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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.

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 I 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 clinicopathological factors.

The MammaPrint service is a microarray-based gene expression analysis of a tumor. The analysis is based on several processes: isolation of RNA from formalin-fixed paraffin embedded (FFPE) tumor tissue sections, DNase treatment of isolated RNA, amplification DNase treated RNA resulting in cDNA, labeling and purification of amplified cDNA, hybridization of the diagnostic microarray, 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 FFPE tissue sample. The result is an expression profile, or fingerprint, of the sample. The molecular profile of the sample is determined (Low Risk) by calculating the MammaPrint index (MPI) by determining the correlation of the sample expression profile to the mean expression profiles of risk templates of tumors with a known good and poor outcome.

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).

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 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. 2. A prognostic indicator for distant recurrence-free survival at 10 years in postmenopausal 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

The required components for the Prosigna™ Breast Cancer Prognostic Gene Signature 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 assay requires microdissection of tumor from FFPE biopsies, isolation of RNA using a Roche RNA isolation kit, transfer of RNA to PCR tubes for hybridization before placing onto the prep station. Two sets of probes specific to each of 58 RNAs are added to the hybridization reaction. These consist of biotin-labeled magnetic probes to purify the RNAs and capture them on the assay cartridge and fluorescent "barcode" probes to detect and quantify individual RNAs. The patient sample and probes are pipetted automatically into the Prosigna test cartridge by the Prep Station. The prep station uses magnetic bead capture and washing to remove excess RNA and un-hybridized probes. The isolated and hybridized RNA species are then bound via biotin on the capture probe randomly to streptavidin on the cartridge. The fluorescent molecules are then aligned on the cartridge by addition of an electric current. The cartridge is then transferred to the Digital Analyzer where the cartridge is scanned and digital analysis software is used to count the number of each RNA species present. The amount of each RNA is then put into a proprietary algorithm to produce a Prosigna score. The test output is a patient specific report which includes a Prosigna score (0-100) and risk category (low/intermediate/high).

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 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).

MammaPrint is a qualitative in vitro diagnostic test service, performed in a central laboratory, using the gene expression profile of fresh breast cancer tissue samples to assess a patient's risk for distant metastasis (up to 10 years for patients less than 61 years old, up to 5 years for patients' ≥ 61 years). The test is performed for breast cancer patients 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 service is a microarray based gene expression analysis of a tumor. The analysis is based on several processes: isolation of RNA from frozen tumor tissue sections. DNA'se treatment of isolated RNA, linear amplification and labeling of DNA'se treated RNA, cRNA purification, hybridization of the cRNA to the MammaPrint microarray, 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).

MammaPrint® is a gualitative in vitro diagnostic test service, performed in a single laboratory, using the gene expression profile of fresh breast cancer tissue samples to assess a patients' risk for distant metastasis (up to 10 years for patients less than 61 years old, up to 5 years for patients ≥ 61 years). The test is performed for breast cancer patients with Stage I or Stage II disease, with a tumor size of ≤ 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 factors.

The MammaPrint service is a microarray based gene expression analysis of a tumor. The analysis is based on several processes: isolation of RNA from frozen tumor tissue sections, DNA'se treatment of isolated RNA, linear amplification and labeling of DNA'se treated RNA, cRNA purification, hybridization of the cRNA to the MammaPrint microarray, scanning the MammaPrint microarray and data acquisition (feature extraction), index calculation and determination of the risk of distant 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 index of the sample is determined (Low Risk, High Risk).

MammaPrint 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 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 service is a microarray based gene expression analysis of a tumor. The analysis is based on several processes: isolation of RNA from frozen turnor tissue sections, DNA'se treatment of isolated RNA, linear amplification and labeling of DNA'se treated RNA, cRNA purification, hybridization of the cRNA to the MammaPrint microarray, 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).

MammaPrint® 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 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 factors.

The MammaPrint service is a microarray based gene expression analysis of a tumor. The analysis is based on several processes: using fresh tissue stored in RNAlater, isolation of RNA from frozen tumor tissue sections, DNA'se treatment of isolated RNA, linear amplification and labeling of DNA'se treated RNA, cRNA purification, hybridization of the cRNA to the MammaPrint microarray, 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).

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).