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ATRX Mutation Analysis Test

Last updated July 26, 2019

Approved by: Krish Tangella MD, MBA, FCAP

The ATRX Mutation Analysis Test detects abnormalities in the ATRX gene. It is used to guide therapy for cancer by aiding in the selection of therapeutic drugs and disqualifying certain drugs from being used.

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

  • ATRX Gene Mutation Test
  • ATRX Gene Sequencing Test
  • ATRX Mutation Test

What is ATRX Mutation Analysis Test? (Background Information)

  • ATRX mutation is an alteration in the ATRX gene, which gives instructions for the ATRX protein (which is also called X-linked helicase II, X-linked nuclear protein, or XNP)
  • ATRX mutations are associated with the following conditions:
    • Grades II and III astrocytomas (71% of the cases)
    • Glioblastoma (71% of the cases)
    • Oligoastrocytomas (68% of the cases)
    • Pancreatic neuroendocrine tumors (19% of the cases)
    • Myelodysplastic syndrome (or MDS, in 13% of the cases)
    • Endometrial tumors (10% of the cases)
    • Colon cancer (8% of the cases)
    • Lung cancers (7% of the cases)
  • The ATRX protein plays a role in regulating protein production. Proteins are normally produced by specialized cellular machinery using instructions provided by the genetic blueprint
  • Access to a given region of the genetic blueprint, and thus, the extent of production of the protein associated with that region of DNA, is tightly controlled
  • The ATRX protein helps control the availability of certain regions of DNA to the protein production machinery, and hence, the degree to which those regions of DNA yield protein products
  • Mutations in the ATRX gene may cause defects in the ATRX protein. The ATRX protein is involved in regulating production of proteins involved in cellular growth and division. Thus, defects in the ATRX protein may lead to uncontrolled cell growth and division, and hence, to cancer
  • The ATRX Mutation Analysis Test detects abnormalities in the ATRX gene. It is used to guide therapy for cancer by aiding in the selection of therapeutic drugs and disqualifying certain drugs from being used

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 the test 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 ATRX Mutation Analysis Test?

Following are the clinical indicators for performing the ATRX Gene Mutation Analysis Test:

  • Monitoring cancer therapy
  • Assessing treatment options for brain, lung, colon, and other cancers

In general, the molecular genetic testing is undertaken in the following situations:

  • To assist (and in some cases, confirm) the initial diagnosis
  • 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 ATRX Mutation Analysis Test?

Following is the specimen collection process for ATRX Mutation Analysis Test:

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 ATRX Mutation Analysis Test:

  • 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 ATRX Mutation Analysis Test Result?

•A positive value for the ATRX Mutation Analysis Test may disqualify certain therapeutic drugs from being used to treat brain, lung, colon, and other cancers

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:

  • Mutations in the ATRX gene often occur alongside mutations in the IDH1 and IDH2 genes
  • 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

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: Dec. 16, 2016
Last updated: July 26, 2019