GlioSeq® - NGS Panel for Brain Tumors
- Adult & Pediatric CNS Tumors
- Small Sample Size
- Fast Turnaround Time
- GlioSeq v2 is utilizing an amplification-based targeted next generation sequencing of DNA and mRNA
- It is strategically designed to sequence clinically relevant genes for mutations in 30 CNS-tumor-related genes, copy number changes in 24 genes, and multiple structural alterations, including BRAF, NTRK1-3, FGFR3, YAP1, and RELA fusions, and EGFRvIII mutation.
- It can be berformed on small stereotactic brain biopsies and resected FFPE tumor specimens
- It has fast turnaround time (7-10 days)
- GlioSeq aids in the diagnosis of both adult and pediatric CNS tumors, including glioma, medullosblastoma, meningioma, and ependymoma
Genes Assayed by GlioSeq
Molecular markers are used to support and enhance the diagnosis, prognosis and treatment of adult and pediatric CNS tumors. The GlioSeq test identifies genetic alterations that are relevant to different CNS tumors subtypes and grades (1). Low grade gliomas (WHO Grade I-II), e.g. pilocytic astrocytoma, pilomyxoid astrocytoma, ganglioglioma, and pleomorphic xanthoastrocytoma often harbor mutations or gene fusions in BRAF (2,3). Neurofibromatosis type 1 associated pilocytic astrocytoma characteristically harbor mutations and/or loss in NF1 gene, resulting in bi-allelic inactivation of the gene (4). Diffusely infiltrative Gliomas (WHO grade II-III) were recently classified into three glioma subtypes based on histopathologic features, molecular alterations, and clinical behavior (5). Lower Grade Glioma (LGG) Type 1 or oligodendrogliomas harbor IDH mutations, 1p/19q co-deletion, TERT promoter mutation and alterations in CIC, and FUBP1 genes. LGG Type 2 or infiltrating astrocytoma of adults harbor IDH, TP53, and ATRX mutations. Both can progress to a higher grade glioma by acquiring additional genomic alterations in the RTK-RAS-PI3K pathway genes. LGG Type 3 do not harbor IDH mutations, but have genetic alterations similar to high grade gliomas (WHO grade IV) and considered to be a precursor to secondary GBMs (5,6). Primary GBMs are IDH wild-type and harbor a number of genetic alterations that lead to dysregulation of critical signaling pathways including i) receptor tyrosine kinase (RTK)/RAS/PI(3)K pathway via amplification and mutation in EGFR, PIK3CA, RAS, NF1, EGFR, and MET and FGFR fusions, ii) TP53 and RB1 pathways via inactivation mutation/loss of TP53, CDKN2A, and RB1 genes, and iii) TERT promoter mutations (6). Pediatric gliomas are unique, featuring mutations and other genetic alterations in H3F3A, SETD2, ATRX, NF1, and BRAF. IDH mutations are rare and usually restricted to adolescent patients. They also can harbors fusions involving BRAF and FGFR genes (7,8).
Medulloblastomas have been recently classified into four groups (WNT (wingless), SHH (sonic hedgehog), Group 3, and Group 4) based on molecular profiling and clinical outcome. Mutations in CTNNB1 or DDX3X can help to identify Wnt pathway medulloblastomas that tend to have a much better prognosis. Tumors with PTCH, SMO, and TERT promoter alterations characterize the Shh class, and have intermediate prognosis between Wnt and group 3/4 tumors. In contrast, MYC or MYCN/CDK6 amplification are characteristic of group 3 and 4 medulloblastomas, respectively, and are far more likely to metastasize and have a poor prognosis even with therapy (7,9). Finally, inactivation of NF2 via mutation or loss of 22q is the most common early genetic alteration in meningiomas and multiple copy number alterations including 1p,10q, and 9p (CDKN2A) loss and TERT promoter mutations are seen in higher grade meningiomas. Recurrent mutations in KLF4, AKT1, and SMO genes are often present in NF2-negative sporadic meningiomas (10,11). These and other genetic alterations can serve as diagnostic, prognostic, and predictive biomarkers for tumor classification, patient risk stratification, and targeted therapies.
- Nikiforova, MN. Targeted next-generation sequencing panel (GlioSeq) provides comprehensive genetic profiling of central nervous system tumors. Neuro Oncol. 2016; 18: 379-87.
- Schindler, G. Analysis of BRAF V600E mutation in 1,320 nervous system tumors reveals high mutation frequencies in pleomorphic xanthoastrocytoma, ganglioglioma and extra-cerebellar pilocytic astrocytoma. Acta Neuropathol. 2011; 121: 397-405.
- Lee, EQ. Characteristics of Patients Who Survived < 3 Months or > 2 Years After Surgery for Spinal Metastases: Can We Avoid Inappropriate Patient Selection?. J Clin Oncol. 2016; 34: 3054-61.
- Gutmann, DH. Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma. Genome Res. 2013; 23: 431-9.
- Brat, DJ. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 2015; 372: 2481-98.
- Aldape, K. Glioblastoma: pathology, molecular mechanisms and markers. Acta Neuropathol. 2015; 129: 829-48.
- Gajjar, A. Cytogenetic prognostication within medulloblastoma subgroups. J Clin Oncol. 2015; 33: 2986-98.
- Korshunov, A. Integrated analysis of pediatric glioblastoma reveals a subset of biologically favorable tumors with associated molecular prognostic markers. Acta Neuropathol. 2015; 129: 669-78.
- Gajjar, AJ. Medulloblastoma-translating discoveries from the bench to the bedside. Nat Rev Clin Oncol. 2014; 11 714-22.
- Clark, VE. Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO. Science. 2013; 339: 1077-80. Suva, ML. Next-generation molecular genetics of brain tumours. Curr Opin Neurol. 2013: 26 681-7.
Examples of GlioSeq Reports
Specimen Requirements and Shipping Instructions
Paraffin embedded tissure sections
- Tissue should be fixed in formalin and not exposed to decalcification solution. The paraffin block should contain no less than 1-3 mm area of tumor.
- Slides should prepared by histology using a specific protocol for cutting molecular sections to avoid contamination of the tissue sections.
- One H&E and 6 unstained sections are required for most of the tests. Ten unstained sections or more are requested if the tissue is small. Please call the lab if you have questions.
- Slides should be properly labeled with a block label that matches the surgical pathology specimen number on the surgical pathology report.
- Slides should be sent ambient temperature in proper storage containers (plastic slide boxes) to protect them during shipment.
- A surgical pathology report and completed requisition must accompany all specimens.
- A minimum of 2 x 2 x 2 mm of frozen tissue is required.
- Collection date and time should be stated.
- Tissue specimen containing at least 50% of tumor cells can be either placed into cryogenic tube and snap frozen in liquid nitrogen, or placed into a tube with preservative solution provided by the Molecular & Genomic Pathology laboratory (request solution from the lab) and frozen at -20° C.
- Ship overnight on dry ice. A surgical pathology and/or cytology report and completed requisition form must accompany all specimens.
7 - 10 days
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