(266 days)
MammaPrint® FFPE is a qualitative in vitro diagnostic test, performed in a central laboratory, using the gene expression profile obtained from formalin-fixed paraffin embedded (FFPE) breast cancer tissue samples to assess a patient's risk for distant metastasis within 5 years.
The test is performed for breast cancer patients, with Stage II disease, with tumor size ≤ 5.0 cm and lymph node negative. The MammaPrint® FFPE result is indicated for use by physicians as a prognostic marker only, along with other clinico-pathological factors.
The MammaPrint® FFPE test is a microarray based gene expression analysis of a tumor. The analysis is based on several processes: isolation of RNA from FFPE breast cancer tissue sections; elimination of gDNA, reverse transcription of RNA resulting in cDNA; amplification of the cDNA, purification and labeling of cDNA; hybridization of the amplified and labeled cDNA to the diagnostic microarray; washing and scanning the diagnostic microarray and data acquisition (feature extraction); calculation and determination of the risk of recurrence.
The MammaPrint® FFPE analysis is designed to determine the expression of specific genes in a tissue sample. The result is an expression profile, or "fingerprint", of the sample. Using this expression profile, the MammaPrint® FFPE Index is calculated and the molecular prognosis profile of the sample is determined (Low Risk, High Risk).
Below is a summary of the acceptance criteria and study details for the Agendia MammaPrint® FFPE device, based on the provided text.
1. Table of Acceptance Criteria and Reported Device Performance
The acceptance criteria for MammaPrint® FFPE are primarily based on demonstrating equivalence to the MammaPrint® Fresh device (K101454) in terms of concordance and clinical performance.
| Test Category | Acceptance Criteria | Reported Device Performance and Confidence Intervals |
|---|---|---|
| Analytical Performance | ||
| Concordance (FFPE vs. Fresh) - 1st Study (n=122) | High concordance between MammaPrint Fresh and FFPE outcomes. | Overall Concordance: 89.34% |
| True Positive/Negative Concordance (non-borderline): 92.7% | ||
| NPA (95% CI): 88.4% (80.5-95) | ||
| PPA (95% CI): 90.6% (79.8-95.9) | ||
| Concordance (FFPE vs. Fresh) - 2nd Study (n=345) | High concordance between MammaPrint Fresh and FFPE outcomes. | Overall Concordance: 89.28% |
| True Positive/Negative Concordance (non-borderline): 93.5% | ||
| NPA (95% CI): 91.5% (86.7-94.7) | ||
| PPA (95% CI): 86.6% (80.4-91.1) | ||
| Intra-sample Reproducibility (4 isolations) | No significant difference in MammaPrint Indices or Outcome across multiple isolations from the same sample. | MammaPrint Indices: p=0.994 (no significant difference) |
| MammaPrint Outcome: p=0.290 (no significant difference) | ||
| Inter-assay Reproducibility (Control samples over time) | Standard deviations of MammaPrint Indices for control samples to meet predefined criteria. | PHTR=0.045 (n=54), PLEP=0.056 (n=52), PHHE=0.072 (n=52) (all passed predefined criteria) |
| Method Precision (Repeatability & Within-lab) | Repeatability and Method Precision results to meet predefined acceptance criteria. | Repeatability (Within-Run): |
| High Risk (1): 0.036 | ||
| High Risk (2): 0.046 | ||
| Low Risk: 0.042 | ||
| Low Risk-Borderline: 0.049 | ||
| Method Precision (Within-Laboratory): | ||
| High Risk (1): 0.044 | ||
| High Risk (2): 0.057 | ||
| Low Risk: 0.050 | ||
| Low Risk-Borderline: 0.066 | ||
| (All met predefined criteria) | ||
| Inter-laboratory Comparison (Irvine vs. Amsterdam) | High agreement in MammaPrint Index and Outcome between laboratories, passing predefined acceptance criteria. | Irvine: Kappa score = 0.90 |
| Amsterdam: Kappa Score = 0.9 | ||
| Intercept close to zero, slope close to 1 (Passing and Bablok regression) | ||
| Microarray Scanner Comparison (Amsterdam) | High agreement in MammaPrint Index and Outcome between different scanners, passing predefined acceptance criteria. | Pearson correlation = 1.0 |
| Kappa score = 1.0 | ||
| NPA (95% CI): 100% (67.6-100) | ||
| PPA (95% CI): 100% (81.6-99.0) | ||
| Intercept close to zero, slope close to 1 | ||
| Microarray Scanner Comparison (Irvine) | High agreement in MammaPrint Index and Outcome between different scanners, passing predefined acceptance criteria. | Pearson correlation = 1.0 |
| Kappa score = 1.0 | ||
| NPA (95% CI): 100% (77.2-100) | ||
| PPA (95% CI): 100% (78.5-100) | ||
| Intercept close to zero, slope close to 1 | ||
| Minimum Input (Dilution Study) | Very stable results even at low input of cDNA expected. | Results showed very stable results even at low input of cDNA. |
| Clinical Performance | ||
| 5-year DRFI (Distant Recurrence Free Interval) | MammaPrint FFPE performance (low and high risk signatures) to fall within the 95% CI of MammaPrint Fresh. | Low Risk Signature: |
| MammaPrint Fresh 2013: 0.976 (0.952-1.000) | ||
| MammaPrint FFPE: 0.977 (0.955-0.999) | ||
| High Risk Signature: | ||
| MammaPrint Fresh 2013: 0.891 (0.840-0.942) | ||
| MammaPrint FFPE: 0.885 (0.830-0.940) | ||
| (All fall within 95% CI) | ||
| 5-year DM1st (Distant Metastasis as first event) | MammaPrint FFPE performance (low and high risk signatures) to fall within the 95% CI of MammaPrint Fresh. | Low Risk Signature: |
| MammaPrint Fresh 2013: 0.976 (0.952-1.000) | ||
| MammaPrint FFPE: 0.977 (0.955-0.999) | ||
| High Risk Signature: | ||
| MammaPrint Fresh 2013: 0.907 (0.860-0.954) | ||
| MammaPrint FFPE: 0.903 (0.854-0.952) | ||
| (All fall within 95% CI) |
2. Sample Size Used for the Test Set and Data Provenance
- Analytical Performance - Concordance Studies:
- First independent validation: n=122 tumor samples (FFPE vs. Fresh from the same tumor). Data provenance is not explicitly stated beyond being "internal" to Agendia but given the global operations might be multi-country. The study appears to be retrospective as it compares processed samples.
- Second independent validation (Raster study): n=345 samples (FFPE tissue vs. Fresh RNA from the same patients). The Raster study is mentioned as the source, which is a clinical study. The geographical origin is not explicitly stated, but clinical studies often involve multiple centers. It's retrospective in the sense that existing samples with follow-up were used.
- Analytical Performance - Reproducibility & Precision:
- Multiple isolations: 30 FFPE samples. Provenance not specified.
- Multiple labeling/hybridizations (control samples): PHTR (n=54), PLEP (n=52), PHHE (n=52) over time. Provenance not specified.
- Precision and Evaluation (P&E): 4 test samples (representing different risk levels) over 20 days. Provenance not specified.
- Analytical Performance - Inter-laboratory Comparison: 25 FFPE samples. Provenance not specified, but involved samples processed in Amsterdam and Irvine laboratories.
- Analytical Performance - Microarray Scanner Validation: 25 samples (Amsterdam), 27 samples (Irvine). Provenance not specified.
- Analytical Performance - Minimum Input: 3 samples and 3 control samples. Provenance not specified.
- Clinical Performance (Comparison with MammaPrint Fresh):
- Raster study: 345 samples with clinical follow-up of 5 years. This data is from the Raster study, which is a clinical prospective study (although the use here for the FFPE comparison would be retrospective on archived samples).
3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications of Those Experts
The document does not specify the number or qualifications of experts used to establish ground truth for the analytical or clinical validation. The "ground truth" for the analytical studies is the result from the established MammaPrint Fresh assay (K101454) for concordance, or statistical assessments of variability for reproducibility/precision. For clinical outcomes, the ground truth is clinical follow-up data (Distant Recurrence Free Interval and Distant Metastasis as first event) over 5 years. This outcome data is typically collected through clinical study follow-up by medical professionals, but not "established by experts" in the sense of a panel review for each case in this context.
4. Adjudication Method for the Test Set
No explicit adjudication method (like 2+1 or 3+1) is mentioned for the test sets. The ground truth for analytical concordance is the result from the predicate device (MammaPrint Fresh), and for clinical performance, it's the 5-year clinical outcome data (DRFI, DM1st) from the Raster study.
5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study was Done
No MRMC comparative effectiveness study involving human readers is described. This device is a gene expression profiling test performed in a central laboratory, not an image-based diagnostic read by human readers. Therefore, the concept of human readers improving with AI assistance is not applicable in this context.
6. If a Standalone (i.e. algorithm only without human-in-the-loop performance) was Done
Yes, the studies described are standalone performance evaluations of the MammaPrint® FFPE algorithm. The "device performance" and "reported device performance" in the table refer to the algorithm's output (Low Risk/High Risk and MammaPrint Index calculation) based on the tissue sample analysis.
7. The Type of Ground Truth Used
- Analytical Performance:
- Concordance: The results from the predicate device, MammaPrint® Fresh (K101454), using fresh tissue samples of the same tumor.
- Reproducibility, Precision, Inter-laboratory, Scanner Validation, Minimum Input: Statistical measures of consistency and variation against predefined internal criteria, using the device's own output.
- Clinical Performance:
- Outcomes Data: 5-year Distant Recurrence Free Interval (DRFI) and 5-year Distant Metastasis as first event (DM1st) collected during the Raster study.
8. The Sample Size for the Training Set
The document does not explicitly state the sample size for a training set for the MammaPrint® FFPE algorithm. The MammaPrint® technology was likely developed and validated using significant cohorts prior to this specific submission, which focuses on extending its use to FFPE samples and demonstrating equivalence. The "Raster study" is mentioned for clinical evaluation, but it's not explicitly stated as a training set. The descriptions focus on the validation of the FFPE version against the established Fresh version and clinical outcomes.
9. How the Ground Truth for the Training Set Was Established
Since a dedicated training set and its ground truth establishment are not described, this information cannot be provided from the given text. MammaPrint is a gene expression profiling test, and the "ground truth" for its original development (not necessarily a "training set" in the machine learning sense for this submission) would typically involve correlating gene expression profiles with long-term clinical outcomes in large patient cohorts to define the prognostic signature. This submission focuses on validating the FFPE version against the already cleared predicate device (MammaPrint Fresh).
§ 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.