NeoTYPE® DNA & RNA - Brain uses targeted next-generation sequencing (NGS) to detect single nucleotide variants, insertions/deletions, and gene fusions in 83 unique genes (62 genes analyzed by DNA and 28 by RNA), plus microsatellite instability (MSI) and tumor mutational burden (TMB). In addition, FISH is performed to detect nine key copy number alterations and PD-L1 immunohistochemistry is performed. MGMT Promoter Methylation Analysis by PCR is an optional add-on. Results are incorporated into one report providing diagnostic, prognostic, and therapeutic implications, as well as potential clinical trial options. A microsatellite instability NGS result of “indeterminate” will create a reflex to MSI by PCR as long as the tumor percentage is ≥40% and paired normal tissue is available. If the sample is insufficient to produce both DNA and RNA results, the available results will be reported and alternate CPT® Codes may apply.
- SNVs/Indels (62 genes): AKT1, APC, ATRX, BAP1, BCOR, BCORL1, BRAF, CDK6, CDKN2A, CDKN2B, CIC, CTNNB1, DICER1, EED, EGFR, EPCAM, ERBB2, ERBB4, FGFR1, FGFR2, FGFR3, FUBP1, GNA11, GNAQ, H3F3A (H3-3A), HIST1H3C (H3C3), HRAS, IDH1, IDH2, KDM6A, KRAS, MAP2K1, MET, MLH1, MSH2, MSH6, MYC, MYCN, NOTCH1, NF1, NF2, NRAS, PDGFRA, PIK3CA, PMS2, PTCH1, PTEN, RB1, SETD2, SF3B1, SMAD4, SMARCA4, SMARCB1, SMO, SRC, SUFU, SUZ12, TERT Promoter, TP53, TSC1, TSC2, and VHL
- RNA Fusions (28 genes): ALK, BRAF, CIC, EGFR including EGFRvIII, EML4, ETV6, EWSR1, FGFR1, FGFR2, FGFR3, FUS, KIAA1549, MAML2, MET, MN1, MYB, MYBL1, NTRK1, NTRK2, NTRK3, PRKCA, RAF1, ROS1, STAT6, TACC3, TFG, YAP1, and ZFTA (C11orf95)
- CNVs by FISH (9 CNVs): 1p/19q co-deletion, +7/-10 (trisomy 7, monosomy 10), CDKN2A (p16) deletion, EGFR amplification, MET amplification, MYCN amplification, PDGFRa amplification, and PTEN deletion (FISH is global only)
- IHC: PD-L1 LDT (tech-only available)
- Other Biomarkers: Microsatellite Instability (MSI) and Tumor Mutation Burden (TMB) included. MGMT Promoter Methylation Analysis may be added.
NeoTYPE® DNA & RNA – Brain is intended to provide a tumor genomic profile that includes the most clinically significant genomic alterations according to the 2021 WHO Classification of Tumors of the CNS, 5th edition. These genomic findings may help inform diagnosis, prognosis, therapeutic decisions, and clinical trial options. This profile is appropriate for patients with newly diagnosed, recurrent, or resistant disease.
FFPE solid tumor tissue: Minimum surface area 10mm2 with ≥20% tumor content. Please use positively-charged slides and 10% NBF fixative. Do not use zinc fixatives.
- Paraffin block: Preferred.
- Cut slides: Send ≥25 unstained sections cut at 5 microns plus one H&E slide (which NeoGenomics will keep). No additional slides are needed if ordering MGMT Promoter Methylation Analysis.
Use cold pack for transport, making sure cold pack is not in direct contact with specimen. Slides can be packed at room temperature.
Add 81287x1 if ordering MGMT Promoter Methylation Analysis.
- Louis DN et al. The 2021 WHO Classification of Tumors of the Central Nervous System: a summary. Neuro-Oncology. 2021;23(8):1231-1251. https://doi.org/10.1093/neuonc/noab106