(246 days)
The Prosigna™ Breast Cancer Prognostic Gene Signature Assay is an in vitro diagnostic assay which is performed on the NanoString nCounter® Dx Analysis System using FFPE breast tumor tissue previously diagnosed as invasive breast carcinoma. This qualitative assay utilizes gene expression data, weighted together with clinical variables to generate a risk category and numerical score, to assess a patient's risk of distant recurrence of disease.
The Prosigna Breast Cancer Prognostic Gene Signature Assay is indicated in female breast cancer patients who have undergone surgery in conjunction with locoregional treatment consistent with standard of care, either as:
-
A prognostic indicator for distant recurrence-free survival at 10 years in post-menopausal women with Hormone Receptor-Positive (HR+), lymph node-negative, Stage I or II breast cancer to be treated with adjuvant endocrine therapy alone, when used in conjunction with other clinicopathological factors.
-
A prognostic indicator for distant recurrence-free survival at 10 years in post-menopausal women with Hormone Receptor-Positive (HR+), lymph node-positive (1-3 positive nodes), Stage II breast cancer to be treated with adjuvant endocrine therapy alone, when used in conjunction with other clinicopathological factors. The device is not intended for patients with 4 or more positive nodes.
Special Conditions for Use: Prosigna is not intended for diagnosis, to predict or detect response to therapy, or to help select the optimal therapy for patients.
Used together, the Prosigna™ Breast Cancer Prognostic Gene Signature Assay and nCounter Dx Analysis System are a nucleic acid hybridization and image analysis system based upon coded probes designed to detect the messenger RNA transcribed from 58 genes. The test input is purified RNA from FFPE breast tumor specimens which are acquired from surgical resection. The Prosigna assay uses gene-specific probe pairs that hybridize directly to the mRNA transcripts in solution. The nCounter Dx Analysis System delivers direct, multiplexed measurements of gene expression through digital readouts of the relative abundance of the mRNA transcripts. Specifications are included as part of the Prosigna Assay to control for sample quality, RNA quality, and process quality. Prosigna simultaneously measures the expression levels of 50 genes used in the PAM50 classification algorithm (Parker et al., 2009), 8 housekeeping genes used for signal normalization, 6 positive controls, and 8 negative controls in a single hybridization reaction, using nucleic acid probes designed specifically to those genes. The Prosigna assay utilizes prototypical expression profiles (centroids) which are associated with and define each of the four PAM50 molecular subtypes of breast cancer. The software algorithm produces a Prosigna Score (referred to as ROR Score or Risk of Recurrence Score in the literature (Dowsett et al., 2013)) based on the similarity of the expression profile to each PAM50 molecular subtype, as well as the gross pathological tumor size and a proliferation score computed from a subset of genes. Three risk categories (low, intermediate and high) were defined based on a study with over 1007 patient samples associating Prosigna score with longterm outcome.
The required components for the Prosigna Assay include the RNA Isolation kit (manufactured by Roche), Prosigna reagents (Reference Sample, CodeSet, Prep Pack, Cartridge(s) and Prep Plate) and the instruments that comprise the nCounter Dx Analysis System; the Prep Station and Digital Analyzer.
The test output is a patient specific report which includes a Prosigna score (0-100) and risk category (low/intermediate/high).
Let's break down the acceptance criteria and the study that proves the device meets those criteria for the Prosigna™ Breast Cancer Prognostic Gene Signature Assay, based on the provided FDA 510(k) summary.
1. Table of Acceptance Criteria and Reported Device Performance
The FDA 510(k) summary for the Prosigna assay demonstrates clinical performance relative to its intended use as a prognostic indicator for distant recurrence-free survival (DRFS) at 10 years. The acceptance criteria are implicit in the statistical significance and magnitude of the prognostic information provided by the Prosigna Score, both as a continuous variable and when categorized into risk groups.
| Acceptance Criteria (Implicit) | Reported Device Performance (ABCSG-8 Study) |
|---|---|
| Primary Clinical Performance: Prosigna Score must add "significant prognostic information" for DRFS over and above existing clinical and treatment variables (CTS). | For DRFS at 10 years: - Prosigna Score as a continuous variable: Added significant prognostic information (p < 0.0001) over and above CTS (ΔLR χ² = 53.49, critical value 3.84 for df=1). - Prosigna Score using risk groups: Added significant prognostic information (p < 0.0001) over and above CTS (ΔLR χ² = 34.12, critical value 5.99 for df=2). |
| Risk Group Separation (Node-Negative): Pre-defined Prosigna Score cutoffs must separate node-negative patients into three risk groups (Low, Intermediate, High) with statistically different outcomes at 10 years DRFS. | Node-Negative Population: - Intermediate vs. Low Prosigna Score: Hazard Ratio = 2.60 (95% CI: 1.44 - 4.70, p = 0.0015). Statistically significantly greater than 1. - High vs. Low Prosigna Score: Hazard Ratio = 3.96 (95% CI: 2.18 - 7.20, p < 0.0001). Statistically significantly greater than 2. - Estimated Percent Without Recurrence at 10 years: - Low Risk: 96.6% [94.4% - 97.9%] - Intermediate Risk: 90.4% [86.3% - 93.3%] - High Risk: 84.3% [78.4% - 88.6%] The low-risk group had 10-year DRFS well above 90% and was separated from the high-risk group by more than a 10% probability of recurrence. |
| Risk Group Separation (Node-Positive, 1-3 nodes): Pre-defined Prosigna Score cutoffs must separate node-positive patients into two risk groups (Low, High) with statistically different outcomes at 10 years DRFS. | Node-Positive (1-3 nodes) Population: - High vs. Low Prosigna Score: Hazard Ratio = 4.22 (95% CI: 1.98 - 9.00, p = 0.0002). Statistically significantly greater than 2. - Estimated Percent Without Distant Recurrence at 10 years: - Low Risk: 94.2% [88.1% - 97.2%] - High Risk: 75.8% [68.9% - 81.4%] The low-risk group had 10-year DRFS well above 90% and was separated from the high-risk group by more than a 10% probability of recurrence. |
| Analytical Precision/Reproducibility: Device must reliably measure differences in Prosigna Score. | - Standard deviation of Prosigna Score from 5 pooled RNA samples: < 1 Prosigna Score unit across 3 sites, 3 reagent lots, and 108 measurements. - Total variability (tissue and RNA Processing): 2.9 Prosigna Score units. This demonstrates the assay can reliably measure a difference of 6.75 Prosigna Score units with 95% confidence. - Concordance in categorical risk classifications across 43 tissue samples in Tissue Reproducibility study: average > 90%. |
| Clinical Utility (Small Score Changes): Small changes in Prosigna Score (5-10 units) should be statistically significant for time to distant recurrence. | C-index analysis showed statistically significant utility for small changes in Prosigna Score (P<0.05) for 5-10 Prosigna Score units. A difference of 7 Prosigna Score units is both statistically reproducible and clinically meaningful. |
2. Sample Size Used for the Test Set and Data Provenance
- Test Set (Clinical Validation):
- The primary clinical validation study was ABCSG-8, with 1,478 patients available for analysis after QC failures (out of 1,620 tissues initially available).
- A prior study, TransATAC, was used to select the Prosigna Score cut-offs for risk categories. This study also demonstrated continuous relation to DRFS.
- Data Provenance: The 510(k) summary states that the validation population for the Prosigna Assay utilized "Treatment arms from a randomized trial conducted in Europe" with a "prospective retrospective study design". Both TransATAC and ABCSG-8 samples were independent from those used to train the Prosigna algorithm.
3. Number of Experts Used to Establish the Ground Truth for the Test Set and Qualifications of Those Experts
The document does not explicitly state the number or qualifications of experts used to establish the ground truth for the test set. However, a "pre-defined pathology review criteria for adequate tumor" was applied to the ABCSG-8 tissue samples, which would typically involve expert pathologists. The clinical endpoints (distant recurrence, distant recurrence-free survival) are outcome data derived from patient follow-up within the clinical trial, rather than ground truth established by expert consensus on images.
4. Adjudication Method for the Test Set
The document does not specify an adjudication method for establishing specific diagnoses or outcomes on a case-by-case basis. The outcomes (distant recurrence, death) are clinical events recorded during patient follow-up, typical of a clinical trial. Pathology review criteria were applied to screen samples, but this is a quality control step, not an adjudication of a device output.
5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done, If So, What Was the Effect Size of How Much Human Readers Improve With AI vs Without AI Assistance
No MRMC comparative effectiveness study involving human readers and AI assistance is mentioned. The Prosigna assay is a gene expression profiling test system, providing a numeric score and risk category directly. It is not designed to assist human readers in interpreting images or other data in the way an AI diagnostic tool might. Its primary purpose is to add prognostic information to clinical variables.
6. If a Standalone (i.e., algorithm only without human-in-the-loop performance) Was Done
Yes, the clinical performance described is a standalone (algorithm only) performance. The Prosigna Assay generates a risk category and numerical score directly from gene expression data and clinical variables. The studies evaluate the prognostic value of this score and risk category on patient outcomes (DRFS) without human interpretation of the assay's raw output. The output is intended for healthcare professionals to consider alongside other clinicopathological factors in treatment decisions.
7. The Type of Ground Truth Used (expert consensus, pathology, outcomes data, etc.)
The ground truth used for the clinical validation studies (TransATAC and ABCSG-8) was patient outcomes data, specifically:
- Distant Recurrence-Free Survival (DRFS) at 10 years.
- Incidence of distant recurrence (events).
The clinical endpoints were derived from long-term follow-up of patients in these retrospective clinical trials.
8. The Sample Size for the Training Set
The document explicitly states that "Both the TransATAC and ABCSG-8 study samples were independent from those samples used to train the Prosigna algorithm." However, the exact sample size for the training set (i.e., the cohort(s) used to develop the PAM50 classification algorithm and subsequently to define the Prosigna Score and risk categories prior to its validation) is not specified in this 510(k) summary. It references "Parker et al., 2009" for the PAM50 classification algorithm and "Dowsett et al., 2013" for the Prosigna Score literature, which would contain details on the training cohorts used for algorithm development and initial risk stratification. The summary notes that "Three risk categories (low, intermediate and high) were defined based on a study with over 1007 patient samples associating Prosigna score with long-term outcome." This "study with over 1007 patient samples" likely refers to the TransATAC study, which was used for defining cut-offs and therefore might be considered part of an extended training/calibration phase before independent validation in ABCSG-8.
9. How the Ground Truth for the Training Set Was Established
Similar to the validation set, the ground truth for the (unspecified) training set would have been established using patient outcomes data, specifically clinical endpoints such as:
- Distant Recurrence-Free Survival
- Overall Survival
- Other breast cancer-specific endpoints.
The "PAM50 classification algorithm" itself was "based on intrinsic subtypes" (Parker et al., 2009), implying that molecular profiling of tumors was correlated with clinical outcomes to identify and define these subtypes, which then formed the basis of the gene signature. The "study with over 1007 patient samples associating Prosigna score with long-term outcome" (likely TransATAC) would also have used patient outcomes data for this association and for defining risk category cut-offs.
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Food and Drug Administration 10903 New Hampshire Avenue Document Control Center - WO66-G609 Silver Spring, MD 20993-0002
July 12, 2016
Nanostring Technologies Sylva Krizan, Ph.D. Regulatory Affairs Specialist 530 Fairview Ave N, Suite 2000 Seattle, WA 98109
Re: K130010
Trade/Device Name: ProsignaTM Breast Cancer Prognostic Gene Signature Assay Regulation Number: 21 CFR §866.6040 Regulation Name: Gene expression profiling test system for breast cancer prognosis Regulatory Class: Class II Product Code: NYI, NSU Dated: August 9, 2013 Received: August 9, 2013
Dear Dr. Krizan:
This letter corrects our substantially equivalent letter of September 6, 2013.
We have reviewed your Section 510(k) premarket notification of intent to market the device referenced above and have determined the device is substantially equivalent (for the indications for use stated in the enclosure) to legally marketed predicate devices marketed in interstate commerce prior to May 28, 1976, the enactment date of the Medical Device Amendments or to devices that have been reclassified in accordance with the provisions of the Federal Food, Drug, and Cosmetic Act (Act) that do not require approval of a premarket approval application (PMA). You may, therefore, market the device, subject to the general controls provisions of the Act. The general controls provisions of the Act include requirements for annual registration. Iisting of devices, good manufacturing practice, labeling, and prohibitions against misbranding and adulteration. Please note: CDRH does not evaluate information related to contract liability warranties. We remind you, however, that device labeling must be truthful and not misleading.
If your device is classified (see above) into either class II (Special Controls) or class III (PMA), it may be subject to additional controls. Existing major regulations affecting your device can be found in the Code of Federal Regulations, Title 21, Parts 800 to 898. In addition, FDA may publish further announcements concerning your device in the Federal Register.
Please be advised that FDA's issuance of a substantial equivalence determination does not mean that FDA has made a determination that your device complies with other requirements of the Act or any Federal statutes and regulations administered by other Federal agencies. You must comply with all the Act's requirements, including, but not limited to: registration and listing (21 CFR Part 807); labeling (21 CFR Parts 801 and 809); medical device reporting (reporting of
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medical device-related adverse events) (21 CFR 803); good manufacturing practice requirements as set forth in the quality systems (QS) regulation (21 CFR Part 820); and if applicable, the electronic product radiation control provisions (Sections 531-542 of the Act); 21 CFR 1000-1050.
If you desire specific advice for your device on our labeling regulation (21 CFR Part Parts 801 and 809), please contact the Division of Industry and Consumer Education at its toll-free number (800) 638-2041 or (301) 796-7100 or at its Internet address
http://www.fda.gov/MedicalDevices/ResourcesforYou/Industry/default.htm. Also, please note the regulation entitled. "Misbranding by reference to premarket notification" (21CFR Part 807.97). For questions regarding the reporting of adverse events under the MDR regulation (21 CFR Part 803), please go to
http://www.fda.gov/MedicalDevices/Safety/ReportaProblem/default.htm for the CDRH's Office of Surveillance and Biometrics/Division of Postmarket Surveillance.
You may obtain other general information on your responsibilities under the Act from the Division of Industry and Consumer Education at its toll-free number (800) 638-2041 or (301) 796-7100 or at its Internet address
http://www.fda.gov/MedicalDevices/ResourcesforYou/Industry/default.htm.
Sincerely.
Reena Philip -S
Reena Philip, Ph.D. Director Division of Molecular Genetics and Pathology Office of In Vitro Diagnostics and Radiological Health Center for Devices and Radiological Health
Enclosure
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510(k) Number (if known): K130010
Device Name: Prosigna™ Breast Cancer Prognostic Gene Signature Assay
Indications for Use:
The Prosigna™ Breast Cancer Prognostic Gene Signature Assay is an in vitro diagnostic assay which is performed on the NanoString nCounter® Dx Analysis System using FFPE breast tumor tissue previously diagnosed as invasive breast carcinoma. This qualitative assay utilizes gene expression data, weighted together with clinical variables to generate a risk category and numerical score, to assess a patient's risk of distant recurrence of disease.
The Prosigna Breast Cancer Prognostic Gene Signature Assay is indicated in female breast cancer patients who have undergone surgery in conjunction with locoregional treatment consistent with standard of care, either as:
A prognostic indicator for distant recurrence-free survival at 10 years in post-menopausal 1. women with Hormone Receptor-Positive (HR+), lymph node-negative, Stage I or II breast cancer to be treated with adjuvant endocrine therapy alone, when used in conjunction with other clinicopathological factors.
- A prognostic indicator for distant recurrence-free survival at 10 years in post-menopausal women with Hormone Receptor-Positive (HR+), lymph node-positive (1-3 positive nodes), Stage II breast cancer to be treated with adjuvant endocrine therapy alone, when used in conjunction with other clinicopathological factors. The device is not intended for patients with 4 or more positive nodes.
Special Conditions for Use: Prosigna is not intended for diagnosis, to predict or detect response to therapy, or to help select the optimal therapy for patients.
Prescription Use x (Part 21 CFR 801 Subpart D)
Over-The-Counter Use _ (21 CFR 801 Subpart C)
(PLEASE DO NOT WRITE BELOW THIS LINE-CONTINUE ON ANOTHER PAGE IF NEEDED)
Concurrence of CDRH, Office of In Vitro Diagnostics and Radiological Health (OIR)
/un fo Au -S
Division Sign-Off Office of In Vitro Diagnostics and Radiological Health
510(k) K130010
Page 1 of 1
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510(k) Summary: K130010
Applicant: NanoString Technologies, Inc.
Establishment Registration Number: 3006389928
Contact person:
Sylva Krizan, Ph.D. Regulatory Affairs Specialist NanoString Technologies 530 Fairview Avenue North, Suite 2000 Seattle, WA 98109
Phone: (206) 432-8854 Fax: (206) 378-6288
Summary Date:
September 6, 2013
Device Name:
Trade name: Prosigna™ Breast Cancer Prognostic Gene Signature Assay Common Name: NanoString gene expression profiling test for breast cancer prognosis
Classification:
21 CFR § 866.6040: Gene expression profiling test system for breast cancer prognosis
Guidance Document:
Class II Special Controls Guidance Document: Gene Expression Profiling Test System for Breast Cancer Prognosis, issued on May 9, 2007
Product Code:
NYI
Indications for Use / Intended Use:
The Prosigna™ Breast Cancer Prognostic Gene Signature Assay is an in vitro diagnostic assay which is performed on the NanoString nCounter® Dx Analysis System using FFPE breast tumor tissue previously diagnosed as invasive breast carcinoma. This qualitative assay utilizes gene expression data, weighted together with clinical variables to generate a risk category and numerical score, to assess a patient's risk of distant recurrence of disease.
The Prosigna Breast Cancer Prognostic Gene Signature Assay is indicated in female breast cancer patients who have undergone surgery in conjunction with locoregional treatment consistent with standard of care, either as:
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- A prognostic indicator for distant recurrence-free survival at 10 years in postmenopausal women with Hormone Receptor-Positive (HR+), lymph node-negative, Stage I or II breast cancer to be treated with adjuvant endocrine therapy alone, when used in conjunction with other clinicopathological factors.
A prognostic indicator for distant recurrence-free survival at 10 years in post-2. menopausal women with Hormone Receptor-Positive (HR+), lymph node-positive (1-3 positive nodes), Stage II breast cancer to be treated with adjuvant endocrine therapy alone, when used in conjunction with other clinicopathological factors. The device is not intended for patients with 4 or more positive nodes.
Special Conditions for Use:
Prosigna™ is not intended for diagnosis, to predict or detect response to therapy, or to help select the optimal therapy for patients.
Device Description:
Used together, the Prosigna™ Breast Cancer Prognostic Gene Signature Assay and nCounter Dx Analysis System are a nucleic acid hybridization and image analysis system based upon coded probes designed to detect the messenger RNA transcribed from 58 genes. The test input is purified RNA from FFPE breast tumor specimens which are acquired from surgical resection. The Prosigna assay uses gene-specific probe pairs that hybridize directly to the mRNA transcripts in solution. The nCounter Dx Analysis System delivers direct, multiplexed measurements of gene expression through digital readouts of the relative abundance of the mRNA transcripts. Specifications are included as part of the Prosigna Assay to control for sample quality, RNA quality, and process quality. Prosigna simultaneously measures the expression levels of 50 genes used in the PAM50 classification algorithm (Parker et al., 2009), 8 housekeeping genes used for signal normalization, 6 positive controls, and 8 negative controls in a single hybridization reaction, using nucleic acid probes designed specifically to those genes. The Prosigna assay utilizes prototypical expression profiles (centroids) which are associated with and define each of the four PAM50 molecular subtypes of breast cancer. The software algorithm produces a Prosigna Score (referred to as ROR Score or Risk of Recurrence Score in the literature (Dowsett et al., 2013)) based on the similarity of the expression profile to each PAM50 molecular subtype, as well as the gross pathological tumor size and a proliferation score computed from a subset of genes. Three risk categories (low, intermediate and high) were defined based on a study with over 1007 patient samples associating Prosigna score with longterm outcome.
The required components for the Prosigna Assay include the RNA Isolation kit (manufactured by Roche), Prosigna reagents (Reference Sample, CodeSet, Prep Pack, Cartridge(s) and Prep Plate) and the instruments that comprise the nCounter Dx Analysis System; the Prep Station and Digital Analyzer.
The test output is a patient specific report which includes a Prosigna score (0-100) and risk category (low/intermediate/high).
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Analytical Performance:
A number of pre-analytical and analytical studies were carried out with the Prosigna Assay to assess the precision, reproducibility, cutoff, sensitivity, specificity and robustness of the assay. Analytical studies also addressed specimen shipping and storage, reagent stability, RNA extraction specifications, tissue requirements, RNA input, cross-hybridization, crosscontamination and tissue interferents testing.
Technical validity was demonstrated in two multi-site (3 sites total), blinded and randomized studies which were designed to test variability across operators, sites, instruments, reagent lots, time, runs and sample position within a 10-sample cartridge. One study assessed reproducibility including pre-analytical factors with a total of 43 tissue samples (FFPE) and the other assessed assay precision with 5 pooled RNA samples. All reproducibility samples were within the intended use patient population indicated by Prosigna, and constituted a large range of Prosigna scores (across 94 Prosigna Score units).
The standard deviation (SD) of the Prosigna Score from the 5 pooled RNA samples was < 1 Prosigna Score unit across 3 sites, 3 reagent lots, and 108 measurements of each RNA sample. Using a linear regression and correlation analysis, the normalized gene expression from the 50 classifier genes was compared between the replicate tumor RNA hybridization measurements from all valid samples tested at each site. The average intercept, slope, and Pearson's correlation (r) of the pair-wise comparisons are reported with the 95 % confidence interval. At each site, the normalized gene expression between RNA replicates was highly correlative with slopes ranging from 0.98 – 1.00, intercepts at 0, and r values of 0.99.
| Pairwise Comparison of Replicate RNA Hybridizations | |||||
|---|---|---|---|---|---|
| Comparison | PairwiseComparisons (n) | Intercept[95% Cl] | Slope[95% Cl] | r[95% CI] | |
| All Sites | 124 | 0.00[-0.01 , 0] | 0.99[0.99 , 1] | 0.99ﺃﻣﺎﻛﻦ ﻣﺄﻫﻮﻟﺔ ﺃﺳﺴﺖ ﻓﻲ 1990 ﻓﻲ ﺇﺳﺒﺎﻧﻴﺎ، ﻭﻳﺘﻤﻴﺰ ﺍﻟﻤﺪﻳﻨﺔ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ ﺍﻟﻤﺘﺤﺪﺓ | |
| Site 1 | 40 | -0.01[-0.01 , 0] | 1.00[0.99 , 1.01] | 0.99[0.99 , 0.99] | |
| Site 2 | 41 | 0.00[-0.01 , 0.01] | 0.98[0.97 , 0.99] | 0.99[0.99 , 0.99] | |
| Site 3 | 43 | 0.00[-0.01 , 0.01] | 0.99[0.99 , 1] | 0.99[0.99 , 0.99] |
Pairwise correlation for Replications from tissue reproducibility study
Using a linear regression and correlation analysis, the normalized gene expression from the 50 classifier genes was also compared between the tissue replicates from all valid specimens tested at each site. The average intercept, slope, and Pearson's correlation (r) of the pair-wise
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comparisons between sites are reported with the 95 % confidence interval. The gene expression between tissue replicates was highly correlative between sites with slopes ranging from 0.97 – 1.00, intercepts at 0, and r values of 0.98 or greater.
| Pairwise Comparison of Tissue Replicates | |||||
|---|---|---|---|---|---|
| Comparison | PairwiseComparisons (n) | Intercept[95% Cl] | Slope[95% Cl] | r[95% Cl] | |
| All Sites | 121 | 0.00[-0.01 , 0.01] | 0.98[0.97 , 0.99] | 0.98[0.98 , 0.98] | |
| Site 1 vs. Site 2 | 40 | 0.00[-0.01 , 0.01] | 0.97[0.95 , 0.98] | 0.98[0.97 , 0.98] | |
| Site 1 vs. Site 3 | 40 | 0.01[0 , 0.02] | 1.00[0.98 , 1.01] | 0.98[0.98 , 0.99] | |
| Site 2 vs. Site 3 | 41 | -0.01[-0.02 , 0] | 0.99[0.97 , 1] | 0.99[0.98 , 0.99] |
Pairwise correlation for Replicate Tissues from tissue reproducibility study
The total variability using the sum of the tissue processing variability (including across sites and within tissue samples) as well as the total RNA Processing Variability from the RNA precision study (averaged across the five tested RNA samples) is summarized as a total standard deviation for tissue and RNA Processing of 2.9 Prosigna Score units. A standard deviation of 2.9 Prosigna Score units demonstrates that the Prosigna Assay can reliably measure a difference between two Prosigna Scores of 6.75 with 95% confidence.
Additionally, the concordance in categorical risk classifications across the 43 tissue samples in the Tissue Reproducibility study (node-negative and positive risk categories) between all sites was very high (average concordance greater than 90%) .
Additional analyses of the gene expression from samples used in the validation studies shows that the gene expression inherent to the intrinsic biology of breast cancer is the primary factor in explaining the differences in expression in this patient population, which is independent of the patient's nodal status. For further details, see Package Insert.
Clinical Performance:
Prosigna's clinical performance has been verified and validated in two large studies using retrospective tissue samples from 2485 patients within the Intended Use patient population. The first study, TransATAC, demonstrated that Prosigna Score was continuously related to Distant Recurrence-Free Survival (DRFS) at 10 years and was used to select the Prosigna Score cut-offs for low, intermediate, and high risk categories. The second study, ABCSG-8 replicated the result that Prosigna Score was continuously related to DRFS at 10 years and validated the
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risk group cut-offs. Both the TransATAC and ABCSG-8 study samples were independent from those samples used to train the Prosigna algorithm.
For the ABCSG-8 study, all samples were sent to, and all tests were performed at, an independent academic pathology laboratory. Of the 1,620 tissues available for testing in the ABCSG-8 study, 25 (1.5%) did not pass pre-defined pathology review criteria for adequate tumor, 73 of the 1595 tissue samples (4.6%) with viable invasive tissue did not pass pre-defined QC specifications for quantity and quality of extracted RNA, and 44 of the 1522 RNA samples (2.9%) failed the Prosigna assay QC specifications leaving a total of 1,478 (91.2%) available for analysis. Of the 1,478 patients available for analysis, 155 had distant recurrences and 194 had local or distant recurrence or death due to breast cancer. The median follow-up for the trial was 10 years.
The table below shows a summary of the primary analysis of the ABCSG-8 study using a Cox proportional hazards model in which (1) Prosigna Score was added to the clinical treatment score (CTS) as a continuous variable and (2) Prosigna Score was added to CTS using the predefined Prosigna Score-based risk groups. In both cases, a null model consisting of CTS alone was compared to an alternate model using a likelihood ratio (LR) test. The table shows the test statistic (ΔLR χ2 = -2ln(LR)), the critical value for the degrees of freedom for the α = 0.05 test, and the p-value based on the χ2 distribution.
| Null Model | Alternate Model | $ΔLR χ²*$ | $χ²$ Critical Value(Degrees of freedom) | $χ²$ p-value |
|---|---|---|---|---|
| CTS | CTS + Prosigna Score | 53.49 | 3.84 (df = 1) | p < 0.0001 |
| CTS | CTS + Risk Groups | 34.12 | 5.99 (df = 2) | p < 0.0001 |
Summary of Primary Analysis Testing from ABCSG-8 clinical validation study
*ΔLR is used to denote twice the difference of the log likelihoods when comparing two models, e.g., CTS and CTS + Prosigna Score. The statistic has an approximate x2 distribution.
CTS is an optimized combination of clinical and treatment variables (patient age, tumor grade, gross pathological tumor size, nodal status, and adjuvant therapy) which is a best-case approximation of how a physician may use these factors in treatment decisions. When adding Prosigna Score either as a continuous variable or using risk-groups, the Prosigna Score was shown to add significant prognostic information (p < 0.0001) for DRFS over and above that contained in the CTS score.
The table below shows the results of Cox modeling when CTS and the two or three Prosigna Score-based risk groups were included as covariates in the ABCSG-8 study, by nodal status.
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| Hazard Ratio | |||||||
|---|---|---|---|---|---|---|---|
| NodeGroup* | Variable | Coefficient | P-value | PointEstimate | Lower95% CL | Upper95% CL | |
| NO | CTS | 0.70 | 0.0013 | 2.01 | 1.31 | 3.08 | |
| Intermediate vs. LowProsigna Score | 0.96 | 0.0015 | 2.60 | 1.44 | 4.70 | ||
| High vs. LowProsigna score | 1.38 | <0.0001 | 3.96 | 2.18 | 7.20 | ||
| N1 | CTS | 0.69 | 0.0098 | 1.99 | 1.18 | 3.34 | |
| High vs. Low ProsignaScore | 1.44 | 0.0002 | 4.22 | 1.98 | 9.00 |
Cox Regression Results for Pre-Defined Risk Groups in ABCSG-8 Clinical Validation Study
*N0: Node-negative, N1: Node-positive (1-3 nodes)
In the node-negative population, the hazard ratio for Intermediate vs. Low Prosigna Score is statistically significantly greater than 1 (95% confidence interval does not include 1) and that for High vs. Low Prosigna Score is statistically significantly greater than 2 (95% confidence interval does not include 2), i.e. the pre-defined Prosigna Score cutoffs separate the patients into three risk groups (low risk, intermediate risk, high risk) with statistically different outcomes at 10 years.
In the node-positive population (1-3 nodes), the hazard ratio for High vs. Low Prosigna Score is statistically significantly greater than 2 (95% confidence interval does not include 2), i.e. the predefined Prosigna Score cutoffs separate the patients into two risk groups (low risk, high risk) with statistically significantly different outcomes at 10 years.
The cutoffs for the risk group classifications were defined based on the results of the TransATAC study:
| Risk Group | Risk of distantrecurrence by 10years | Prosigna Score RangeforNode-Negative | Prosigna Score Range forNode-Positive (1-3 Nodes) |
|---|---|---|---|
| Low | < 10% | 0-40 | 0-40 |
| Intermediate | 10 - 20% | 41-60 | 0-40 |
| High | > 20% | 61-100 | 41-100 |
The following figures are the Kaplan-Meier curves showing the percent of patients without distant recurrence by risk-group through 10 years for all patients from the ABCSG-8 study, by nodal status.
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DRFS by Risk Group for Node-Negative Patients
Image /page/9/Figure/1 description: This image is a Kaplan-Meier plot showing the percent without distant recurrence over a 10-year follow-up period for three risk groups: low-risk, intermediate-risk, and high-risk. The y-axis represents the percent without distant recurrence, ranging from 0 to 1, while the x-axis represents the follow-up time in years, ranging from 0 to 10. The low-risk group has the highest percentage without distant recurrence, followed by the intermediate-risk group, and then the high-risk group.
Summary: DRFS by Risk Group for Node-Negative Patients
| Risk Group | Number of Patients (%) | Number of Events Through 10 Years | Estimated Percent Without Recurrence at 10 years [95% CI] |
|---|---|---|---|
| Low | 487 (47%) | 15 | 96.6% [94.4% - 97.9%] |
| Intermediate | 335 (32%) | 28 | 90.4% [86.3% - 93.3%] |
| High | 225 (21%) | 32 | 84.3% [78.4% - 88.6%] |
| Total | 1,047 (100%) | 75 |
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DRFS by Risk Group for Node-Positive (1-3 nodes) Patients
Summary: DRFS by Risk Group for Node-Positive (1-3 nodes) Patients
| Risk Group | Number of Patients (%) | Number of EventsThrough 10 Years | Estimated Percent Without DistantRecurrence at 10 years [95% CI] |
|---|---|---|---|
| Low | 158 (41%) | 7 | 94.2% [88.1%-97.2%] |
| High | 224 (59%) | 46 | 75.8% [68.9%-81.4%] |
| Total | 382 (100%) | 53 |
The Prosigna Score was demonstrated to add significant prognostic information over and above the standard clinical and treatment variables both when included as a continuous measure and when included using pre-defined risk groups. The low-risk groups (each of node-negative and node-positive patients) had 10-year DRFS well above 90% and was separated from the high-risk group by more than a 10% probability of recurrence at 10 years. The Prosigna Score (continuous and risk-group based) showed similar prognostic information in various subgroups.
A C-index analysis was used to evaluate the correlation between the Prosigna Score and the time to distant recurrence. The C-index analysis was restricted to comparing patient samples with Prosigna Scores that differed by only 5-10 Prosigna Score units. This analysis showed that there is statistically significant in small changes in Prosigna Score (P<0.05). Based on the analytical precision and reproducibility studies and the restricted C-index analysis of 5-10 ΔProsigna Score units, a difference of Prosigna Score of 7 is shown to be both a reliable measure of difference of the Prosigna test performance (statistically reproducible based on analytical studies), and of clinical utility (clinically meaningful based on restricted C-index analysis).
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The analytical performance studies in combination with pre-analytical studies validate that the Prosigna assay is appropriate for use as a distributed gene expression profiling test system for breast cancer prognosis. The clinical studies demonstrate the validity of a risk classifier that includes High, Intermediate and Low risk groups (where indicated) as well as a continuous risk score that outputs an integer Prosigna Score of 0-100.
Predicate Device: Agendia, MammaPrint K062694, K081092
| Substantial Equivalence Comparison Table | ||
|---|---|---|
| Device | New Device (Prosigna™ Breast Cancer Prognostic Gene Signature Assay) | Predicate Device (MammaPrint, K062694, K081092) |
| Intended Use | The Prosigna™ Breast Cancer Prognostic Gene Signature Assay is an in vitro diagnostic assay which is performed on the NanoString nCounter® Dx Analysis System using FFPE breast tumor tissue previously diagnosed as invasive breast carcinoma. This qualitative assay utilizes gene expression data, weighted together with clinical variables to generate a risk category and numerical score, to assess a patient's risk of distant recurrence of disease.The Prosigna Breast Cancer Prognostic Gene Signature Assay is indicated in female breast cancer patients who have undergone surgery in conjunction with locoregional treatment consistent with standard of care, either as:1. A prognostic indicator for distant recurrence-free survival at 10 years in post-menopausal women with Hormone Receptor-Positive (HR+), lymph node-negative, Stage I or II breast cancer to be treated with adjuvant endocrine therapy alone, when used in conjunction with other clinicopathological factors.2. A prognostic indicator for | K062694MammaPrint 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 lymph node negative. The MammaPrint result is indicated for use by physicians as a prognostic marker only, along with other clinicopathological factorsK081092MammaPrint is a qualitative in vitro diagnostic test service, performed in a single laboratory, using the gene expression profile of fresh breast cancer tissue samples to assess a patient's risk for distant metastasis.The test is performed for breast cancer patients, with |
| distant recurrence-free survival at10 years in post-menopausal womenwith Hormone Receptor-Positive(HR+), lymph node-positive (1-3positive nodes), Stage II breastcancer to be treated with adjuvantendocrine therapy alone, when usedin conjunction with otherclinicopathological factors.Thedevice is not intended for patientswith 4 or more positive nodes. | Stage I or Stage 11 disease,with tumor size <= 5.0 cm andwho are lymph node negative.The MammaPrint result isindicated for use by physiciansas a prognostic marker only,along with otherclinicopathological factors. | |
| Indications | Same as intended use | Same as intended use |
| Special conditions foruse statement(s) | For prescription use only.Prosigna™ is not intended fordiagnosis, to predict or detectresponse to therapy, or to helpselect the optimal therapy forpatients | For prescription use only.MammaPrint® is not intendedfor diagnosis, or to predict ordetect response to therapy, orto help select the optimaltherapy for patients |
| Device Description | Prosigna™ Breast Cancer PrognosticGene Signature Assay and nCounterDx Analysis Platform; all elementscleared by FDA as a distributed testand platform | Microarray-based assayperformed as a service at asingle site; includesinstrumentation that iscleared for use at thedesignated site |
| Test Sample | FFPE tumor samples | Fresh frozen or freshpreserved tissue sections |
| Extraction/amplificationreagents/amplificationprocedures | No amplification required;procedure for processing FFPEtumor samples provided; includesRNA isolation, multiplexhybridization in solution, automatedpurification on a liquid handlingrobot and analysis on an automatedepifluorescence microscope | Amplification required; singlesite handles entire protocolstarting from tissue; includesRNA isolation, labelingamplification, microarrayhybridization and scanning |
| Validation population | Treatment arms from a randomizedtrial conducted in Europe;prospective retrospective studydesign | European cohort; literaturebased support |
| Method ComparisonResults | Not applicable | Not applicable |
| Clinical Studies | 1478 patients evaluated resulting inoverall percentage without distantrecurrence at 10 years separated bythree risk groups in node-negativepatients (n=1047): low risk 96.6% | 302 patients evaluated(K062694) resulting in ametastasis-free survival byprofile at 10 yrs (for patientsless than 61 years old): lowrisk profile 90% (85-96%), high |
| 90.4% (86.3%-93.3%), high risk84.3% (78.4%-88.6%) and by two riskgroups in node-positive (1-3 nodes)patients (n=382): low risk 94.2%(88.1%-97.2%), high risk 75.8%(68.9%-81.4%) | risk profile 71% (65-78%) (at 5yrs: 95% (91%-99%) and 78%(72%-84%) respectively)131 patients were evaluated(K081092) for 5 year survival.The study showed that thedevice could categorize risk ofmetastatic disease within 5years for patients ≥ 61 yearswith PPV = 0.22 (0.12-0.38)NPV = 0.93 (0.85-0.97) |
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Based on the Intended Use of the Prosigna Breast Cancer Prognostic Gene Signature Assay and the results of the performance and analytical studies provided in the 510(k), the Prosigna Breast Cancer Prognostic Gene Signature Assay is found to be Substantially Equivalent to the predicate device, Mammaprint.
References:
Dowsett M. et al. on behalf of the ATAC and LATTE Trialists Group. Comparison of PAM50 Risk of Recurrence Score With Oncotype DX and IHC4 for Predicting Risk of Distant Recurrence After Endocrine Therapy. Journal of Clinical Oncology. ePub ahead of print July 1, 2013 as 10.1200/JCO.2012.46.1558
Parker J.S., et. al., Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes. Journal of Clinical Oncology, v27 No.8 (2009) 1160-1167
§ 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.