Mutational Testing

Exon Mutations Affect Response Rate

Whether GIST tumors have mutations in the KIT or PDGFRA gene and the location of those mutations has proven to be the most powerful predictor of how a patient will respond to treatment with targeted drugs such as Gleevec and Sutent.

Mutational testing has become increasingly important over the years and is now recommended for metastatic and high-risk GIST patients (NCCN Task Force Report, 4-20101; ESMO clinical practice guidelines for diagnosis, treatment and follow-up, 20102). Despite these recommendations only about 6% of GIST patients in the United States have mutational testing performed3.

KIT & PDGFRA mutations in GIST: A to Z by Dr. Michael Heinrich

Looking for kinase mutations in GISTs: how, when and why? by Dr. Christopher Corless

KIT Mutational Status Predicts Clinical Response to Glivec in Patients With Metastatic GIST

Correlation of target kinase genotype with clinical activity of imatinib mesylate (IM) in patients with metastatic GI stromal tumors (GISTs) expressing KIT (KIT+)

Routine mutational testing and plasma level testing: The time has come

KIT exon mutations in GIST

The information in genes is divided into different sections called exons and introns. Exons contain coding information and introns do not. Mutations in different exons in the gene cause changes in shape in different parts of the KIT receptor. Mutations in the following exons of the c-kit gene are known to occur in GIST.

Exon 11 - This is the most commonly mutated exon in GIST. In phase II trials, exon 11 mutations were found in 68% of cases. Mutations in exon 11 generally respond to treatment with Gleevec better than mutations in other exons.

Exon 9 - Exon 9 mutations are the second most common mutation. In phase II trials, exon 9 mutations were found in 16% of cases. They occur in the small bowel and colon in about 98% of the patients that have an exon 9 mutation; however, they do NOT make up the majority of cases that occur in the small bowel or colon. In fact, about 2/3 of the cases that occur in the small bowel or colon are KIT exon 11 mutations. GISTs with exon 9 mutations have a lower response rate to Gleevec therapy when compared to exon 11 mutations and they seem to require a higher dosage of Gleevec. They also seem to respond fairly well to Sutent.

Exon 13 and exon 17 mutations are rare in GIST.

PDGFRA mutations in GIST

Some GIST tumor cells do not contain c-kit mutations. In about 5-8% of all GIST cases, a closely related gene, PDGFRA, is mutated. About 1/3 of the PDGFRA mutations may still respond to Gleevec and/or Sutent, but up to 2/3 of PDGFRA mutations do not respond to these drugs. These mutations occur in one specific spot in exon 18 of the gene and are called a D842V mutation (PDGFRA mutation, exon 18, D842V). A phase II trial for a specific D842V inhibitor, CP-868,596, opened in the United States in April, 2011 for advanced/metastatic GIST. Another phase II trial of a different type of drug, a monoclonal antibody, IMC-3G3, that inhibits PDGFRA, is expected to open in May, 2011 (NCT01316263).

Wild-type GIST

GIST tumors that do not have a mutation in KIT or PDGFRA are called "wild-type" GIST, although we are now finding that some of these tumors have mutations in other genes such as BRAF or SDH mutations (2007-2008). GIST with wild-type tumors do not respond as well as other types, but since some signaling may still occur through the KIT receptor treatment with Gleevec is beneficial in some cases. Gleevec however, is not a very potent inhibitor of wild-type KIT. More potent inhibitors of wild-type KIT, especially Sutent and Tasigna (nilotinib), may provide more benefit for wild-type GIST. Wild-type GIST has also been shown to overexpress a protein called IGF1R in about 2/3 of the cases studied. As a result, trials with IGF1R are being planned for GIST (2009). For more information see Wild-type GIST.

SDH and BRAF mutations

NOTE: Testing for SDH and BRAF mutations are not yet part of a standard mutational test. BRAF testing is available through both Oregon Health Sciences University (OHSU) and Memorial Sloan Kettering Cancer Center (MSKCC). SDH testing is available from the National Institutes of Health (NIH).

In 2007, Dr. P. Aidan Carney, Dr. Constantine Stratakis and other members of the Carney-Stratakis Dyad Consortium reported that some GIST patients have a familial type of GIST caused by mutations in one of the four genes involved in producing the succinate dehydrogenase (SDH) protein. This type of inherited mutation can result in a condition called Carney-Stratakis Syndrome. For additional information see Carney-Stratakis Syndrome.

Researchers at Memorial Sloan-Kettering Cancer Center (MSKCC) in New York have found a rare mutation in some GIST tumors. In a series of 61 patients with wild-type GIST, they found that three of them (5%) had mutations in a gene called BRAF. This same mutation, a “V600E” mutation in exon 15 of the BRAF gene, occurs frequently in melanoma. They also found the same mutation in one of 28 GIST patients that were resistant to Gleevec. For more information see MSK team finds rare new mutation. On August 17, 2011, the FDA approved an inhibitor of the BRAF V600E mutation, a drug called Zelboraf, for patients with advanced/metastatic melonoma. This drug is not approved for BRAF V600E mutation patients with other types of cancer including GIST.

KIT & PDGFRA gene mutation screening

Background Data and Interpretation

Testing for mutations in the KIT and PDGFRA genes is available through the Molecular Diagnostics Laboratory of Oregon Health & Science University (OHSU) and is increasingly becoming available in other labs. See below for a list of labs that we are aware of. This testing can provide physicians and their patients information on the likelihood of response to therapy with imatinib mesylate (STI571; Gleevec), as detailed below. Regardless of the test results, however, all patients in need of treatment should be offered the drug. Even among patients with tumors lacking a detectable KIT or PDGFRA gene mutation, the response to imatinib mesylate is higher than the response to traditional chemotherapy (<5%).

Approximately 80-85% of gastrointestinal stromal tumors (GISTs) have an oncogenic mutation in the gene encoding KIT tyrosine kinase. Another 5-7% of GISTs have a mutation in the gene encoding the related kinase PDGFRA (platelet-derived growth factor receptor alpha). KIT and PDGFRA mutations are mutually exclusive in GISTs. In both genes, the observed mutations result in expression of a mutant form of kinase that is constitutively “turned on” and helps drive the growth of the tumor. Approximately 10-15% of GISTs have no detectable KIT or PDGFRA gene mutation.

Based on an interim analysis of the CSTI-B2222 phase II trial of imatinib mesylate in the treatment of non-operable malignant GI stromal tumor, there is a relationship between the kinase mutation status of a GIST and the likelihood of drug response, as summarized in the table below.

In addition to having a higher rate of response to therapy, patients with GISTs harboring an exon 11 mutation have more durable responses and better overall survival than those with exon 9 mutations or those with no mutation detected in either gene.

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Methods

Testing is performed in two stages. KIT exons 9 and 11 are screened first, as approximately 80% of GISTs will have a mutation in one of these two exons. KIT exons 13 and 17, and PDGFRA exons 12 and 18 are screened in the second stage. If no mutations are found in these exons, the tumor is presumed to be “wild-type”, although there remains a small (less than 1%) possibility that a mutation was missed elsewhere in either gene.

DNA is extracted and purified from paraffin-embedded tumor tissue. The indicated exons of the KIT and PDGFRA genes are amplified by PCR, and the products are screened for mutations by denaturing HPLC (WAVE system, Transgenomic, Inc.). Based on analysis of over 400 GIST samples, the sensitivity and specificity of this combined HPLC plus sequencing approach are >98%.

How to Order the Test

Requests for KIT and PDGFRA mutation screening must originate from a pathologist or treating physician. One paraffin block of the tumor (either biopsy or surgical specimen) or 15 unstained sections of the tumor should be sent to address listed below. A copy of the original pathology report as well as the patient’s insurance information must be included.

KIT/PDGRRA Mutation Screening Service (Heinrich/Corless lab website)

View list of medical codes and charges for mutational screening to provide to your insurance provider

Other Mutational Testing Sites:

Expert Opinions: KIT & PDGFRA mutations in GIST: A to Z by Michael Heinrich, M.D.
Looking for kinase mutations in GISTs: how, when and why? by Christopher Corless, M.D., PhD.

References