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PTPN11 Mutation Analysis Test

Last updated March 18, 2018

Approved by: Krish Tangella MD, MBA, FCAP

The PTPN11 Mutation Analysis Test detects abnormalities in the PTPN11 gene. It is used to diagnose cancer. It also aids in the treatment of cancer by guiding chemotherapy drug selection.

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

  • BPTP3 Mutation Analysis Test
  • Protein Tyrosine Phosphatase, Non-Receptor type 11 (Noonan Syndrome 1) Mutation Analysis Test
  • SHP2 Phosphatase Mutation Analysis Test

What is PTPN11 Mutation Analysis Test? (Background Information)

  • PTPN11 mutation refers to an alteration in the PTPN11 gene. It is associated with a wide range of cancers, including lung, prostate, breast, and other cancers
  • The PTPN11 gene gives instructions for a protein called SHP-2. SHP-2 is important for communication between cells. It activates a signal transmission pathway called the RAS/MAPK pathway inside cells. This pathway enacts changes in the cell that stimulate growth and division.
  • Normally, SHP-2 receives input from chemical signals outside the cell, and only then does it stimulate growth and division by activating RAS/MAPK pathway
  • Mutations in the PTPN11 gene may result in a SHP-2 protein that is overactive. This overactive protein activates RAS/MAPK independently of outside signals, causing uncontrolled growth of the cell, resulting in cancer
  • The PTPN11 Mutation Analysis Test detects abnormalities in the PTPN11 gene. It is used to diagnose cancer. It also aids in the treatment of cancer by guiding chemotherapy drug selection

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 PTPN11 Mutation Analysis Test?

Following are the clinical indications for performing the PTPN11 Mutation Analysis Test:

  • A characteristic facial appearance
  • Short stature
  • Heart defect present at birth (congenital heart defect)
  • A broad or webbed neck
  • Minor eye problems, such as strabismus, in up to 95% of individuals
  • Bleeding problems, such as a history of abnormal bleeding or bruising
  • An unusual chest shape with widely-spaced and low-set nipples
  • Developmental delay of varying degrees, but usually mild
  • In males, undescended testes (cryptorchidism)
  • Fatigue
  • Abdominal pain
  • Unexplained weight loss

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 PTPN11 Mutation Analysis Test?

Following is the specimen collection process for PTPN11 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 PTPN11 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 PTPN11 Mutation Analysis Test Result?

The presence of an alteration in the PTPN11 gene indicates a positive result for the PTPN11 Mutation Analysis Test. This may point to a diagnosis of any of the following:

  • Lung cancer
  • Breast cancer
  • Prostate cancer
  • Noonan syndrome
  • Metachondromatosis

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:

  • The PTPN11 gene is found in location 12q24.13 i.e., the long (q) arm of chromosome 12 in position 24.13
  • 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, 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: May 29, 2017
Last updated: March 18, 2018