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Molecular Testing for Clear-Cell Sarcoma

Last updated Feb. 28, 2017

Molecular Testing for Clear-Cell Sarcoma is a genetic test that is helpful in aiding a diagnosis of clear-cell sarcoma.

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

  • Gene Mutation Analysis for Clear-Cell Sarcoma
  • Molecular Testing for CCS
  • Test for Molecular Diagnosis of Clear-Cell Sarcoma

What is Molecular Testing for Clear-Cell Sarcoma? (Background Information)

  • Molecular Testing for Clear-Cell Sarcoma is a genetic test that is helpful in aiding a diagnosis of clear-cell sarcoma. The lab test results may also be subsequently useful in taking appropriate treatment decisions
  • Clear-cell sarcoma (CCS) of soft tissue is an infrequent, aggressive, but often rapidly developing tumor, without any presenting signs and symptoms in the early stages
  • The tumor occurs in the soft tissues, especially in the tendons and aponeurosis (flat, fibrous membranes that anchor muscles)
  • They are regarded as a kind of high-grade malignant cancer that spreads and infiltrates the surrounding tissues, tendons, muscles, and organs
  • CCS of soft tissue is seen to peak during 3rd and 4th decade (i.e., between 20-40 years). These tumors are normally located deep inside the body tissues, with common sites being the upper and lower limbs

The cause of clear-cell sarcoma is due to genetic mutations. Currently, studies indicate defects in the following genes:

  • EWSR1-ATF1 causing chromosomal translocation abnormality namely t(12;22)(q13;q12)
  • EWSR1-CREB1 causing chromosomal translocation abnormality namely t(2;22)(q33;q12)

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 clear-cell sarcoma 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 Clear-Cell Sarcoma Test?

Molecular Testing for Clear-Cell Sarcoma is undertaken in the following situations: 

  • To assist (and in some cases, confirm) the initial diagnosis of clear-cell sarcoma
  • 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 Clear-Cell Sarcoma?

Following is the specimen collection process for Molecular Testing for Clear-Cell Sarcoma:

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 required:
    • 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


  • Depending on the location of testing, it may take up to 2 weeks’ turnaround time, to obtain the test results
  • Occasionally, additional samples may be required to either repeat the test or to perform follow-up testing
  • 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 Clear-Cell Sarcoma:

  • 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 Clear-Cell Sarcoma Result?

The significance of Molecular Testing for Clear-Cell Sarcoma is explained:

  • Presence of a positive test result helps aid, and in some cases, confirm the diagnosis of clear-cell sarcoma
  • 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:

  • 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.

What are some Useful Resources for Additional Information?

The following DoveMed website link is a useful resource for additional information:


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


References and Information Sources used for the Article:

https://ghr.nlm.nih.gov/primer/testing/genetictesting (accessed on 02/17/2017)

https://www.cdc.gov/mmwr/preview/mmwrhtml/rr5806a1.htm (accessed on 02/17/2017)

http://www.nature.com/gim/journal/v10/n5/full/gim200852a.html (accessed on 02/17/2017)

http://pediatrics.aappublications.org/content/106/6/1494 (accessed on 02/17/2017)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097407/ (accessed on 02/17/2017)

https://www.ncbi.nlm.nih.gov/pubmed/19561568 (accessed on 02/17/2017)

http://sarcomahelp.org/clear-cell-sarcoma.html (accessed on 02/17/2017)

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Druker, B. J. Perspectives on the development of a molecularly targeted agent. Cancer Cell 1, 31–36 (2002)

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Pinkel, D., et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genetics 20, 207–211 (1998) doi:10.1038/2524

Speicher, M. R., et al. Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nature Genetics 12, 368–375 (1996) doi:10.1038/ng0496-368

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Goldblum, J. R., Weiss, S. W., & Folpe, A. L. (2013). Enzinger and Weiss's soft tissue tumors. Elsevier Health Sciences.

Weiss, S. W. (2012). Histological typing of soft tissue tumours. Springer Science & Business Media.

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Reviewed and Approved by a member of the DoveMed Editorial Board
First uploaded: Feb. 28, 2017
Last updated: Feb. 28, 2017