ArticleNeuro-oncology2016
Targeted next-generation sequencing panel (GlioSeq) provides comprehensive genetic profiling of central nervous system tumors.
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Article in Neuro-oncology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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69citing papers in PubMed
6.7field-weighted citation impact, top 2% of its field
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69 citing papers in PubMed, 116 citations in OpenAlex.
- Targeted next-generation sequencing panel (TruSight Tumor 170) in diffuse glioma: a single institutional experience of 135 cases.Journal of neuro-oncology · 2019Trial
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- Detection of Copy-Number Variations in CNS Tumours From Off-Target Reads of Hybrid-Capture Sequencing.Neuropathology and applied neurobiology · 2026Article
- Disrupting PDGFRA-driven immune evasion in glioma: vaccine-based strategies on the horizon.Frontiers in oncology · 2026Review
- Unveiling the BRAF fusion structure variations through DNA and RNA sequencing.British journal of cancer · 2025Article
- The radiogenomic and spatiogenomic landscapes of glioblastoma and their relationship to oncogenic drivers.Communications medicine · 2025Article
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- Implementing Massive Parallel Sequencing into Biliary Samples Obtained through Endoscopic Retrograde Cholangiopancreatography for Diagnosing Malignant Bile Duct Strictures.International journal of molecular sciences · 2024Article
- Diffuse, IDH-wildtype gliomas in adults with minimal histological change and isolated TERT promoter mutation: not simply CNS WHO grade 4.Acta neuropathologica · 2024Article
- Development of a rapid and comprehensive genomic profiling test supporting diagnosis and research for gliomas.Brain tumor pathology · 2024Article
- Molecular neuropathology: an essential and evolving toolbox for the diagnosis and clinical management of central nervous system tumors.Virchows Archiv : an international journal of pathology · 2024Review
- Characterization of low-grade epilepsy-associated tumor from implanted stereoelectroencephalography electrodes.Epilepsia open · 2024Article
- Molecular diagnostic tools for the World Health Organization (WHO) 2021 classification of gliomas, glioneuronal and neuronal tumors; an EANO guideline.Neuro-oncology · 2023Article
- IDH-mutant diffuse gliomas: tips and tricks in the era of genomic tumor classification.Histology and histopathology · 2023Review
- The Glioma-IRE project - Molecular profiling in patients with glioma: steps toward an individualized diagnostic and therapeutic approach.Journal of translational medicine · 2023Article
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- Prospective, Multi-Institutional, Real-Time Next-Generation Sequencing of Pancreatic Cyst Fluid Reveals Diverse Genomic Alterations That Improve the Clinical Management of Pancreatic Cysts.Gastroenterology · 2023Article
- Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects.Frontiers in molecular biosciences · 2023Review
- Droplet digital PCR-based analyses for robust, rapid, and sensitive molecular diagnostics of gliomas.Acta neuropathologica communications · 2022Article
- Detection ofBiomedicines · 2022Review
9 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 5 institutions in 1 country.
Marina N NikiforovaDepartment of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).
Abigail I WaldDepartment of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).
Melissa A MelanDepartment of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).
Somak RoyDepartment of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).
Shan ZhongDepartment of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).
Ronald L HamiltonDepartment of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).
Frank S LiebermanDepartment of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).
Jan DrappatzDepartment of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).
Nduka M AmankulorDepartment of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).
Ian F PollackDepartment of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).
Yuri E NikiforovDepartment of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).
Craig HorbinskiDepartment of Pathology, Division of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (M.N.N, A.I.W., M.A.M., S.R., S.Z., Y.E.N.); Department of Pathology, Division of Neuropathology, University of Pittsburgh Medical Center, Presbyterian Hospital, Pittsburgh, Pennsylvania (R.L.H.); Division of Hematology/Oncology, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (F.S.L., J.D.); Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (N.M.A., I.F.P.); Departments of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois (C.H.).
Northwestern University · USUPMC Hillman Cancer Center · USUPMC Presbyterian · USNeurological Surgery · USUniversity of Pittsburgh Medical Center · US
Funding
MOLECULAR MARKERS AS PREDICTORS OF OUTCOME IN GLIOMASR01NS037704 · NINDS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI POLLACK, IAN F. · 1998 to 2015
$4.5MThe Significance of Isocitrate Dehydrogenase Mutations in GliomasK08CA155764 · NCI · UNIVERSITY OF KENTUCKY · PI HORBINSKI, CRAIG MICHAEL · 2011 to 2015
$857kNCI NIH HHS K08 CA155764NCI NIH HHS K08CA155764NINDS NIH HHS R01 NS037704NINDS NIH HHS R01NS37704
Abstract
backgroundIdentification of genetic changes in CNS tumors is important for the appropriate clinical management of patients. Our objective was to develop a next-generation sequencing (NGS) assay for simultaneously detecting the various types of genetic alterations characteristic for adult and pediatric CNS tumors that can be applied to small brain biopsies.
methodsWe report an amplification-based targeted NGS assay (GlioSeq) that analyzes 30 genes for single nucleotide variants (SNVs) and indels, 24 genes for copy number variations (CNVs), and 14 types of structural alterations in BRAF, EGFR, and FGFR3 genes in a single workflow. GlioSeq performance was evaluated in 54 adult and pediatric CNS tumors, and the results were compared with fluorescence in-situ hybridization, Sanger sequencing, and reverse transcription PCR.
resultsGlioSeq correctly identified 71/71 (100%) genetic alterations known to be present by conventional techniques, including 56 SNVs/indels, 9 CNVs, 3 EGFRvIII, and 3 KIAA1549-BRAF fusions. Only 20 ng of DNA and 10 ng of RNA were required for successful sequencing of 100% frozen and 96% formalin-fixed, paraffin-embedded tissue specimens. The assay sensitivity was 3%-5% of mutant alleles for SNVs and 1%-5% for gene fusions. The most commonly detected alterations were IDH1, TP53, TERT, ATRX. CDKN2A, and PTEN in high-grade gliomas, followed by BRAF fusions in low-grade gliomas and H3F3A mutations in pediatric gliomas.
conclusionsGlioSeq NGS assay offers accurate and sensitive detection of a wide range of genetic alterations in a single workflow. It allows rapid and cost-effective profiling of brain tumor specimens and thus provides valuable information for patient management.
Indexed as
Genetic Predisposition to DiseaseHigh-Throughput Nucleotide SequencingAdolescentAdultCentral Nervous System NeoplasmsChildChild, PreschoolDNA Copy Number VariationsGliomaHumansMutationProto-Oncogene Proteins B-rafProto-Oncogene Proteins B-rafCNS tumorsgene fusionsmutationsnext generation sequencingparaffin
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