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MammaPrint® is a qualitative in vitro diagnostic test service, performed in a single laboratory, using the gene expression profile of fresh frozen breast cancer tissue samples to assess a patients' risk for distant metastasis.
The test is performed for breast cancer patients who are less than 61 years old, with Stage I or Stage II disease, with tumor size ≤ 5.0 cm and who are lymph node negative. The MammaPrint® result is indicated for use by physicians as a prognostic marker only. along with other clinicopathological factors.
The MammaPrint® test is performed and provided as a service by Agendia Laboratory. The test is a microarray based gene expression analysis of RNA extracted from breast tumor tissue. The test is a custom-designed array chip manufactured by Agilent Technologies using the Agilent oligonucleotide microarray platform which assesses the mRNA expression of the 70 genes in triplicate. The MammaPrint® microarray features eight 1900-feature subarrays per glass slide which can each be individually hybridized. Per subarray 232 reporter genes are printed in triplicate, including the 70 genes which make up the MammaPrint® prognostic profile. Each subarray additionally includes 915 normalization genes and 289 spots for hybridization and printing quality control.
The analysis is based on several processes: isolation of RNA from frozen tumor tissue sections, DNAse treatment of isolated RNA, linear amplification and labeling of DNAse treated RNA, cRNA purification, hybridization of the cRNA to the MammaPrint® microaray, scanning the MammaPrint® microarray and data acquisition (feature extraction), calculation and determination of the risk of recurrence in breast cancer patients.
The MammaPrint® analysis is designed to determine the gene activity of specific genes in a tissue sample compared to a reference standard. The result is an expression profile, or fingerprint, of the sample. The correlation of the sample expression profile to a template (the mean expression profile of 44 tumors with a known good clinical outcome) is calculated and the molecular profile of the sample is determined (Low Risk, High Risk, Low Risk Borderline, High Risk Borderline).
Here's a detailed breakdown of the acceptance criteria and the study that proves the MammaPrint® device meets them, based on the provided text:
Acceptance Criteria and Reported Device Performance
| Acceptance Criteria Category | Specific Metric | Reported Device Performance | Study Proving Performance |
|---|---|---|---|
| Prognostic Performance (5-year) | Negative Predictive Value (NPV) for distant metastasis | 0.95 (0.91-0.99) | TRANSBIG Study (Independent European Validation) |
| Prognostic Performance (5-year) | Positive Predictive Value (PPV) for distant metastasis | 0.22 (0.16-0.28) | TRANSBIG Study |
| Prognostic Performance (5-year) | Low Risk Group: Metastasis-free survival probability | 0.95 | TRANSBIG Study (Kaplan-Meier data) |
| Prognostic Performance (5-year) | High Risk Group: Metastasis-free survival probability | 0.78 | TRANSBIG Study (Kaplan-Meier data) |
| Prognostic Performance (10-year) | Negative Predictive Value (NPV) for distant metastasis | 0.90 (0.85-0.96) | TRANSBIG Study |
| Prognostic Performance (10-year) | Positive Predictive Value (PPV) for distant metastasis | 0.29 (0.22-0.35) | TRANSBIG Study |
| Prognostic Performance (10-year) | Low Risk Group: Metastasis-free survival probability | 0.90 | TRANSBIG Study (Kaplan-Meier data) |
| Prognostic Performance (10-year) | High Risk Group: Metastasis-free survival probability | 0.71 | TRANSBIG Study (Kaplan-Meier data) |
| Analytical Reproducibility (RNA pool) | MammaPrint Index SD (LRC pool) | 0.026 | Internal reproducibility study from RNA pool |
| Analytical Reproducibility (RNA pool) | MammaPrint Index SD (HRC pool) | 0.02747 | Internal reproducibility study from RNA pool |
| Analytical Reproducibility (RNA pool) | MammaPrint Index SD (BLS sample) | 0.031 | Internal reproducibility study from RNA pool |
| Repeatability (Individual patients) | Intra-class correlation coefficient (ICC) | 0.9953 | Internal repeatability study (46 patients) |
| Repeatability (Hybridization) | MammaPrint Index SD (one labeled sample, 8 hybridizations) | 0.020 | Internal repeatability study (one labeled sample) |
| Tissue % cut-off | Minimum tumor cell content required | 30% tumor epithelial cells | Internal validation experiment (adapted from original 50% cutoff) |
Study Details for Clinical Performance (TRANSBIG Study)
2. Sample Size Used for the Test Set and Data Provenance:
- Sample Size: 302 patients
- Data Provenance: Retrospective, from five European centers (Villejuif, France; Stockholm, Sweden; Saint-Cloud, France; London, U.K.; Oxford, U.K.). No US patients were included.
3. Number of Experts Used to Establish the Ground Truth for the Test Set and Their Qualifications:
The document does not explicitly state the number or specific qualifications of experts used to establish the "ground truth" (i.e., metastasis events or metastasis-free survival) for the TRANSBIG test set. However, it mentions:
- "Paraffin embedded tumor samples from this validation series were independently evaluated." This implies a pathologist, but no specific number or qualifications are given.
- Clinical outcome (metastatic disease within 5 or 10 years) is an objective outcome and generally requires clinical follow-up data, not primary expert interpretation of the initial diagnostic material in the way an imaging study would.
4. Adjudication Method for the Test Set:
The document does not explicitly describe an adjudication method (like 2+1 or 3+1 consensus) for establishing the ground truth outcomes (metastasis events) in the TRANSBIG study. The outcome data appears to be based on observed clinical events over time.
5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done, and the Effect Size:
- No, an MRMC comparative effectiveness study was not done in the context of comparing human readers with and without AI assistance.
- The MammaPrint® is a standalone gene expression profiling test, not a tool for human readers to interpret clinical images or data with AI assistance.
- The study did report an unadjusted hazard ratio for time to distant metastases of 2.32 (95% CI: 1.35 to 4.00), which reflects the standalone performance of the gene signature in predicting outcomes, not its assistive effect on human readers. When adjusted for clinical factors (Adjuvant online), the hazard ratio was 2.13 (95% CI: 1.19 to 3.82). This indicates the gene signature provides additional prognostic information beyond standard clinical factors.
6. If a Standalone (Algorithm Only Without Human-in-the-Loop Performance) Was Done:
- Yes, a standalone performance study was done. The entire clinical validation (TRANSBIG study) describes the performance of the MammaPrint® algorithm (the 70-gene signature) without human interpretation in the loop. The device directly outputs a "Low Risk" or "High Risk" classification. The hazard ratios and NPV/PPV values directly reflect this standalone performance.
7. The Type of Ground Truth Used:
- The primary ground truth for the clinical studies (especially TRANSBIG) was outcomes data and pathology. Specifically, the ground truth was the occurrence or non-occurrence of distant metastasis within specific timeframes (5 and 10 years) and the pathology confirmation of breast cancer.
8. The Sample Size for the Training Set:
- Nature Paper (1): 78 patients
- This paper describes the "Development of breast cancer prognosis 70-gene profile."
9. How the Ground Truth for the Training Set Was Established:
- The Nature paper (1) description states it was for "Development of breast cancer prognosis 70-gene profile." While the specific methodology for establishing ground truth isn't detailed in this summary, typically for such studies, it would involve adjudicated clinical outcomes (e.g., metastasis-free survival status) confirmed through patient follow-up and medical records, often correlating with pathology reports for initial diagnosis and tumor characteristics. The mention of "metastasis risk" directly implies reliance on long-term clinical outcome data.
§ 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.