EoGenius Frequently Asked Questions

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What is “gene expression”?

Gene expression is the process by which the information encoded in a gene is used to direct the assembly of a protein molecule.

DNA is the blueprint which contains all the information needed to make an organism what it is. A gene is a functional part of the DNA which codes for a specific product (usually protein). DNA is located in the nucleus; however, protein synthesis takes place in the cytoplasm. For this to happen, the region of the DNA or the gene is copied or “transcribed” onto messenger RNA, which can cross over from the nucleus to the cytoplasm where the code is “translated” into protein. This is the process of gene expression. Regulation of gene expression allows a cell to produce the gene products as needed, e.g. the amount of insulin or thyroid hormone. Depending on need, the expression of the genes is either up-regulated (increased gene expression and therefore the product) or down-regulated (repressed gene expression and therefore the product).

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How does the EoGenius test use gene expression to suggest a diagnosis of EoE?

Marc E. Rothenberg, MD, PhD, and his group at Cincinnati Children’s Hospital first identified about 574 genes that showed “altered” expression (up- or down-regulated) in cases of eosinophilic esophagitis (EoE). From this set they identified a subset of genes that could identify EoE reliably from non-EoE patients. The test uses the “signature pattern” of this subset of genes and uses an algorithm based on the genes that are known to be up or down regulated in EoE to determine if the patient falls into the EoE or non-EoE group.

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What is the sensitivity and specificity of the EoGenius test?

Per Dr. Rothenberg’s study, which was primarily done on the pediatric population, the sensitivity is 96% and specificity is 98%.

A subsequent independent study conducted by Evan Dellon, MD, MPH, at University of North Carolina School of Medicine, was performed on adults and resulted in the following values:

  • Positive predictive value/PPV (probability that patients with a positive EoGenius test truly have EoE): 91%.
  • Negative predictive value/NPV (probability that patients with a negative EoGenius test truly do not have EoE): 90%.
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What percent of adult patients will have an indeterminate result by the EoGenius test?

Approximately 10–12% of adult patients are expected to receive an “Indeterminate” result.

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What are the limitations of the EoGenius test?

  • The results of the EoGenius test depend on the quality of the RNA, which can be adversely affected by the type of fixative (other than 10% neutral buffered formalin or RNAlater), duration of fixation (>48 hours), and conditions and duration of storage (>1 year).
  • FFPE sections should be freshly cut to avoid RNA degradation (<48 hours to start RNA extraction).
  • Although the performance characteristics of the test are good, there is a possibility of a false-positive or false-negative result.
  • The claims of this assay are based on retrospective clinical studies, which included fresh samples preserved in RNAlater as well as an FFPE comparison group using a smaller subset of samples.
  • The results of the assay should be interpreted in conjunction with pathologic findings and clinical context and should not be used alone to make therapeutic decisions.
  • The test has not been cleared or approved by the U.S. Food and Drug Administration, however FDA clearance or approval is not currently required for clinical use.
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If the EoGenius test uses RNA, why does it have to come from the esophagus (versus a swab, for example)?

The studies to date have been performed on esophageal biopsies, and the EoGenius test is validated on this tissue. It is not established that the test is viable for other sample types. The EoGenius test requires a good quality and quantity of RNA, which is difficult to obtain from a swab, and there is no evidence to date about the validity of such results. 

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Can specimens be processed from formalin jars directly?

Formalin is a fixative and penetrates the tissue to form bonds with the tissue components. The extraction process for the EoGenius test cannot get DNA or RNA from “wet” formalin specimens directly. The tissue has to go through routine processing, i.e., formalin fixation and paraffin embedding (FFPE), for the test to be performed.

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What type of specimen does Miraca need to run the assay?

The test requires only one type of specimen (block, curls, or fresh tissue in RNAlater) from one site (preferably mid-esophagus but specimens from upper and lower or random sites can be used).

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What additional information does Miraca need to run the assay?

Miraca needs the date of collection, site of biopsy, and type of sample (block or curls or fresh tissue in RNAlater) with the ID number from the processing lab, and an ICD-10 code (if available). A pathology report would be most helpful for Miraca to derive this data and to verify that the correct blocks or curls have been received.

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How long is a specimen stable or acceptable for testing?

For FFPE blocks: Best RNA retrieval occurs when the collection date is within a year of testing. Place the FFPE block in the small zip lock bag provided in the EoGenius kit. If you need to request this from an outside pathology lab (not Miraca), use Miraca’s Patient Material Request form.

For FFPE curls: A minimum of 80 microns should be cut (10 microns x 8 sections) and placed directly into the conical bottom empty tube in the kit. These are not slide sections. If you need to request curls from a third-party pathology lab, use a Patient Material Request form.

For RNAlater: A tissue biopsy at the time of procedure should be put into the round bottom tube in the kit which contains the RNAlater (labeled).

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What are the instructions for cutting curls or scrolls from an FFPE block?

  • Clean the microtome blade, chuck, and tray in between each block with 70% alcohol to prevent cross contamination.
  • Each microtome blade should be used only once on each edge to prevent cross contamination.
  • Clean forceps with 70% alcohol between blocks to prevent contamination.
  • Label the PCR tube (conical bottom tube) with the accession number and patient name.
  • All sections should be cut preferably at 10 microns. Discard the first 2 sections.
  • Cut a series (8–10) of sections. (Sections should be full face, be careful not to efface the block).
  • Using forceps, pick up the curls (sections or scrolls), and after visually matching the block and the labeled PCR tube, place curls in the labeled PCR tube.
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If my practice or center is an existing Miraca client, how can we order the EoGenius test?

  • EoGenius can be ordered up-front for cases provided to the Miraca laboratory. On your GI pathology requisition, select the EoGenius test in the SPECIAL REQUESTS section. If your practice uses an EMR with an interface to Miraca, enter EoGenius in the special requests section of your electronic pathology requisition.
  • The GI pathology team will select a block to be sent to Miraca’s Phoenix lab for the EoGenius test. To add EoGenius testing to an existing case for which Miraca already has the tissue, you do not need to use a separate kit—simply check the EoGenius test box on the requisition or enter it electronically.
  • If you choose to use separate fresh tissue for the EoGenius test, use the EoGenius kit, put the biopsy specimen directly into the RNAlater tube, complete the requisition, and send the kit to Miraca’s Phoenix lab directly.
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If my practice or lab is not a Miraca client, how can we order the EoGenius test?

  • If you want the EoGenius test performed on a case that was already collected and sent to another lab, use the EoGenius Patient Material Request form to get the block or curls and have them shipped to Miraca.
    • Alternatively, provide the EoGenius kit to the other pathology lab and have them ship the block or curls to us.
  • If you want to split samples at collection, send the formalin jars to your usual lab, and use the RNAlater in the EoGenius kit to send the RNAlater-preserved tissue to Miraca.
  • Please note that these instructions are for the EoGenius test only (without histologic interpretation).
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What is the turnaround time for the EoGenius test?

Currently the turnaround time for the EoGenius test is 7–10 days from date of receipt. Tissue processing and testing takes three days, and if repeats are needed, up to five days

How to Order the EoGenius Test

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Miraca Client Services Contact Information

Phone: 866.588.3280
Fax: 866.688.3280
Email: ClientServices@MiracaLS.com

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