81540 Oncology (tumor of unknown origin), mRNA, gene expression profiling by real-time RT-PCR of 92 genes (87 content and 5 housekeeping) to classify tumor into main cancer type and subtype, utilizing formalin-fixed paraffin-embedded tissue, algorithm reported

Name of the Procedure:

Oncology Tumor Profiling by mRNA Gene Expression (Real-Time RT-PCR)
Other names: Gene Expression Profiling, mRNA Tumor Classification

Summary

This procedure analyzes the gene expression of 92 specific genes in a tumor sample to classify it into its main cancer type and subtype. It utilizes formalin-fixed, paraffin-embedded tissues and a technique called real-time reverse transcription-polymerase chain reaction (RT-PCR). The results help identify the tumor even if its origin is unknown.

Purpose

The procedure aims to identify the type and subtype of a tumor whose origin is unknown by examining the activity of certain genes. The goal is to provide a more accurate diagnosis, which can guide appropriate treatment and management.

Indications

• Suspected cancer with unknown primary origin.
• Atypical tumor presentation that complicates diagnosis through standard histological techniques.
• Patients presenting with metastatic cancer without a known primary site.

Preparation

• No specific patient preparation is required for this procedure.
• The clinician will obtain a sample of the tumor, typically from a biopsy already performed.
• The tissue sample must be preserved in formalin and embedded in paraffin.

Procedure Description

1. A small sample of the tumor tissue, preserved in formalin and embedded in paraffin (FFPE), is prepared.
2. RNA is extracted from the FFPE tissue sample.
3. The extracted RNA undergoes reverse transcription to produce complementary DNA (cDNA).
4. Real-time RT-PCR is performed to quantify the expression levels of 92 genes (87 content and 5 housekeeping genes).
5. The expression data are analyzed using a specialized algorithm to classify the tumor into its main cancer type and subtype.
6. A report is generated detailing the classification results, which are then reviewed by the oncologist.

Duration

The procedure, from RNA extraction to final report generation, typically takes several days to a week.

Setting

The procedure is performed in a specialized laboratory equipped for molecular diagnostics.

Personnel

• Pathologists
• Molecular biologists
• Laboratory technicians
• Oncologists (for interpretation of results)

Risks and Complications

• Minimal risk directly associated with the profiling itself.
• Potential for inconclusive results if the RNA quality is poor.
• False negatives or positives depending on the variability of gene expression.

Benefits

• More accurate identification of the tumor type, leading to targeted and effective treatment plans.
• Faster diagnosis compared to traditional methods.
• Provides critical information for tumors that are difficult to classify otherwise.
• Results can be instrumental in guiding personalized medicine approaches.

Recovery

• There is no recovery period required for the procedure itself as it involves analysis of an already obtained tissue sample.
• Follow-up appointments may be needed to discuss results and treatment options.

Alternatives

• Immunohistochemistry (IHC)
• Next-Generation Sequencing (NGS)
• Fluorescence In Situ Hybridization (FISH)
• Pros of alternatives: Different techniques may provide complementary information.
• Cons of alternatives: May be more time-consuming, expensive, or less specific compared to gene expression profiling.

Patient Experience

• Since this procedure utilizes an existing biopsy sample, there are no additional physical experiences for the patient.
• Patients might experience anxiety while waiting for diagnosis results.
• Effective communication from healthcare providers can help manage patient expectations and provide support.