Skip to main content
Premium Trial:

Request an Annual Quote

Agendia to Offer FFPE Sample Analysis for Symphony Suite of Breast Cancer Diagnostics


By Turna Ray

This story was originally posted Dec. 19.

Agendia has added technology to its Symphony suite of breast cancer assays that will allow the company to accept and analyze paraffin-embedded tissue samples.

"Coming early 2012, Agendia is able to perform the Symphony cancer assays on formalin-fixed, paraffin-embedded tissue from a paraffin block or unstained slides," Agendia states on its website.

In a statement, Agendia CEO David Macdonald said that the company's ability to analyze both fresh and FFPE specimens will "further assist physicians in delivering personalized treatment options."

The Symphony suite of tests includes the breast cancer recurrence test MammaPrint; the molecular subtyping assay BluePrint; a test for determining patients' estrogen-receptor, progesterone receptor, and HER2 status, called TargetPrint; and TheraPrint, which identifies alternative treatments for metastatic breast cancer.

MammaPrint, approved by the US Food and Drug Administration in 2007, originally only analyzed fresh samples. The test operates on an Agilent microarray-based platform.

Agendia told PGx Reporter this week over e-mail that the company will continue to accept both fresh and paraffin-embedded specimens for analysis. The company uses Asuragen's FDA-cleared RNA isolation kit RNARetain for both FFPE and fresh tissue samples.

"Fresh is best for discovery and validation of new assays and technology and Agendia will always start in fresh [specimens] for unbiased selection of biomarkers," a company spokesperson said.

The spokesperson noted that Agendia considered some issues with handling FFPE specimens, such as cross-linking and RNA degradation, when adding this capability to its test offerings. "FFPE needs to be under strict regulation and guidance of use," the spokesperson said.

Agendia has validated the concordance and reproducibility of its tests on FFPE samples, but the spokesperson said the company could not release details of these studies since it is submitting the data to the FDA.

"FFPE is substantially equivalent to fresh [specimens] for the Symphony assays (MammaPrint, BluePrint, and TargetPrint)," the spokesperson said via e-mail.

The spokesperson added that the American Society for Clinical Oncology now recommends that tissue be fixed in formalin within an hour of removal, and that the company developed a collection process that "does not compromise the specimen."

The company has also updated the amplification method used for its tests. "Agendia was also able to show substantially equivalent (data) for FFPE vs. fresh specimens" using these new methods, the spokesperson said. "Data show [that the] … new technology [is] as good as and concordance is substantially equivalent [to a] CLIA validated LDT."

MammaPrint was the first in vitro diagnostic multivariate index assay to receive clearance from the FDA. Agendia is planning to seek FDA clearance for MammaPrint's use with FFPE samples. According to the company, TargetPrint and BluePrint do not require FDA clearance because they are Class I, low-risk devices under FDA regulations.

"Agendia is in the process of voluntarily bringing all of its products through the FDA clearance process, expanding the product claims appropriately," the Agendia spokesperson said, adding that the company plans to submit BluePrint for regulatory approval even though the test is exempt from having to garner FDA clearance as a Class I device. TheraPrint is not yet commercially available.

The ability to analyze FFPE specimens could help Agendia gain some traction in the breast cancer testing market. Industry observers have viewed the fact that the test only analyzed fresh tissue as a limitation that would bar adoption in the US, where samples are commonly preserved in paraffin.

Although Agendia plans to stick with fresh specimens for discovery of biomarkers and validation of its tests, many experts in the field believe that since archived FFPE samples are more widely accessible, they can more readily facilitate retrospective studies for investigating gene-expression patterns linked to diseases.

The market leader in the breast cancer recurrence testing sector, Genomic Health's Oncotype DX, is an RT-PCR-based test that analyzes FFPE samples. The company believes Oncotype DX falls under FDA's ongoing "enforcement discretion" policy for LDTs, and has not sought approval for the test from the agency.

Have topics you'd like to see covered in Pharmacogenomics Reporter? Contact the editor at tray [at] genomeweb [.] com.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.