• Test Code:
    6515
  • Department:
    Solid Tumors Cancer Cytogenetics
  • Test Synonyms:
    Glioma arrayGlioma copy number analysisGlioma gene/targeted region
  • CPT Code(s):
    81406
Background:

Based on the WHO 2016 classification of gliomas (Louis et al. 2016) subtyping, therapeutic regimen selection, and response to therapy may be informed using molecular techniques, such as IDH mutation studies and chromosomal microarray for detection of relevant copy number changes.

Chromosomal microarray has recently supplanted fluorescent in situ hybridization (FISH) for detection of copy number changes in glioma because microarray can detect the same changes at higher resolution, and can also, for instance, discriminate whole chromosome arm loss of 1p and 19q from the smaller deletions detected by FISH.  Additionally, the SNP microarray used here can detect copy number neutral absence of heterozygosity (AOH), which is not detectable by FISH and may provide information relevant to the mutation status of genes in the region.  Such copy number and SNP analysis can aid classification and have prognostic implications (Louis et al. 2016, Crespo et al. 2011, Cimino et al. 2017, Buckner et al. 2017).

Currently, the Glioma Microarray Targeted Gene Panel focuses on:

  1. Deletion or LOH of chromosome 1p
  2. Deletion or LOH of chromosome 19q
  3. EGFR amplification or gain of chromosome 7
  4. Deletion or LOH of chromosome 10q or monosomy 10 (including both PTEN and DMBT genes)
  5. Deletion of CDKN2A/B (9p21)
  6. Chromosome 6 monosomy
  7. MYC amplification
  8. MYCN amplification
  9. CDK4 amplification
  10. CDK6 amplification
  11. CCND1 amplification
  12. CCND2 amplification
  13. PDGRFA amplification
  14. MET amplification

Methodology:

After pathologist review and tumor identification, DNA is macro-dissected from FFPE slides, isolated, fluorescently labeled and hybridized (with labeled reference DNA) to an Oxford Genome Technology-designed CCMC oncology array, printed by Agilent.  The CCMC+SNP array is comprised of a collection of oligonucleotide probes covering 495 oncology-associated genes at gene-level resolution, plus region-specific and backbone probes; additionally, SNP probes are used to determine copy number neutral (LOH); 180,000 elements in total (oligos+SNP) on each array.

*Please note: depending on oligo/SNP coverage, additional genes and areas may be interrogated at request.

Specimen Requirements:

  • Unstained FFPE slides at room temperature.
  • Preferred slice thickness is 5 micrometer on positively charged slides.
  • Please submit 10 unstained slides; 15 sections for small biopsies.
  • Contact Client Services with questions.
  • Tumor samples should be selected from viable areas, with as little normal or necrotic material as possible.
  • After collection, keep at room temperature until shipping.
  • Contact Client Services at (855) 535-1522 for shipping kits and instructions.
A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include details clinical information.

Test Performed (Days):

Weekly

Turn Around Time:

7-12 Days - Contact Lab at 855-KDL-1LAb (535-1522)

Shipment Sensitivity Requirements:

  • Keep specimen at room temperature during transit.
  • Do not use the cold pack provided in the KDL shipping kit.
  • Ship the specimen overnight express, using the FedEx priority overnight label provided.

References:

  • Louis et al. 2016 Acta Neuropath 131(6)
  • Cimino et al. 2017 Acta Neuropath Commun 5(1).
  • Buckner et al. 2017 Nat Rev Neurol 13(6).
  • Crespo et al. 2011 J Mol Diag 13(6).

Additional Info: