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Familial Gastrointestinal Stromal Tumors (GISTs) via the PDGFRA Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
PDGFRA 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8025PDGFRA81479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Yuan Xue, PhD

Clinical Features and Genetics

Clinical Features

Gastrointestinal stromal tumors (GISTs) are rare mesenchymal tumors found in the gastrointestinal tract. In most cases, GISTs spontaneously arise due to somatic mutations in the KIT gene, and less frequently in the PDGFRA gene. Families with GISTs and germline mutations in the KIT and PDGFRA genes have been described. Familial GISTs are often distinct from sporadic GISTs in that they are multiple in number, smaller in size, and present hyperplasia of interstitial cells of Cajal (ICC). Individuals with PDGFRA mutations show clinical manifestations similar to patients with KIT germline mutations, including dysphagia, hyperpigmentation and urticaria pigmentosa; however patients with germline PDGFRA mutations have distinct clinical features, such as large hands, lipomas, intestinal neurofibromatosis, and small intestine fibrous tumors. (Postow and Robson. Clinical Sarcoma Research 2:16, 2012) . In addition, patients with a germline PDGFRA mutation appear to have better outcomes compared to individuals with KIT germline mutations (Maleddu et al. Journal of Translational Medicine 9:75, 2011; Antonescu. Seminars in Diagnostic Pathology 23:63-69, 2006). Interestingly, individuals who are positive for either KIT and PDGFRA tumor mutations are treated with Imatinib, a KIT and PDGFRA inhibitor, which has been successfully used in the treatment of metastatic GISTs (Lasota and Miettinen. Histopathology 53, 245–266, 2008). Other diseases in which germline PDGFRA mutations are present include Hypereosinophilic syndrome, Vitiligo vulgaris, and isolated cleft palate.

Genetics

Familial GISTs are inherited as an autosomal dominant disease caused by mutations in KIT and PDGFRA. While the majority of mutations are found in the KIT gene, several families have been found to have causative mutations in the PDGFRA gene. PDGFRA encodes a trans-membrane receptor that belongs to the type III tyrosine kinase family whose natural ligands are stem cell factor (SCF) and platelet derived growth factor (Maleddu et al., 2011). Ligand binding promotes autophosphorylation of the PDGRA receptor and activation of downstream targets, such as the Ras/MAP kinase, Rac/Rho-JNK, PI3K/AKT, and SFK/STAT signaling networks (Antonescu, 2006). These pathways are involved in cellular differentiation and growth. Deregulation leads to tumorigenesis. The majority of causative germline mutations in the PDFRA gene are missense mutations, and are mostly similar to those found in sporadic GISTs (Lasota and Miettinen, 2008). No consistent genotype-phenotypes correlations exist for Familial GISTs.

Clinical Sensitivity - Sequencing with CNV PG-Select

Approximately 90% of individuals with Familial GISTS will have a mutation in the KIT and PDGFRA genes. PDGFRA causative mutations are found in approximately 1/3 of patients who test negative for KIT mutations (Antonescu. Seminars in Diagnostic Pathology 23:63-69, 2006).

Testing Strategy

This test provides full coverage of all coding exons of the PDGFRA gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Candidates for this test are patients with a history of familial GISTs, and especially those who have tested negative for KIT germline mutations. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue. This test can also be used for testing PDGFRA mutation status in Hypereosinophilic syndrome, Vitiligo vulgaris, and isolated cleft palate.

Gene

Official Gene Symbol OMIM ID
PDGFRA 173490
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Citations

  • Antonescu. (2006). "Gastrointestinal stromal tumor (GIST) pathogenesis, familial GIST, and animal models." Seminars in Diagnostic Pathology 23:63-69. PubMed ID: 17193819
  • Lasota and Miettinen. (2008). "Clinical significance of oncogenic KIT and PDGFRA mutations in gastrointestinal stromal tumours." Histopathology 53, 245266. PubMed ID: 18312355
  • Maleddu et al. (2011). "The role of mutational analysis of KIT and PDGFRA in gastrointestinal stromal tumors in a clinical setting."Journal of Translational Medicine 9:75. PubMed ID: 21605429
  • Postow and Robson. (2012). "Inherited gastrointestinal stromal tumor syndromes: mutations, clinical features, and therapeutic implications." Clinical Sarcoma Research 2:16,. PubMed ID: 23036227

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.


Specimen Types

Specimen Requirements and Shipping Details

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ORDER OPTIONS

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2) Select Additional Test Options

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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