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Test Code LAB3970 Neoplasia Methylation Profiling

Important Note

This test is currently restricted to CNS tumors.

This test can only be ordered by placing a Pathology Add-on Request to a sample that has already been processed by the laboratory.

Synonyms

Hypermethylation, Hypomethylation, Methylation array, Methylome

Description

DNA methylation profiling is used to subclassify central nervous system (CNS) tumors. This test can classify CNS tumors based on the methylation profiling. The main output is a classification score (range 0-1) that indicates CNS tumor class. Testing is performed by UWMC - Montlake DLMP Clinical Genomics Laboratory.

Sample Requirements

Acceptable Specimen Types: Extracted DNA, Fresh or Frozen Tumor, FFPE Slides or Block, Tumor Culture

Fresh Frozen Tumor Tissue:

  • 50-150mg (0.15-2.0 cm3) fresh tissue snap-frozen. Store at -20°C. Ship on minimum of 10 lb of dry ice in insulated container by overnight courier.

FFPE Tumor Slides:

  • If tumor content is <70% send 10 unstained 10μm FFPE slides. Send one image of an H&E stained slide that has the area of tumor marked.
  • If tumor content is >70% send 10 x 10μm curls in two 1.5 mL tubes (5 per tube). Send one H&E stained slide for QC.
  • Include a copy of corresponding surgical pathology report.
  • Mail slides in a protected mailing container at room temperature and protect from excessive heat.

FFPE Tumor Block:

  • Please send curls or slides if possible. Contact lab (206-616-4062) if block is the only option.

Solid Tumor Cultures:

  • Two T-25 flasks of cultured tumor cells that are 80-100% confluent. Keep at room temperature.

Extracted DNA:

  • 3-10 micrograms (minimum 1 microgram) at a concentration of 100 nanograms per microliter (or higher), suspended in water. Keep at room temperature. We can only accept DNA isolated in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the College of American Pathologists and/or the Centers for Medicare and Medicaid Services.

Processing Instructions

Reject due to: See specimen type.

Spin: N

Aliquot: N

Temp: RT. If sample is received frozen, maintain and send on dry ice.

 

Storage location:

Specimen Type Temperature Storage Instructions
FFPE Blocks/Slides, Tumor Culture, Extracted DNA RT RT Sendouts Bin
Fresh Frozen Tumor Tissue -20°C or -70°C -20°C CPA Freezer, Sendouts Rack

Stability

Specimen Type Temperature    Time   
FFPE Blocks/Slides, Tumor Culture, Extracted DNA RT  
Fresh Frozen Tumor Tissue -20°C or -70°C  

Availability

STAT Performed TAT
N   2 - 3 w

Performing Laboratory

University of Washington Medical Center

Clinical Genomics Laboratory
University of Washington Health Sciences Building
Room H-561
1959 NE Pacific St
Seattle, WA 98195

Phone Number: (206) 520-4600

206-598–6429

Department

Department: Send Outs/Genetic

Phone: (206) 987-2563

Methodology

Methods Summary: Genomic DNA extraction from the patient specimen was performed according to manufactures instruction. For fresh/frozen specimen, Gentra Puregene Blood Kit or DNeasy Blood & Tissue Kit was used (Qiagen, Germantown, MD). For formalin-fixed paraffin-embedded (FFPE) tissue curls or sections mounted on slides, after macro-dissection to enrich for viable tumor content if needed, AllPrep DNA/RNA FFPE Kit was used (Qiagen, Germantown, MD). The DNA was bisulfite converted using EZ DNA Methylation Kit (Zymo Research, Irvine, CA), then restored using Infinium HD FFPE DNA Restore Kit for FFPE specimen (Illumina Inc, San Diego, CA), and subsequently processed using Infinium MethylationEPIC BeadChip v2.0 (Illumina Inc, San Diego, CA) according to manufactures instructions. The microarray was scanned using iScan reader (Illumina Inc, San Diego, CA). Intensity ratio data of the fluorescent signals were generated using iScan Control Software (Illumina Inc, San Diego, CA). Genome build GRCh37 was used. Signal processing and methylation-based CNS tumor classification analysis were performed using the Heidelberg Epignostix CNS Tumor Classifier v12.8 implemented through the epxCNS v1.1.3 analysis pipeline. Classification using methylation profiling is based on a published algorithm (Capper et al. Nature 2018). A score between 0 and 1 is generated for every class. All class prediction scores theoretically add up to 1. For a prediction, a methylation class score has to be above the cutoff of 0.9 (Capper et al., Acta Neuropathol. 2018).

Interferences and Limitations: This test has limited ability to classify tumors with low-level tumor content (<70% of cells with an abnormality). Small genetic alterations, such as point mutations, indels, small copy number alterations, balanced alterations, or copy neutral loss of heterozygosity, are not be detected by this analysis.

References:

Capper D, Jones DTW, Sill M, Hovestadt V et al., Nature. 2018 Mar 22;555(7697):469-474.

Capper D, Stichel D, Sahm F et al., Acta Neuropathol. 2018 Aug;136(2):181-210.

Bady P, Sciuscio D, Diserens AC et al., Acta Neuropathol. 2012 Oct;124(4):547-60. PMID: 22810491.

Send Out Instructions

Reference Test Name:

Neoplasia Microarray Analysis with DNA Methylation Profiling [UWMC Clinical Genomics Laboratory]
Reference Test Number: 1067
Instructions: Send out Monday - Friday with the UW courier.

CPT Codes

0020M