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Molecular Testing for Gastrointestinal Stromal Tumor

Last updated June 19, 2019

Approved by: Krish Tangella MD, MBA, FCAP

Molecular Testing for Gastrointestinal Stromal Tumor is a genetic test that is helpful in aiding a diagnosis of gastrointestinal stromal tumor.

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

  • Gene Mutation Analysis for Gastrointestinal Stromal Tumor
  • Molecular Testing for GIST
  • Test for Molecular Diagnosis of Gastrointestinal Stromal Tumor

What is Molecular Testing for Gastrointestinal Stromal Tumor? (Background Information)

  • Molecular Testing for Gastrointestinal Stromal Tumor is a genetic test that is helpful in aiding a diagnosis of gastrointestinal stromal tumor. The lab test results may also be subsequently useful in taking appropriate treatment decisions
  • A gastrointestinal stromal tumor (GIST) is a type of tumor that occurs in the gastrointestinal tract. The most common location of this tumor is the stomach or the small intestine
  • The origin of the tumor is uncertain. Some researchers believe that these tumors originate from a special type of cells that are present in the gastrointestinal tract, called the interstitial cells of Cajal (ICCs)
  • GIST can either be benign or malignant, depending on various characteristics. Also, most tumors occur randomly, while some originate due to a family history of the condition

The cause of gastrointestinal stromal tumor is due to genetic mutations. Currently, studies indicate defects in the following genes:

  • KIT
  • BRAF
  • CDKN2A and CDKN2B (both showing 9p21 loss)

Additionally, the following chromosomal aberrations (loss) may be noted:

  • Partial loss or monosomy of chromosome 14 with/without partial loss or monosomy of chromosome 22
  • Mutations in chromosome 1 due to deletion in 1p (short arm)
  • Mutations in chromosome 9 due to deletions in 9p (short arm) and 9q (long arm)
  • Mutations in chromosome 10 due to deletions
  • Mutations in chromosome 11 due to deletion in 11p (short arm)
  • Mutations in chromosome 13 due to deletion in 13q (long arm)

Additionally, the following chromosomal aberrations (gains) may be noted:

  • Mutations in chromosome 5 causing gains/amplification on 5p (short arm)
  • Mutations in chromosome 3 causing gains/amplification on 3q (long arm)
  • Mutations in chromosome 8 causing gains/amplification on 8q (long arm)
  • Mutations in chromosome 17 causing gains/amplification on 17q (long 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 gastrointestinal stromal tumor 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 Gastrointestinal Stromal Tumor Test?

Molecular Testing for Gastrointestinal Stromal Tumor is undertaken in the following situations:

  • To assist (and in some cases, confirm) the initial diagnosis of gastrointestinal stromal tumor
  • 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 Gastrointestinal Stromal Tumor?

Following is the specimen collection process for Molecular Testing for Gastrointestinal Stromal Tumor:

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 Embryonal Rhabdomyosarcoma:

  • 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 Gastrointestinal Stromal Tumor Result?

The significance of Molecular Testing for Gastrointestinal Stromal Tumor is explained:

  • Presence of a positive test result helps aid, and in some cases, confirm the diagnosis of gastrointestinal stromal tumor
  • 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.

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:

Helpful Peer-Reviewed Medical Articles:

Reviewed and Approved by a member of the DoveMed Editorial Board
First uploaded: March 8, 2017
Last updated: June 19, 2019