative Oncology Group (ECOG) clinical trial (E1900) for AML diagnosis. This appears to be retrospective data from a specific clinical trial. The country of origin is implied to be the US given the ECOG trial.
3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications
- Analytical Specificity: "one technologist" evaluated 100 metaphase nuclei per sample. No specific qualifications are provided for this technologist beyond being a "technologist."
- Analytical Sensitivity: "two technologists" evaluated 100 nuclei per specimen. No specific qualifications provided.
- Verification of Normal Cut-off: "two technologists" evaluated 100 nuclei per specimen. No specific qualifications provided.
- Clinical Utility (Agreement with Karyotype): The ground truth for this section is based on "karyotype" results. While the text refers to a publication by Vance et al. from an ECOG clinical trial, it does not explicitly state the number or qualifications of the experts establishing the karyotype ground truth for this specific study. However, karyotyping is a specialized cytogenetic analysis performed by trained professionals (cytogeneticists/pathologists).
4. Adjudication Method for the Test Set
- Analytical Specificity, Sensitivity, Normal Cut-off: The text mentions evaluation by one or two technologists. For cases where two technologists evaluated, it doesn't explicitly state an adjudication method if discrepancies occurred. It simply states "Each technologist evaluated..." or "evaluated by two technologists." This suggests independent evaluation, but no formal adjudication process is described for reconciling differences.
- Reproducibility: A mean and standard deviation were calculated across replicates and sites/lots, indicating a statistical comparison of results, not a consensus-based adjudication of individual cases.
- Clinical Utility (Agreement with Karyotype): The comparison is against established karyotype results, which are considered the ground truth. There's no further adjudication stated for these 181 specimens beyond that initial karyotype.
5. Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study
No Multi-Reader Multi-Case (MRMC) comparative effectiveness study was done comparing human readers with AI assistance vs. without AI assistance. This device is a FISH probe kit, not an AI-assisted diagnostic tool.
6. Standalone (Algorithm Only) Performance
This device is a physical FISH probe kit designed for laboratory use with microscopic interpretation by trained personnel. It does not involve a standalone algorithm or AI for interpretation. Performance metrics like analytical specificity, sensitivity, and reproducibility are for the kit's ability to produce expected signal patterns when interpreted by human technologists.
7. Type of Ground Truth Used
- Analytical Specificity: Metaphase chromosomes from karyotypically normal individuals, with "correct locus" hybridization serving as the ground truth.
- Analytical Sensitivity: Expected normal signal pattern (2R2G) in interphase nuclei from karyotypically normal or deletion-free bone marrow specimens.
- Verification of Normal Cut-off: Normal bone marrow specimens that were karyotypically normal or 5p15.2 and 5q31 deletion-free.
- Reproducibility: Known status of specimens (high-positive, low-positive, normal) created by mixing positive and normal bone marrow cells.
- Clinical Utility (Agreement with Karyotype): Cytogenetic results (karyotype) from clinical AML diagnosis ("-5/del5q" vs. normal karyotype).
8. Sample Size for the Training Set
The document does not explicitly describe a separate "training set" in the context of machine learning or algorithm development, as this device is a probe kit. The studies described are for analytical validation and clinical correlation.
9. How the Ground Truth for the Training Set Was Established
Not applicable, as there's no mention of a traditional "training set" for an algorithm in this submission. The validation studies rely on established biological principles and comparisons to conventional cytogenetic methods.
§ 866.6040 Gene expression profiling test system for breast cancer prognosis.
(a)
Identification. A gene expression profiling test system for breast cancer prognosis is a device that measures the ribonucleic acid (RNA) expression level of multiple genes and combines this information to yield a signature (pattern or classifier or index) to aid in prognosis of previously diagnosed breast cancer.(b)
Classification. Class II (special controls). The special control is FDA's guidance document entitled “Class II Special Controls Guidance Document: Gene Expression Profiling Test System for Breast Cancer Prognosis.” See § 866.1(e) for the availability of this guidance document.