Background:
Central nervous system tumor diagnosis relies on microscopic examination of tumor tissue, along with identification of signature genetic alterations that define certain brain tumor subtypes. Genome-wide DNA methylation profiling is an adjunct to conventional histochemical and molecular testing that can provide useful information for diagnosis and risk stratification in brain and spinal cord tumors, particularly in challenging or histologically ambiguous cases (1). Note that DNA copy number (gains, losses and amplifications) and MGMT promoter methylation status may also be observed using this technique (1) and will be reported.
The Knight Diagnostic Laboratories uses the Infinium MethylationEPIC platform from Illumina to generate genome-wide DNA methylation output data, which is then classified according to the German Cancer Research Center brain tumor methylation and copy number classifier (1,2). The classifier output is interpreted in the context of the histology and other available molecular results for final interpretation.
Methodology:
After pathological identification of tumor cells from FFPE or fresh frozen tissue, tumor cells are isolated by microdissection and DNA is extracted and processed according to the Infinium MethylationEPIC 450 BeadChip array kit instructions (Illumina). Data is analyzed and classified using the German Cancer Research Center brain tumor methylation and copy number classifier and genome-wide methylation, MGMT promoter methylation, and genome-wide copy number data are interpreted and reported within the context of histology and other relevant clinical and laboratory findings.
Specimen Requirements:
- Tumor samples should be selected from viable areas, with as little normal or necrotic material as possible.
- It is preferable to collect the specimen before initiation of chemotherapy in the patient.
- FFPE Slides: Specimen Requirements: A paraffin block or 10-20 unstained FFPE slides at room temperature. Preferred slice thickness is 5 micrometer on positively charged slides.
- Fresh Tumor Samples: Tumor specimens of at least 0.5 cm3 (up to 3 inches in diameter) are immediately collected with sterile methods into closable containers with sterile transport medium.* Needle biopsies will be accepted, but are often difficult to grow. Deliver the specimen in transport medium to the laboratory within a day, if possible, with decreased success rates as specimens are delayed in transit. Protect sample from temperature extremes during shipping.
*Sterile Ringer’s solution, either lactated or non-lactated and sterile isotonic saline are alternatives, if no complete RPMI is available. Contact Client Services for more information on media requirements.
• Unacceptable specimens are acellular, necrotic specimens, septic specimens, specimens in fixative, or specimens collected more than one week previously.
A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include detailed clinical information.
Test Performed (Days):
weekly
Turn Around Time:
2-3- weeks
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.
• Contact Client Services at (855) 535-1522 for shipping kits and instructions.
References:
- Capper D et al. Practical implementation of DNA methylation and copy-number-based CNS tumor diagnostics: the Heidelberg experience. Acta Neuropathol. 2018 Aug;136(2):181-201. PMID 29967940.
- Capper D et al. DNA methylation-based classification of central nervous system tumors. Nature 2018 Mar22;555(7697):469-474. PMID 29539639.
Additional Info: