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Test ID: PDGFRA
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PDGFRA Mutation Analysis
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PDGFRA mutation detection by DNA sequencing.
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Useful For
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Screening for KIT and PDGFRA kinase mutations can be useful for patient management as different mutations can predict responsiveness to imatinib therapy. Predictive molecular biomarker in patients with GIST.
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Method name and description
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PCR amplification is done by using primers specific for exons 9, 11, 13, 17 and 18 of the KIT gene and exon 12 and 18 of PDGFRA gene. The resulting PCR products are purified and sequenced to look for the presence of mutations. Sequencing analysis is performed using Genetic analyzer.
Bidirectional DNA sequencing is used to determine the order of the nucleotide bases (adenine, guanine, cytosine, and thymine) in a molecule of DNA.
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Reporting name
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For GIST cases: Reflex testing for GIST (cKIT – PDGFRA mutation analysis).
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Clinical information
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Gastrointestinal stromal tumors (GISTs) can have activating mutations in either the KIT or PDGFRA genes. The immunostain for CD117 (c-KIT) does not give information on the location and type of mutation, and GISTs that contain activating mutations in PDGFRA are negative for c-KIT expression. Screening for KIT and PDGFRA kinase mutations can be useful in-patient management as different mutations can predict responsiveness to imatinib therapy. For example, mutation of exon 11 of the c-KIT gene comprises ~70% of all mutations and it is a strongest predictor of imatinib response.
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Specimen type / Specimen volume / Specimen container
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FFPE tissue:
Option 1: Tissue sections of 10X (5-7 µm) fixed on non-charged slides with an H&E stained slide with marked tumor area.
Option 2: Tissue curls of 6 sections (10 µm) collected in 2 mL tube (e.g. Eppendorf).
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Collection instructions / Special Precautions / Timing of collection
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Specimens are arranged from Sunday to Wednesday from the Anatomical Pathology Department to the Molecular Genetics Laboratory at room temperature.
Please avoid direct sun light exposure.
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Relevant clinical information to be provided
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The following points must be provided:
- The tumor rich area on the must be marked by a consultant pathologist.
- Tumor percentage.
- Cancer type.
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Storage and transport instructions
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The specimens are stored and transported at Room Temperature (16 - 25° C).
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Specimen Rejection Criteria
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Consistent with Diagnostic Genomic Division policies
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Biological reference intervals and clinical decision values
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Detected amplifications of the mutant target with mutant allele frequency >20% are referred as Detected.
No amplification of the mutant allele due to low mutant allele frequency (<20%) or due to absence of mutant target are referred as No mutation detected.
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Factors affecting test performance and result interpretation
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This test was validated for DNA extraction from FFPE, the FFPE process has effect on the DNA quality and might result on DNA degradation. In addition, PCR inhibitors due to FFPE fixation might affect the PCR amplification.
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Turnaround time / Days and times test performed / Specimen retention time
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Days Test is Performed: Arranged by laboratory Rota.
Single gene testing: 10 working days.
Reflex testing: 10 working days for the first test and an additional week (5 working days) for every following test.
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