KIT and PDGFRA GIST

Please note that KIT and PDGFRA testing is intended for solid tumors, for testing related to hematologic malignancies, please order - Heme Single Gene by NGS [HCAPSG]. Consultation with a Director can be requested to determine the appropriate testing. Please contact the laboratory at 206-598-6429 for further questions.

Mutations in KIT or PDGFRA are observed in ~85 % of gastrointestinal stromal tumors (GIST). Activating mutations in KIT and PDGFRA have been shown to be responsive to imatinib and resistance mutations have also been described. Tissues will be evaluated for mutations in KIT (exons 9, 11, 13, and 17) and PDGFRA (exons 12 and 18).

Mutations in KIT or PDGFA are observed in ~85 % of gastrointestinal stromal tumors (GISTs) and can be associated with response to tyrosine kinase inhibitors such as imatinib. The approximate distribution of mutations is 62% KIT exon 11, 9% KIT exon 9, 6% PDGFA exon 18, and 1% PDGFR exon 12. Very rare activating mutations, and resistance mutations are observed in KIT exons 13 and 17. GIST patients with KIT Exon 9 mutations may benefit from higher doses of imatinib (800mg per day vs. 400mg per day). No significant difference has been observed between 400mg and 800mg imatinib dosing for GIST patients with exon 11 mutations.

Next-generation sequencing.

Coding and flanking intronic regions of selected exons of KIT (including exons 8, 9, 11, 13, and 17), and PDGFRA (including 12 and 18) are amplified and sequenced bidirectionally according to the test indication as outlined above. The reference sequences for the KIT and PDGFRA coding regions are NM_000222 and NM_006206, respectively, with nucleotide 1 corresponding to the A of the ATG initiation codon. The genomic reference sequence is the GRCh37 (hg19, Feb. 2009) of the human genome assembly. This test was developed and its performance characteristics determined by the Department of Laboratory Medicine at the University of Washington.

Requirements for Specimen Selection

• To ensure clinically relevant results, the most recent and/or metastatic sample is preferred to older specimens, provided sufficient tumor is present (see point 2).
• To ensure detection of all types of mutations there should be at least 10% tumor cells in the tissue area processed for DNA for mutation detection and 20% tumor cells for microsatellite instability evaluation. If there is more than one tissue block, please provide the block that has the greatest percentage of neoplastic nuclei.
• Tissue samples and pathology reports will be reviewed by directors upon receipt for acceptability prior to testing. Director consultation for tissue selection is available if needed (contact Genetics lab).

Specimen Types

Tissue samples

Send one of the following:

1. Slides: 1 slide at 4-micron thickness stained with hematoxylin-and-eosin (H&E) AND 10 unstained, non-baked slides at 10-micron thickness (a minimum of 5 unstained slides is acceptable). Unstained slides can be on charged or uncharged slides.
2. Tissue Blocks: Provide complete formalin-fixed tissue block containing tumor tissue. Tissue block will be returned at completion of testing.
3. Fresh/frozen tissue: 5 microgram tissue in cell culture medium or frozen tissue stored at -20C. Tumor percentage will not be determined prior to sequencing studies.

NOTE: In order to ensure that enough DNA is obtained, the minimum acceptable tissue area is 10 square millimeters when ten 10-micron slides are supplied (1 cubic millimeter of tissue).

Purified DNA

5 micrograms ANDa reference hematoxylin-and-eosin (H&E) stained slide and pathology report required.

Bone Marrow

1 to 2 mL Bone Marrow in LAVENDER TOP (EDTA) tube

Blood

6 mL blood in LAVENDER TOP (EDTA) tube.

Alternative specimens may be acceptable with approval (contact: 206-598-1149).

For ADD-ON after prior testing, contact Genetics lab.

Unacceptable samples

We cannot accept decalcified samples or tissue samples treated with fixatives other than formalin.

Quantity:

Requested:

• Tissue: 10 unstained slides (10-micron thickness) plus one H&E-stained slide.
• Extracted DNA: 5 microgram Bone Marrow: 2 mL
• Blood: 6 mL

Minimum:

• Tissue: 5 unstained slides (10-micron thickness) plus one H&E-stained slide.
• Extracted DNA: 100-250 nanograms Bone Marrow: 1 mL
• Blood: 3 mL

Genetics Requisition

Providers with access to the UW implementation of Epic (i.e., FHCC, HMC, SCCA, UWMC, UWNW) may order this test using the order "UW Genetics and Solid Tumor Test Request." See tip sheet for more information (internal link).

Attach a copy of the pathology report for the tumor sample being submitted.

Hold slides or tissue blocks at room temperature.

Outside Laboratories: Ship at room temperature.

Stability: unstained slides or tissue blocks stable at room temperature for at least 2 years.

Hold slides or tissue blocks at room temperature.

Outside Laboratories: Ship at room temperature.

Stability: unstained slides or tissue blocks stable at room temperature for at least 2 years.