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.

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 Sarcoma tumors can be used to
  • confirm the WHO Sarcoma tumor classification determined by pathology and routine molecular testing. The 5th edition of WHO Sarcoma Tumor Classification offers DNA methylation profiles as a route to meet diagnostic criteria for many different tumor types. 
  • 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.

Synonyms

  • MASAR
  • Methylation Array
  • Sarcoma
  • Sarcoma Methylation
  • Methylation
  • Cancer
  • Solid Tumor
  • Tumor

LIS Mnemonic

MEARY

Test Notes

Genomic DNA is extracted from the tumor tissue followed by bisulfite conversion using EZ-96 DNA Methylation-Lightning MagPrep kit.  Converted DNA undergoes whole genome amplification and is processed utilizing the Infinium MethylationEPIC Array v.2 (Illumina). Raw IDAT files are processed through the Sarcoma methylation classifier developed by the Molecular Neuropathology group at the German Cancer Research Center (DKFZ) [Koelsche 2021, PMID: 33479225]. Methylation Class and Methylation subclass calibrated scores are provided by the classifier. 

Tumor molecular subclasses included in the training dataset for the Heidelberg Epignostix Sarcoma classifier v13.1: (atypical) fibrous histiocytoma, adamantinoma (group A), adamantinoma (group B), alveolar rhabdomyosarcoma, alveolar soft part sarcoma, aneurysmal bone cyst, angioleiomyoma (CNS type), angioleiomyoma (peripheral type), angiomatoid fibrous histiocytoma, angiosarcoma (group A), angiosarcoma (group B), atypical fibroxanthoma, atypical lipomatous tumor, chondroblastoma, chondromyxoid fibroma, chondrosarcoma (group A), chondrosarcoma (group B), chondrosarcoma IDH (group A), chondrosarcoma IDH (group B), chordoma, chordoma poorly differentiated, CIC-rearranged sarcoma, clear cell chondrosarcoma, clear cell sarcoma of soft parts, clear cell sarcoma of the kidney, control bone, control muscle tissue, control reactive tissue, control whole blood leukocytes, dedifferentiated liposarcoma, dermatofibroma, dermatofibrosarcoma protuberans, desmoid fibromatosis, desmoplastic small round cell tumor, embryonal rhabdomyosarcoma, embryonal rhabdomyosarcoma DICER1-mutant, endometrial stromal sarcoma high grade, endometrial stromal sarcoma low grade, epithelioid nerve sheath tumor, epithelioid sarcoma, Ewing sarcoma, EWSR1::NFATC2 sarcoma, extraskeletal myxoid chondrosarcoma, fibrous dysplasia/ossifying fibroma, fibrous hamartoma of infancy, gastrointestinal stromal tumour (adult type), gastrointestinal stromal tumour (pediatric type), giant cell tumor of bone, granular cell tumor, hemangioendothelioma epithelioid, hemangioendothelioma kaposiform, histiocytic sarcoma (group A), histiocytic sarcoma (group B), infantile fibrosarcoma (group A), infantile fibrosarcoma (group B), inflammatory myofibroblastic tumor, intimal sarcoma, intranodal palisaded myofibroblastoma, juvenile nasopharyngeal angiofibroma, juvenile/adult xanthogranuloma, Kaposi sarcoma, Langerhans cell histiocytosis, leiomyoma, leiomyosarcoma, leiomyosarcoma (uterine type), lipoblastoma, lipoma, low grade central osteosarcoma, low-grade fibromyxoid sarcoma, malignant melanotic nerve sheath tumor, malignant peripheral nerve sheath tumor, malignant rhabdoid tumour, melanocytoma/uveal melanoma, melanoma desmoplastic, melanoma/melanoma mucosal, mesenchymal chondrosarcoma, mesoblastic nephroma, mesothelioma epithelioid/biphasic, mesothelioma sarcomatoid, myofibroma, myopericytoma, myositis ossificans, myxofibrosarcoma, myxoid liposarcoma, myxoma intramuscular, myxoma nerve sheath, nerve sheath tumor, ERBB2-mutant, neurofibroma, neurofibroma plexiform, nodular fasciitis, non-ossifying fibroma, NTRK-rearranged spindle cell neoplasm, ossifying fibroma, ossifying fibromyxoid tumour (group A), ossifying fibromyxoid tumour (group B), osteoblastoma, osteofibrous dysplasia/osteofibrous dysplasia-like adamantinoma, osteosarcoma (group A), osteosarcoma (group B), ovarian fibroma, PeComa, pleomorphic dermal sarcoma, pleomorphic liposarcoma, pleomorphic rhabdomyosarcoma, pleuropulmonary blastoma, proliferative myositis, sarcoma MPNST-like, sarcoma with BCOR genetic alterations, schwannoma, sclerosing epithelioid fibrosarcoma, small cell carcinoma of the ovary, hypercalcemic type, solitary fibrous tumor  (peripheral type), solitary fibrous tumor (CNS type), spindle cell-sclerosing rhabdomyosarcoma, squamous cell carcinoma (cutaneous), synovial sarcoma, undifferentiated pleomorphic sarcoma, uterine sarcoma, SMARCA4-deficient, uterine tumor resembling ovarian sex chord tumor, well differentiated liposarcoma

Molecular Testing Notes

The Methylation Array for Sarcomas assay uses DNA from the sarcoma 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 sarcomas [Koelsche 2021, PMID: 33479225]. The methylation profiling and classifier are intended to provide supplementary information for diagnosis. Correlation with other omics results and clinical, pathological, and radiological features is recommended. 

This analysis is based on the current understanding of the methylation profiles of Sarcomas. 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

81479

Billing (EAP) Codes

809017
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 Sarcoma tumors can be used to
  • confirm the WHO Sarcoma tumor classification determined by pathology and routine molecular testing. The 5th edition of WHO Sarcoma Tumor Classification offers DNA methylation profiles as a route to meet diagnostic criteria for many different tumor types. 
  • 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.

Synonyms

  • MASAR
  • Methylation Array
  • Sarcoma
  • Sarcoma Methylation
  • Methylation
  • Cancer
  • Solid Tumor
  • Tumor

LIS Mnemonic

MEARY

Test Notes

Genomic DNA is extracted from the tumor tissue followed by bisulfite conversion using EZ-96 DNA Methylation-Lightning MagPrep kit.  Converted DNA undergoes whole genome amplification and is processed utilizing the Infinium MethylationEPIC Array v.2 (Illumina). Raw IDAT files are processed through the Sarcoma methylation classifier developed by the Molecular Neuropathology group at the German Cancer Research Center (DKFZ) [Koelsche 2021, PMID: 33479225]. Methylation Class and Methylation subclass calibrated scores are provided by the classifier. 

Tumor molecular subclasses included in the training dataset for the Heidelberg Epignostix Sarcoma classifier v13.1: (atypical) fibrous histiocytoma, adamantinoma (group A), adamantinoma (group B), alveolar rhabdomyosarcoma, alveolar soft part sarcoma, aneurysmal bone cyst, angioleiomyoma (CNS type), angioleiomyoma (peripheral type), angiomatoid fibrous histiocytoma, angiosarcoma (group A), angiosarcoma (group B), atypical fibroxanthoma, atypical lipomatous tumor, chondroblastoma, chondromyxoid fibroma, chondrosarcoma (group A), chondrosarcoma (group B), chondrosarcoma IDH (group A), chondrosarcoma IDH (group B), chordoma, chordoma poorly differentiated, CIC-rearranged sarcoma, clear cell chondrosarcoma, clear cell sarcoma of soft parts, clear cell sarcoma of the kidney, control bone, control muscle tissue, control reactive tissue, control whole blood leukocytes, dedifferentiated liposarcoma, dermatofibroma, dermatofibrosarcoma protuberans, desmoid fibromatosis, desmoplastic small round cell tumor, embryonal rhabdomyosarcoma, embryonal rhabdomyosarcoma DICER1-mutant, endometrial stromal sarcoma high grade, endometrial stromal sarcoma low grade, epithelioid nerve sheath tumor, epithelioid sarcoma, Ewing sarcoma, EWSR1::NFATC2 sarcoma, extraskeletal myxoid chondrosarcoma, fibrous dysplasia/ossifying fibroma, fibrous hamartoma of infancy, gastrointestinal stromal tumour (adult type), gastrointestinal stromal tumour (pediatric type), giant cell tumor of bone, granular cell tumor, hemangioendothelioma epithelioid, hemangioendothelioma kaposiform, histiocytic sarcoma (group A), histiocytic sarcoma (group B), infantile fibrosarcoma (group A), infantile fibrosarcoma (group B), inflammatory myofibroblastic tumor, intimal sarcoma, intranodal palisaded myofibroblastoma, juvenile nasopharyngeal angiofibroma, juvenile/adult xanthogranuloma, Kaposi sarcoma, Langerhans cell histiocytosis, leiomyoma, leiomyosarcoma, leiomyosarcoma (uterine type), lipoblastoma, lipoma, low grade central osteosarcoma, low-grade fibromyxoid sarcoma, malignant melanotic nerve sheath tumor, malignant peripheral nerve sheath tumor, malignant rhabdoid tumour, melanocytoma/uveal melanoma, melanoma desmoplastic, melanoma/melanoma mucosal, mesenchymal chondrosarcoma, mesoblastic nephroma, mesothelioma epithelioid/biphasic, mesothelioma sarcomatoid, myofibroma, myopericytoma, myositis ossificans, myxofibrosarcoma, myxoid liposarcoma, myxoma intramuscular, myxoma nerve sheath, nerve sheath tumor, ERBB2-mutant, neurofibroma, neurofibroma plexiform, nodular fasciitis, non-ossifying fibroma, NTRK-rearranged spindle cell neoplasm, ossifying fibroma, ossifying fibromyxoid tumour (group A), ossifying fibromyxoid tumour (group B), osteoblastoma, osteofibrous dysplasia/osteofibrous dysplasia-like adamantinoma, osteosarcoma (group A), osteosarcoma (group B), ovarian fibroma, PeComa, pleomorphic dermal sarcoma, pleomorphic liposarcoma, pleomorphic rhabdomyosarcoma, pleuropulmonary blastoma, proliferative myositis, sarcoma MPNST-like, sarcoma with BCOR genetic alterations, schwannoma, sclerosing epithelioid fibrosarcoma, small cell carcinoma of the ovary, hypercalcemic type, solitary fibrous tumor  (peripheral type), solitary fibrous tumor (CNS type), spindle cell-sclerosing rhabdomyosarcoma, squamous cell carcinoma (cutaneous), synovial sarcoma, undifferentiated pleomorphic sarcoma, uterine sarcoma, SMARCA4-deficient, uterine tumor resembling ovarian sex chord tumor, well differentiated liposarcoma

Molecular Testing Notes

The Methylation Array for Sarcomas assay uses DNA from the sarcoma 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 sarcomas [Koelsche 2021, PMID: 33479225]. The methylation profiling and classifier are intended to provide supplementary information for diagnosis. Correlation with other omics results and clinical, pathological, and radiological features is recommended. 

This analysis is based on the current understanding of the methylation profiles of Sarcomas. 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.
 
Result Interpretation
Administrative

CPT Codes

81479

Billing (EAP) Codes

809017

Requisition

Test Order Form
https://redcap.chop.edu/surveys/?s=LY9N74RXF8X9NH9A

×
Learn More Remind Me Later Dismiss