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Molecular Testing for Benign PEComa

Last updated Aug. 7, 2019

Approved by: Krish Tangella MD, MBA, FCAP

Molecular Testing for Benign PEComa is a genetic test that is helpful in aiding a diagnosis of benign PEComa.

What are other Names for this Test? (Equivalent Terms)

  • Gene Mutation Analysis for Benign PEComa
  • Test for Molecular Diagnosis of Benign PEComa

What is Molecular Testing for Benign PEComa? (Background Information)

  • Molecular Testing for Benign PEComa is a genetic test that is helpful in aiding a diagnosis of benign PEComa. The lab test results may also be subsequently useful in taking appropriate treatment decisions
  • PEComa is a group of soft tissue tumors that show perivascular epithelioid-cell (PEC) differentiation. PEComa tumors may be benign, malignant, or they may be of uncertain malignant potential
  • Benign PEComa tumors can be associated with a syndrome (tuberous sclerosis) in some cases. In a majority of cases, it may not be associated with a syndrome or genetic disorder. The cause of tumor formation is due to genetic defects or mutations
  • It can occur at various locations in the body, such as the abdominal cavity, pelvic region (uterus in women), and the gastrointestinal tract. Small-sized tumors may not present any significant signs and symptoms, while large tumors may compress the surrounding organs and structures causing pain and mass effect

The cause of benign PEComa is due to genetic mutations. Currently, studies indicate defects in the following genes:

  • TSC2 and TFE3
  • A gene fusion (involving the SFPQ and TFE3 genes) was noted in one case of PEComa tumor

Additionally, the following abnormalities may be noted:

  • Mutations in chromosome 16 due to loss of 16p (short arm)

The above genetic abnormalities can be detected using molecular studies, which may play a significant role in identifying the tumor type, and in some cases, helping the healthcare provider take appropriate treatment decisions.

The molecular testing, in general, can be performed using a variety of methods. Some of these methods include:

  • In situ hybridization technique, such as fluorescence in situ hybridization (FISH)
  • Immunohistochemistry (IHC)
  • Next-generation sequencing (NGS)
  • Polymerase chain reaction (PCR)
  • Comparative genomic hybridization (CGH)
  • Karyotyping including spectral karyotyping
  • mRNA analysis
  • Tissue microarrays (TMAs)
  • Southern blot test
  • Northern blot test
  • Western blot test
  • Eastern blot test

The methodology used for benign PEComa may vary from one laboratory to another. 

Note: Molecular testing has limitations due to the molecular method and genetic mutational abnormalities being tested. This can affect the results on a case-by-case basis. Consultation with your healthcare provider will help in determining the right test and right molecular method, based on individual circumstances.

What are the Clinical Indications for performing the Molecular Testing for Benign PEComa Test?

Molecular Testing for Benign PEComa is undertaken in the following situations:

  • To assist (and in some cases, confirm) the initial diagnosis of benign PEComa
  • To distinguish other tumors/conditions that have similar histological features, when examined by a pathologist under the microscope
  • To help in determining treatment options
  • To confirm recurrence of the tumor: Tumor recurrence can either be at the original tumor site, or at a distant location (away from the initial site)

How is the Specimen Collected for Molecular Testing for Benign PEComa?

Following is the specimen collection process for Molecular Testing for Benign PEComa:

The specimen sample requirements may vary from lab to lab. Hence, it is important to contact the testing lab for exact specimen requirements, before initiating the testing process.

  • Sample on which the test is performed may include:
    • Fresh tumor tissue during biopsy
    • Formalin-fixed paraffin-embedded solid tumor tissue (FFPE tumor tissue), often referred to as paraffin block of the tumor
    • Unstained tissue slides
  • Process of obtaining the sample: As outlined by the laboratory testing facility
  • Preparation required: As outlined by the laboratory testing facility


  • In some cases, a different source of specimen (such as peripheral blood, bone marrow biopsy specimen, or other body fluids) may be acceptable to the laboratory performing the test
  • Occasionally, additional samples may be required to either repeat the test or to perform follow-up testing
  • Depending on the location of testing, it may take up to 2 weeks’ turnaround time, to obtain the test results
  • Many hospitals preserve the paraffin blocks for at least 7 years. In general, older paraffin blocks (over 5 years) may affect the detection of specific mutations, due to degradation of the tumor specimen over time

Cost of Molecular Testing for Benign PEComa:

  • The cost of the test procedure depends on a variety of factors, such as the type of your health insurance, annual deductibles, co-pay requirements, out-of-network and in-network of your healthcare providers and healthcare facilities
  • In many cases, an estimate may be provided before the test is conducted. The final amount may depend upon the findings during the test procedure and post-operative care that is necessary (if any)

What is the Significance of the Molecular Testing for Benign PEComa Result?

The significance of Molecular Testing for Benign PEComa is explained:

  • Presence of a positive test result helps aid, and in some cases, confirm the diagnosis of benign PEComa
  • The result can help exclude other tumors with similar histological features
  • It can help determine the prognosis of the patient
  • In some cases, the test results may help in taking treatment decisions

The laboratory test results are NOT to be interpreted as results of a "stand-alone" test. The test results have to be interpreted after correlating with suitable clinical findings and additional supplemental tests/information. Your healthcare providers will explain the meaning of your tests results, based on the overall clinical scenario.

Additional and Relevant Useful Information for Molecular Testing for Benign PEComa:

  • Many laboratories may not have the capability to perform this test. Only highly-specialized labs with advanced facilities and testing procedures may perform this test
  • Additional mutations are still being discovered in many of these tumors. This may further contribute towards tumor diagnosis and treatment. Please consult with your healthcare provider for any information updates

Certain medications that you may be currently taking may influence the outcome of the test. Hence, it is important to inform your healthcare provider of the complete list of medications (including any herbal supplements) you are currently taking. This will help the healthcare provider interpret your test results more accurately and avoid unnecessary chances of a misdiagnosis.

Please visit our Laboratory Procedures Center for more physician-approved health information:


References and Information Sources used for the Article:

Helpful Peer-Reviewed Medical Articles:

Reviewed and Approved by a member of the DoveMed Editorial Board
First uploaded: March 19, 2017
Last updated: Aug. 7, 2019