Search Results
Found 2 results
510(k) Data Aggregation
(526 days)
MammaPrint FFPE NGS Kit
The MammaPrint FFPE NGS kit is a qualitative in vitro diagnostic test for use by clinical laboratories using target enrichment Next Generation Sequencing (NGS) technology for gene expression profiling of the 70-gene MammaPrint Breast Cancer signature on formalin-fixed, paraffin-embedded (FFPE) breast cancer tissue samples. The test is used to assess a patient's risk to develop distant metastasis within 5 years and up to 10 years after diagnosis.
The MammaPrint FFPE NGS kit is performed for breast cancer patients with Stage I or Stage II disease, with tumor size ≤ 5.0 cm and lymph node negative. The test result is indicated for use by physicians as a prognostic marker only, along with other clinicopathological factors.
The MammaPrint FFPE NGS kit is a sequencing-based gene expression analysis of a tumor. The analysis is based on several processes: isolation of RNA from FFPE breast cancer tissue sections; library preparation of RNA resulting in cDNA adapter-ligated sequences; enrichment of the 70 genes (capture step); sequencing of the enriched library in the flow cell and data acquisition; MammaPrint Index calculation of the risk classification in breast cancer patients.
Data analysis is performed according to the MammaPrint FFPE NGS algorithm (resulting in MammaPrint Index or MPI). This algorithm was designed and programmed by Agendia and incorporated into a proprietary software program, which loads the FASTQ data file. The software loads file, performs quality control checks and determines the molecular profile of the sample by calculating the MammaPrint index by determining the correlation of the sample's 70 gene expression profile to the mean expression profiles of tumors with a known good and poor outcome.
The provided text describes the acceptance criteria and the study that proves the MammaPrint FFPE NGS kit meets these criteria, primarily by demonstrating substantial equivalence to its predicate device (MammaPrint FFPE microarray).
Here's a breakdown of the requested information:
1. Table of Acceptance Criteria and Reported Device Performance
The document doesn't explicitly outline a formal "acceptance criteria" table with pre-defined thresholds for performance metrics. Instead, it demonstrates performance through concordance studies and reproducibility assessments against the predicate device, or by showing high agreement for controls. The clinical performance is demonstrated by comparing the survival outcomes of the new device to those of the predicate device on the same patient cohort from the RASTER study.
Acceptance Criteria (Implied by the study design and results presented):
| Performance Metric | Implied Acceptance Criteria (Achieved by the device) | Reported Device Performance |
|---|---|---|
| Method Comparison (Study-1): | ||
| OPA (High vs. Low) | High concordance with predicate device. | 97.42% (95% Cl: 93.55, 98.99) |
| NPA (High vs. Low) | High concordance with predicate device. | 93.85% (95% C1: 85.22, 97.58) |
| PPA (High vs. Low) | High concordance with predicate device. | 100.00% (95% CI: 95.91, 100.00) |
| Method Comparison (Study-2): | ||
| OPA (ranging across sites) | High concordance with predicate device. | 91.09% to 92.41% |
| PPA (ranging across sites) | High concordance with predicate device. | 91.39% to 99.34% |
| NPA (ranging across sites) | High concordance with predicate device. | Lower: 82.89% to 93.42% (noted as impacted by borderline samples) |
| Repeatability of RNA Isolation (Categorical Results): | 100% agreement between repeat isolations. | 100% agreement (95%Cl: High Risk: 86.2-100.0, Low Risk: 81.6-100.0, Borderline: 34.2 –100.0) |
| Reproducibility of Controls (Categorical Results): | 100% agreement for known controls across sites/operators/lots. | 100% agreement for both CTRL-HR and CTRL-LR (Table 1: 94.2%-100% CI for both). |
| Precision/Reproducibility (Categorical Results: Study-1): | High agreement for different risk categories. | PREC-BD (Borderline): 81% (72.0, 88.5) (Table 3) |
| PREC-HR (High Risk): 100% (96.9, 100) (Table 3) | ||
| PREC-LR (Low Risk): 100% (96.9, 100) (Table 3) | ||
| Precision/Reproducibility (Categorical Results: Study-2): | High agreement, especially for samples not near threshold. | Range from 58% to 100% (Table 5). Samples 2 (Low Risk) and 5 (High Risk) had 83% and 58% agreement respectively. |
| Detection Limit (Valid Rates): | Acceptable valid rates at specified RNA input and quality. | DV200 "poor" (35-49%) with ≥100 ng RNA: 80% to 100% valid rates. |
| DV200 "Standard" (35-80%) with ≥100 ng RNA: 80% to 100% valid rates. | ||
| Clinical Performance (DRFI): | Similar survival outcomes to predicate device. | Kaplan-Meier plots suggest significant difference in survival curves among different risk groups for MammaPrint FFPE NGS kit, p=0.001. |
| 5-year DRFI: Low Risk 98.1%, Borderline 92.6%, High Risk 88.2% (Table 6). | ||
| 10-year DRFI: Low Risk 95.2%, Borderline 92.6%, High Risk 82.0% (Table 6). | ||
| The results "indicated that both devices show similar clinical performance" based on RASTER study follow-up. |
2. Sample Sizes and Data Provenance
- Method Comparison Study-1: 155 samples used. Data acquired retrospectively as these samples were "previously processed on MammaPrint FFPE microarray as part of routine diagnostics."
- Method Comparison Study-2: 303 samples used. Data acquired retrospectively from "previously collected patient samples."
- Repeatability of RNA Isolation: Not explicitly stated, but implies multiple FFPE tumor blocks, each sectioned twice.
- Reproducibility of Controls: 2 control samples (CTRL-HR, CTRL-LR), each processed 50 times across 4 external sites, 2 operators per site, 6 NGS runs, and 3 lot numbers. Total of 100 measurements for controls.
- Precision/Reproducibility Assessment-Study-1: 3 samples (High Risk, Borderline, Low Risk). Each processed 96 times (4 external sites x 2 operators x 6 NGS runs x 2 duplicates per run).
- Precision/Reproducibility Assessment-Study-2: 8 samples. Each processed repeatedly (from RNA isolation to sequencing) by 2 operators at 3 sites, with 4 runs per site and 2 replicates per run. This results in 16-24 replicates per sample (table indicates N of 16 or 24).
- Detection Limit: 8 FFPE breast cancer samples with "poor" DV200 quality were evaluated, with various dilutions. Additional unstated number of "Standard" DV200 samples.
- Clinical Validation (RASTER Study):
- Original RASTER enrollment: 427 patients.
- Subset of FFPE samples from RASTER study used for NGS kit validation: 345 samples.
- Samples successfully processed for analysis: 316 samples.
- Data provenance: Multicenter observational study conducted in the Netherlands between 2004 and 2006 (for initial RASTER study). The current analysis uses updated 5- and 10-year follow-up data. This is prospective observational data with the device evaluated retrospectively on archived samples.
3. Number of Experts and Qualifications for Ground Truth
The document does not mention the use of experts to establish ground truth for the analytical or reproducibility test sets. The ground truth for these studies is based on comparisons against the predicate device's results or known control sample values.
For the clinical validation, the ground truth for distant recurrence-free interval (DRFI) and breast cancer specific survival (BCSS) is outcomes data from the RASTER study, defined as distant breast cancer recurrence or death from breast cancer. The establishment of these clinical outcomes likely involved clinical experts (e.g., oncologists, pathologists, and medical records review) over the 10-year follow-up period, but the specific number and qualifications of these experts are not detailed in this submission.
4. Adjudication Method for Test Set
The document does not describe an adjudication method (such as 2+1 or 3+1) for the test sets. For analytical studies, agreement is based on direct comparison of results between NGS and microarray platforms or within the NGS platform itself (repeatability/reproducibility). For the clinical study, outcomes (DRFI, BCSS) are established from patient follow-up data.
5. Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study
No MRMC comparative effectiveness study was performed as this device is a gene expression profiling test system, not an imaging device requiring human reader interpretation. The comparison is between the new NGS-based assay and the predicate microarray-based assay.
6. Standalone Performance
The "standalone" performance shown is the analytical performance of the MammaPrint FFPE NGS kit itself (repeatability, reproducibility, detection limit) and its clinical prognostic ability, which is an algorithm-only output (MammaPrint Index). The clinical validation study (RASTER) assesses the algorithm's ability to stratify patients by risk based on actual clinical outcomes. The device performance (result classification: High Risk, Borderline, Low Risk) is reported directly from the algorithm without a human-in-the-loop component for classification.
7. Type of Ground Truth Used
- Analytical Performance (Method Comparison, Repeatability, Reproducibility): The ground truth is effectively the predicate device's results or the known values of control samples. For repeatability/reproducibility, the ground truth is consistency of the device's own output.
- Clinical Validation: The ground truth is outcomes data (Distant Recurrence-Free Interval - DRFI, and Breast Cancer Specific Survival - BCSS) from prospectively collected clinical follow-up in the RASTER study. This is directly observed patient outcomes over 5 and 10 years.
8. Sample Size for the Training Set
The document focuses on the performance of the MammaPrint FFPE NGS kit, which is stated to use an "unchanged" 70-gene signature and scoring algorithm from the predicate device. The original MammaPrint 70-gene signature was developed much earlier. The description states: "This algorithm was designed and programmed by Agendia and incorporated into a proprietary software program, which loads the FASTQ data file." The specifics of the training set for the original MammaPrint algorithm are not provided in this document. This submission is for a new platform (NGS) of an existing and cleared diagnostic system, demonstrating its equivalence, rather than a new algorithm development.
9. How the Ground Truth for the Training Set was Established
As noted above, the original training of the MammaPrint algorithm is not detailed here. The clinical validation in this document uses the RASTER study data, where the ground truth is clinical outcome data (DRFI, BCSS) established through follow-up. This RASTER data is used for validation of the new NGS platform, not for training a new algorithm.
Ask a specific question about this device
(266 days)
MAMMAPRINT FFPE
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).
Ask a specific question about this device
Page 1 of 1