Neoplasia Microarray Analysis with DNA Methylation Profiling [UWMC Clinical Genomics Laboratory]

single page view

General Information

Lab Name
Lab Code
1067
Description

DNA methylation profiling is used to subclassify central nervous system (CNS) tumors. This test can classify CNS tumors based on the methylation profiling and simultaneously detect large copy number variants. The main output is a classification score (range 0-1) that indicates CNS tumor class, a low resolution copy number plot, and MGMT promoter methylation status. Testing is performed by UWMC - Montlake DLMP Clinical Genomics Laboratory.

Epic Ordering:

  • Test Name: Lab Undefined Order
  • Order Code: LABUND
  • In the order Comments, describe the test "Neoplasia Microarray Analysis with DNA Methylation Profiling" and the performing laboratory "UWMC Clinical Genomics Lab"
  • A paper test request form must accompany the sample
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.

Forms & Requisitions

Outside Providers: CGL Neoplasia Test Request Form

Synonyms
Hypermethylation, Hypomethylation, Methylation array, Methylome

Interpretation

Method

Methods Summary: Genomic DNA extraction from the patient specimen is performed according to manufacturer's instruction. For fresh/frozen specimen, Gentra Puregene Blood Kit or DNeasy Blood & Tissue Kit is 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 is used (Qiagen, Germantown, MD). The DNA is 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 v1.0 (Illumina Inc, San Diego, CA) according to manufacturer's instructions. The microarray is scanned using iScan reader (Illumina Inc, San Diego, CA). Intensity ratio data of the fluorescent signals are generated using iScan Control Software (Illumina Inc, San Diego, CA). Genome build GRCh37 is used. The signal processing, methylation-based tumor classification and MGMT promoter methylation analysis are carried out using an in-house Tumor Classifier software pipeline as well as DKFZ classifier and NCI Classifier. 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). Prediction of MGMT promoter methylation status is based on the study by Bady et al. (Acta Neuropathol. 2012). An open source software Conumee is used for copy number analysis (Hovestadt and Zapatka; doi:10.18129/B9.bioc.conumee).

Interferences and Limitations

This test has limited ability to classify tumors with low-level tumor content (<40% 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.

Ordering & Collection

Specimen Type
Extracted DNA, Fresh or Frozen Tumor, FFPE Slides or Block, Tumor Culture
Collection

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.
Forms & Requisitions

Outside Providers: CGL Neoplasia Test Request Form

Handling Instructions

Outside Laboratories:

  • A completed test request form must accompany all orders.
  • Samples are accepted Monday-Friday.
  • Ship sample to:
    • Clinical Genomics Laboratory
    • University of Washington Health Sciences Building
    • Room H-561
    • 1959 NE Pacific St
    • Seattle, WA 98195
Quantity
requested: Varies; refer to Collection information.
minimum: Varies; refer to Collection information.

Processing

Processing

Hold samples at room temperature. If sample was frozen when received, keep frozen until pick up.

  • Call UWMC - Montlake DLMP Clinical Genomics Laboratory at (206) 616-4062 for pick up.

Performance

LIS Dept Code
Performing Location(s)
Pathology Clinical Genomics Laboratory
206-598-8684
Other Locations/Notes

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

Ph: (206) 616-4062

Frequency
Performed upon receipt of sample. TAT: 2-3 weeks.
Available STAT?
No, but please communicate with lab if urgent

Billing & Coding

CPT codes
Billing Comments

CPT Code: 81277

Prior Insurance Authorization: Contact gpab@uw.edu for details

LOINC