Fresh Tissue 150 mg or 1.0-2.0 cm3 fresh tissue in transport media. Deliver within 24 hours at room temperature.
Fresh Frozen Tissue 150 mg or 1.0-2.0 cm3 tissue snap frozen at -20°C. Store at -20°C. Ship on minimum of 10 lbs. of dry ice in an insulated container by overnight courier.
FFPE sample: Preferably 4 to 6 scrolls or 10 slides (minimum acceptable specimen: 3 scrolls or 5 slides) that are freshly cut before shipping to us via overnight delivery. It would be best to cut and ship Wednesday to arrive on Thursday. Alternatively, a whole FFPE block can be sent.
Any questions regarding the test, interpretation of the results, and availability of additional tests should be referred to the directors and genetic counselors in the Center for Diagnostic Innovation, Cancer Genomic Laboratory at cdicancergenomics@chop.edu.
Unacceptable Conditions
This assay requires tumor content > 50%. Tumor content below 50% will affect the Methylation Class calibrated score and the sensitivity of the assay. This assay is qualitative and should not be used for residual diseases.
Unacceptable conditions include specimens lacking tumor cells or specimens processed or fixed in alternative fixatives.
Storage/Transport Temperature
See the Collect section above.
Volume Required
See the Collect section above.
Minimum Required
See the Collect section above.
Phlebotomy Draw
No.
Performing Lab
Center for Diagnostic Innovation (CDI)
Performed
Monday through Friday 9 to 5
Reported
21 days
Detection Rate
This methylation-based classification is intended to provide supplementary information for diagnosis.
Utility
DNA methylation is an epigenetic modifier involved in gene expression. The pattern of gene methylation observed in tumor tissue is reflective of the cells of origin, as well as the altered methylation pattern caused by cancer.
The DNA methylation class of CNS tumors can be used to
confirm the WHO CNS tumor classification determined by pathology and routine molecular testing. The 5th edition of WHO CNS Tumor Classification offers DNA methylation profiles as a route to meet diagnostic criteria for many different CNS tumor types including gliomas and glioneuronal tumors.
aid in the classification of difficult to diagnose cases.
assign a molecular subgroup based on gene expression pattern, which cannot be determined via routine molecular testing. Both medulloblastomas and ependymomas are CNS tumors with DNA methylation-based molecular subgroupings.
Genomic DNA is extracted from the tumor tissue followed by bisulfite conversion using Zymo EZ-96 DNA Methylation-Lightning MagPrep. Converted DNA undergoes whole genome amplification and is processed utilizing the Infinium MethylationEPIC Array v2 (Illumina). Raw IDAT files are processed through the CNS methylation classifier developed by the Molecular Neuropathology group at the German Cancer Research Center (DKFZ)[ Capper 2018, PMID: 29539639]. Methylation Class Family and Methylation Class calibrated scores are provided by the classifier. Based on our validation results, the concordance rate (134/144), 87.5% (21/24), and 56.3% (9/16), respectively.
Tumor molecular subclasses included in the training dataset for the Heidelberg Epignostix Brain Tumor classifier v12.8: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted; Oligosarcoma, IDH-mutant; Astrocytoma, IDH-mutant, low and high grade; Adult-type diffuse high grade glioma, IDH-wildtype, subtype B, E, and F; Glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (novel); Glioblastoma, IDH-wildtype, [atypical mesenchymal type]; Glioblastoma, IDH-wildtype, RTK1 and RTK2 subtype; Glioblastoma, IDH-wildtype, with primitive neuronal component; High-grade diffuse glioma of the midline/posterior fossa, H3/IDH-wildtype; Central neurocytoma; Choroid plexus carcinoma, adult and pediatric subtype; Choroid plexus papilloma, adult and pediatric subtype; Chordoid glioma, PRKCA-mutant; Subependymal giant cell astrocytoma; Control tissue, cerebellar hemisphere; Control tissue, hemispheric cortex; Control tissue, hypothalamus; Control tissue, optic pathway; Control tissue, pituitary gland (anterior lobe); Control tissue, pons; Control tissue, white matter (corpus callosum); Control tissue, blood; Control tissue, reactive tumour microenvironment; Cauda equina neuroendocrine tumour [paraganglioma], subtype non-CIMP; Malignant melanotic nerve sheath tumour; Plexiform neurofibroma; Malignant peripheral nerve sheath tumour [spinal or atypical type]; Malignant peripheral nerve sheath tumour [typical type]; CNS Schwannoma, VGLL-fused; Schwannoma; High-grade astrocytoma with piloid features; Pleomorphic xanthoastrocytoma; Diffuse glioneuronal tumour, subtype A; Diffuse leptomeningeal glioneuronal tumour, subclass 1 and 2; Myxopapillary ependymoma; Posterior fossa group A (PFA) ependymoma, subclass 1a-f; Posterior fossa group A (PFA) ependymoma, subclass 2a-c; Posterior fossa group B (PFB) ependymoma, subclass 1-5; Posterior fossa subependymoma; Spinal ependymoma; Spinal ependymoma, MYCN-amplified; Spinal subependymoma [subtype A and B]; Supratentorial ependymoma, YAP1-fused; Supratentorial ependymoma, ZFTA fusion-positive, subtype ZFTA-RELA fused, subclass A and B; Supratentorial ependymoma, ZFTA fusion-positive, subclass C-E; Olfactory neuroblastoma; Germinoma, subtype KIT mutant (novel); Germinoma, subtype KIT wildtype (novel); Teratoma; Yolk sac tumour; Plasmacytoma of the CNS; Primary diffuse large B cell lymphoma of the CNS; Langerhans cell histiocytosis; Astroblastoma, MN1-altered, MN1:BEND2-fused; Neuroepithelial tumour, MN1:CXXC5-fused; Inflammatory microenvironment; Intraocular medulloepithelioma; Liponeurocytoma; Angiocentric glioma, MYB/MYBL1-altered; Diffuse astrocytoma, MYB or MYBL1-altered, subtype B-D; Desmoplastic infantile ganglioglioma / desmoplastic infantile astrocytoma; Ganglioglioma; Polymorphous low-grade neuroepithelial tumour of the young; Diffuse glioneuronal tumour with oligodendroglioma-like features and nuclear clusters; Dysembryoplastic neuroepithelial tumour; Extraventricular neurocytoma; Myxoid glioneuronal tumour, PDGFRA-mutant; Papillary glioneuronal tumour; Rosette-forming glioneuronal tumour; Infratentorial pilocytic astrocytoma; Infratentorial pilocytic astrocytoma, FGFR1-altered; Supratentorial midline pilocytic astrocytoma; Supratentorial pilocytic astrocytoma; Medulloblastoma Group 3, subclass I-IV; Medulloblastoma Group 4, subclass V-VIII; Medulloblastoma, SHH-activated, IDH-mutant; Medulloblastoma, SHH-activated, subtype 1-4; Medulloblastoma, WNT activated; Medullomyoblastoma; Melanocytoma; Meningioma, subclass benign 1-3; Meningioma, subclass intermediate A-B; Meningioma, malignant; Meningioma, SMARCE1-altered; Solitary fibrous tumour / haemangiopericytoma; Chordoma; CIC-rearranged sarcoma; Ewing sarcoma; Primary intracranial sarcoma, DICER1-mutant; Haemangioblastoma; Melanoma [metastatic]; Neuroblastoma, MYCN subtype; Neuroblastoma, subtype ALT/TERT TMM positive; Neuroblastoma, subtype TMM negative; Neuroepithelial tumour with PATZ1 fusion; Neuroepithelial tumour, PLAGL1-fused; Atypical teratoid rhabdoid tumour, MYC activated; Atypical teratoid rhabdoid tumour, SHH activated; Atypical teratoid rhabdoid tumour, Tyrosinase activated; CNS tumour with EP300:BCOR(L1) fusion; CNS tumour with BCOR internal tandem duplication; CNS embryonal tumour with BRD4:LEUTX fusion; CNS Embryonal tumour with PLAG-family amplification; CNS neuroblastoma, FOXR2-altered; Cribriform neuroepithelial tumour; Embryonal tumour with multilayered rosettes, atypical; Embryonal tumour with multilayered rosettes, C19MC altered; Diffuse midline glioma, H3 K27-altered, subtype EGFR-altered; Diffuse midline glioma, H3 K27-altered, subtype H3 K27-mutant or EZHIP expressing; Diffuse hemispheric glioma, H3 G34-mutant; Diffuse paediatric-type high grade glioma, H3 wildtype and IDH wild type, Subtype A and B; Diffuse paediatric-type high grade glioma, MYCN subtype; Diffuse paediatric-type high grade glioma, RTK1 subtype, subclass A-C (novel); Diffuse paediatric-type high grade glioma, RTK2 subtype, subclass A and B (novel); Infant-type hemispheric glioma; Control tissue, pineal gland; Retinoblastoma; Retinoblastoma, MYCN-activated; Pineocytoma; Pineal parenchymal tumour of intermediate differentiation, subclass A and B; Pineal retinoblastoma; Pineoblastoma, miRNA pathway altered, group 1A and 1B; Pineoblastoma, miRNA pathway altered, group 2; Pineoblastoma, MYC/FOXR2-activated; Papillary tumour of the pineal region, subclass A and B; Rhabdomyosarcoma, alveolar subtype; Rhabdomyosarcoma, embryonal subtype; Rhabdomyosarcoma, MYOD1-mutant; Sinonasal undifferentiated carcinoma, IDH2-mutant; Adamantinomatous craniopharyngioma; Papillary craniopharyngioma; Pituicytoma, granular cell tumour of the sellar region, and spindle-cell oncocytoma; Pituitary adenoma, ACTH-producing; Pituitary adenoma, gonadotrophin-producing; Pituitary adenoma, prolactin-producing; Pituitary adenoma, STH-producing, subclass densely granulated A and B; Pituitary adenoma, STH-producing, subclass sparsely granulated; Pituitary adenoma, TSH-producing
Molecular Testing Notes
The Methylation Array for CNS Tumor assay uses DNA from the CNS tumor sample to evaluate the genome-wide methylation profile of the tumor and matches the profile to the established tumor methylation profiles using a machine learning algorithm for the classification of central nervous system (CNS) tumors [Capper 2018, PMID: 29539639; Louis 2021, PMID: 34185076]. The methylation profiling and classifier are intended to provide supplementary information for diagnosis.
This analysis is based on the current understanding of the methylation profiles of CNS tumors. Clinical decisions on patient care must be based on the independent medical judgment of the treating physician, taking into consideration all relevant information about the patient's condition, including patient medical and family history, physical examinations, information from other diagnostic tests, and patient preferences. The results of this test must always be interpreted in the context of all relevant clinical and pathological data and should not be used alone for diagnosis or patient care decisions. and the sensitivity of the assay. This assay requires tumor content > 50%. Tumor content below 50% will affect the Methylation Class calibrated score and the sensitivity of the assay. This assay is qualitative and should not be used for residual diseases.
CPT Codes
81524
Billing (EAP) Codes
808954
Collection
Collect
Fresh Tissue 150 mg or 1.0-2.0 cm3 fresh tissue in transport media. Deliver within 24 hours at room temperature.
Fresh Frozen Tissue 150 mg or 1.0-2.0 cm3 tissue snap frozen at -20°C. Store at -20°C. Ship on minimum of 10 lbs. of dry ice in an insulated container by overnight courier.
FFPE sample: Preferably 4 to 6 scrolls or 10 slides (minimum acceptable specimen: 3 scrolls or 5 slides) that are freshly cut before shipping to us via overnight delivery. It would be best to cut and ship Wednesday to arrive on Thursday. Alternatively, a whole FFPE block can be sent.
Any questions regarding the test, interpretation of the results, and availability of additional tests should be referred to the directors and genetic counselors in the Center for Diagnostic Innovation, Cancer Genomic Laboratory at cdicancergenomics@chop.edu.
Unacceptable Conditions
This assay requires tumor content > 50%. Tumor content below 50% will affect the Methylation Class calibrated score and the sensitivity of the assay. This assay is qualitative and should not be used for residual diseases.
Unacceptable conditions include specimens lacking tumor cells or specimens processed or fixed in alternative fixatives.
Storage/Transport Temperature
See the Collect section above.
Volume Required
See the Collect section above.
Minimum Required
See the Collect section above.
Phlebotomy Draw
No.
Ordering
Performing Lab
Center for Diagnostic Innovation (CDI)
Performed
Monday through Friday 9 to 5
Reported
21 days
Detection Rate
This methylation-based classification is intended to provide supplementary information for diagnosis.
Utility
DNA methylation is an epigenetic modifier involved in gene expression. The pattern of gene methylation observed in tumor tissue is reflective of the cells of origin, as well as the altered methylation pattern caused by cancer.
The DNA methylation class of CNS tumors can be used to
confirm the WHO CNS tumor classification determined by pathology and routine molecular testing. The 5th edition of WHO CNS Tumor Classification offers DNA methylation profiles as a route to meet diagnostic criteria for many different CNS tumor types including gliomas and glioneuronal tumors.
aid in the classification of difficult to diagnose cases.
assign a molecular subgroup based on gene expression pattern, which cannot be determined via routine molecular testing. Both medulloblastomas and ependymomas are CNS tumors with DNA methylation-based molecular subgroupings.
Genomic DNA is extracted from the tumor tissue followed by bisulfite conversion using Zymo EZ-96 DNA Methylation-Lightning MagPrep. Converted DNA undergoes whole genome amplification and is processed utilizing the Infinium MethylationEPIC Array v2 (Illumina). Raw IDAT files are processed through the CNS methylation classifier developed by the Molecular Neuropathology group at the German Cancer Research Center (DKFZ)[ Capper 2018, PMID: 29539639]. Methylation Class Family and Methylation Class calibrated scores are provided by the classifier. Based on our validation results, the concordance rate (134/144), 87.5% (21/24), and 56.3% (9/16), respectively.
Tumor molecular subclasses included in the training dataset for the Heidelberg Epignostix Brain Tumor classifier v12.8: Oligodendroglioma, IDH-mutant and 1p/19q-codeleted; Oligosarcoma, IDH-mutant; Astrocytoma, IDH-mutant, low and high grade; Adult-type diffuse high grade glioma, IDH-wildtype, subtype B, E, and F; Glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (novel); Glioblastoma, IDH-wildtype, [atypical mesenchymal type]; Glioblastoma, IDH-wildtype, RTK1 and RTK2 subtype; Glioblastoma, IDH-wildtype, with primitive neuronal component; High-grade diffuse glioma of the midline/posterior fossa, H3/IDH-wildtype; Central neurocytoma; Choroid plexus carcinoma, adult and pediatric subtype; Choroid plexus papilloma, adult and pediatric subtype; Chordoid glioma, PRKCA-mutant; Subependymal giant cell astrocytoma; Control tissue, cerebellar hemisphere; Control tissue, hemispheric cortex; Control tissue, hypothalamus; Control tissue, optic pathway; Control tissue, pituitary gland (anterior lobe); Control tissue, pons; Control tissue, white matter (corpus callosum); Control tissue, blood; Control tissue, reactive tumour microenvironment; Cauda equina neuroendocrine tumour [paraganglioma], subtype non-CIMP; Malignant melanotic nerve sheath tumour; Plexiform neurofibroma; Malignant peripheral nerve sheath tumour [spinal or atypical type]; Malignant peripheral nerve sheath tumour [typical type]; CNS Schwannoma, VGLL-fused; Schwannoma; High-grade astrocytoma with piloid features; Pleomorphic xanthoastrocytoma; Diffuse glioneuronal tumour, subtype A; Diffuse leptomeningeal glioneuronal tumour, subclass 1 and 2; Myxopapillary ependymoma; Posterior fossa group A (PFA) ependymoma, subclass 1a-f; Posterior fossa group A (PFA) ependymoma, subclass 2a-c; Posterior fossa group B (PFB) ependymoma, subclass 1-5; Posterior fossa subependymoma; Spinal ependymoma; Spinal ependymoma, MYCN-amplified; Spinal subependymoma [subtype A and B]; Supratentorial ependymoma, YAP1-fused; Supratentorial ependymoma, ZFTA fusion-positive, subtype ZFTA-RELA fused, subclass A and B; Supratentorial ependymoma, ZFTA fusion-positive, subclass C-E; Olfactory neuroblastoma; Germinoma, subtype KIT mutant (novel); Germinoma, subtype KIT wildtype (novel); Teratoma; Yolk sac tumour; Plasmacytoma of the CNS; Primary diffuse large B cell lymphoma of the CNS; Langerhans cell histiocytosis; Astroblastoma, MN1-altered, MN1:BEND2-fused; Neuroepithelial tumour, MN1:CXXC5-fused; Inflammatory microenvironment; Intraocular medulloepithelioma; Liponeurocytoma; Angiocentric glioma, MYB/MYBL1-altered; Diffuse astrocytoma, MYB or MYBL1-altered, subtype B-D; Desmoplastic infantile ganglioglioma / desmoplastic infantile astrocytoma; Ganglioglioma; Polymorphous low-grade neuroepithelial tumour of the young; Diffuse glioneuronal tumour with oligodendroglioma-like features and nuclear clusters; Dysembryoplastic neuroepithelial tumour; Extraventricular neurocytoma; Myxoid glioneuronal tumour, PDGFRA-mutant; Papillary glioneuronal tumour; Rosette-forming glioneuronal tumour; Infratentorial pilocytic astrocytoma; Infratentorial pilocytic astrocytoma, FGFR1-altered; Supratentorial midline pilocytic astrocytoma; Supratentorial pilocytic astrocytoma; Medulloblastoma Group 3, subclass I-IV; Medulloblastoma Group 4, subclass V-VIII; Medulloblastoma, SHH-activated, IDH-mutant; Medulloblastoma, SHH-activated, subtype 1-4; Medulloblastoma, WNT activated; Medullomyoblastoma; Melanocytoma; Meningioma, subclass benign 1-3; Meningioma, subclass intermediate A-B; Meningioma, malignant; Meningioma, SMARCE1-altered; Solitary fibrous tumour / haemangiopericytoma; Chordoma; CIC-rearranged sarcoma; Ewing sarcoma; Primary intracranial sarcoma, DICER1-mutant; Haemangioblastoma; Melanoma [metastatic]; Neuroblastoma, MYCN subtype; Neuroblastoma, subtype ALT/TERT TMM positive; Neuroblastoma, subtype TMM negative; Neuroepithelial tumour with PATZ1 fusion; Neuroepithelial tumour, PLAGL1-fused; Atypical teratoid rhabdoid tumour, MYC activated; Atypical teratoid rhabdoid tumour, SHH activated; Atypical teratoid rhabdoid tumour, Tyrosinase activated; CNS tumour with EP300:BCOR(L1) fusion; CNS tumour with BCOR internal tandem duplication; CNS embryonal tumour with BRD4:LEUTX fusion; CNS Embryonal tumour with PLAG-family amplification; CNS neuroblastoma, FOXR2-altered; Cribriform neuroepithelial tumour; Embryonal tumour with multilayered rosettes, atypical; Embryonal tumour with multilayered rosettes, C19MC altered; Diffuse midline glioma, H3 K27-altered, subtype EGFR-altered; Diffuse midline glioma, H3 K27-altered, subtype H3 K27-mutant or EZHIP expressing; Diffuse hemispheric glioma, H3 G34-mutant; Diffuse paediatric-type high grade glioma, H3 wildtype and IDH wild type, Subtype A and B; Diffuse paediatric-type high grade glioma, MYCN subtype; Diffuse paediatric-type high grade glioma, RTK1 subtype, subclass A-C (novel); Diffuse paediatric-type high grade glioma, RTK2 subtype, subclass A and B (novel); Infant-type hemispheric glioma; Control tissue, pineal gland; Retinoblastoma; Retinoblastoma, MYCN-activated; Pineocytoma; Pineal parenchymal tumour of intermediate differentiation, subclass A and B; Pineal retinoblastoma; Pineoblastoma, miRNA pathway altered, group 1A and 1B; Pineoblastoma, miRNA pathway altered, group 2; Pineoblastoma, MYC/FOXR2-activated; Papillary tumour of the pineal region, subclass A and B; Rhabdomyosarcoma, alveolar subtype; Rhabdomyosarcoma, embryonal subtype; Rhabdomyosarcoma, MYOD1-mutant; Sinonasal undifferentiated carcinoma, IDH2-mutant; Adamantinomatous craniopharyngioma; Papillary craniopharyngioma; Pituicytoma, granular cell tumour of the sellar region, and spindle-cell oncocytoma; Pituitary adenoma, ACTH-producing; Pituitary adenoma, gonadotrophin-producing; Pituitary adenoma, prolactin-producing; Pituitary adenoma, STH-producing, subclass densely granulated A and B; Pituitary adenoma, STH-producing, subclass sparsely granulated; Pituitary adenoma, TSH-producing
Molecular Testing Notes
The Methylation Array for CNS Tumor assay uses DNA from the CNS tumor sample to evaluate the genome-wide methylation profile of the tumor and matches the profile to the established tumor methylation profiles using a machine learning algorithm for the classification of central nervous system (CNS) tumors [Capper 2018, PMID: 29539639; Louis 2021, PMID: 34185076]. The methylation profiling and classifier are intended to provide supplementary information for diagnosis.
This analysis is based on the current understanding of the methylation profiles of CNS tumors. Clinical decisions on patient care must be based on the independent medical judgment of the treating physician, taking into consideration all relevant information about the patient's condition, including patient medical and family history, physical examinations, information from other diagnostic tests, and patient preferences. The results of this test must always be interpreted in the context of all relevant clinical and pathological data and should not be used alone for diagnosis or patient care decisions. and the sensitivity of the assay. This assay requires tumor content > 50%. Tumor content below 50% will affect the Methylation Class calibrated score and the sensitivity of the assay. This assay is qualitative and should not be used for residual diseases.
