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Title:
Next-generation sequencing in routine brain tumor diagnostics enables an integrated diagnosis and identifies actionable targets | Acta Neuropathologica
Description:
With the number of prognostic and predictive genetic markers in neuro-oncology steadily growing, the need for comprehensive molecular analysis of neuropathology samples has vastly increased. We therefore developed a customized enrichment/hybrid-capture-based next-generation sequencing (NGS) gene panel comprising the entire coding and selected intronic and promoter regions of 130 genes recurrently altered in brain tumors, allowing for the detection of single nucleotide variations, fusions, and copy number aberrations. Optimization of probe design, library generation and sequencing conditions on 150 samples resulted in a 5-workday routine workflow from the formalin-fixed paraffin-embedded sample to neuropathological report. This protocol was applied to 79 retrospective cases with established molecular aberrations for validation and 71 prospective cases for discovery of potential therapeutic targets. Concordance of NGS compared to established, single biomarker methods was 98.0 %, with discrepancies resulting from one case where a TERT promoter mutation was not called by NGS and three ATRX mutations not being detected by Sanger sequencing. Importantly, in samples with low tumor cell content, NGS was able to identify mutant alleles that were not detectable by traditional methods. Information derived from NGS data identified potential targets for experimental therapy in 37/47 (79 %) glioblastomas, 9/10 (90 %) pilocytic astrocytomas, and 5/14 (36 %) medulloblastomas in the prospective target discovery cohort. In conclusion, we present the settings for high-throughput, adaptive next-generation sequencing in routine neuropathology diagnostics. Such an approach will likely become highly valuable in the near future for treatment decision making, as more therapeutic targets emerge and genetic information enters the classification of brain tumors.
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article, pubmed, google, scholar, sequencing, cancer, cas, heidelberg, research, german, germany, center, nextgeneration, sahm, acta, capper, central, dkfz, analysis, brain, tumor, schrimpf, david, clinical, dna, jones, reuss, accessed, oct, neuropathol, content, data, information, routine, koelsche, neuropathology, access, pathol, idh, consortium, privacy, cookies, diagnostics, targets, kratz, christian, korshunov, wiestler, wick, witt,
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/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v216-software-guide-15051736 org/packages/release/bioc/html/conumee formalin-fixed paraffin-embedded sample formalin-fixed paraffin-embedded dna customized enrichment/hybrid-capture-based month download article/chapter andreas von deimling christel herold-mende accurate long-read alignment formalin-fixed tissues egfrviii-targeted vaccination therapy neuro-oncology steadily growing io/hts-specs/samv1 io/hts-specs/vcfv4 mutation-specific monoclonal antibody tumor rna-seq data neuropathology-haarlem consensus guidelines idh mutant diffuse copy number aberrations ruprecht-karls-university heidelberg identifies actionable targets high-throughput sequencing data routine neuropathology diagnostics melanie bewerunge-hudler von deimling de la orden clinical sequencing applications privacy choices/manage cookies full article pdf related subjects potential therapeutic targets andrey korshunov generation molecular genetics translational cancer research louis dn diffuse astrocytoma treatment decision making target capture experiments haplotype-based approaches identify mutant alleles 5-workday routine workflow reuss de therapeutic targets emerge german cancer aid pilocytic astrocytoma comprehensive molecular analysis combined molecular analysis melting curve analysis pediatric neurooncology dna sequencing genomics
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headline:Next-generation sequencing in routine brain tumor diagnostics enables an integrated diagnosis and identifies actionable targets
description:With the number of prognostic and predictive genetic markers in neuro-oncology steadily growing, the need for comprehensive molecular analysis of neuropathology samples has vastly increased. We therefore developed a customized enrichment/hybrid-capture-based next-generation sequencing (NGS) gene panel comprising the entire coding and selected intronic and promoter regions of 130 genes recurrently altered in brain tumors, allowing for the detection of single nucleotide variations, fusions, and copy number aberrations. Optimization of probe design, library generation and sequencing conditions on 150 samples resulted in a 5-workday routine workflow from the formalin-fixed paraffin-embedded sample to neuropathological report. This protocol was applied to 79 retrospective cases with established molecular aberrations for validation and 71 prospective cases for discovery of potential therapeutic targets. Concordance of NGS compared to established, single biomarker methods was 98.0 %, with discrepancies resulting from one case where a TERT promoter mutation was not called by NGS and three ATRX mutations not being detected by Sanger sequencing. Importantly, in samples with low tumor cell content, NGS was able to identify mutant alleles that were not detectable by traditional methods. Information derived from NGS data identified potential targets for experimental therapy in 37/47 (79 %) glioblastomas, 9/10 (90 %) pilocytic astrocytomas, and 5/14 (36 %) medulloblastomas in the prospective target discovery cohort. In conclusion, we present the settings for high-throughput, adaptive next-generation sequencing in routine neuropathology diagnostics. Such an approach will likely become highly valuable in the near future for treatment decision making, as more therapeutic targets emerge and genetic information enters the classification of brain tumors.
datePublished:2015-12-15T00:00:00Z
dateModified:2015-12-15T00:00:00Z
pageStart:903
pageEnd:910
sameAs:https://doi.org/10.1007/s00401-015-1519-8
keywords:
Medulloblastoma
Pilocytic Astrocytoma
FFPE Tissue
Copy Number Aberration
Diffuse Glioma
Pathology
Neurosciences
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headline:Next-generation sequencing in routine brain tumor diagnostics enables an integrated diagnosis and identifies actionable targets
description:With the number of prognostic and predictive genetic markers in neuro-oncology steadily growing, the need for comprehensive molecular analysis of neuropathology samples has vastly increased. We therefore developed a customized enrichment/hybrid-capture-based next-generation sequencing (NGS) gene panel comprising the entire coding and selected intronic and promoter regions of 130 genes recurrently altered in brain tumors, allowing for the detection of single nucleotide variations, fusions, and copy number aberrations. Optimization of probe design, library generation and sequencing conditions on 150 samples resulted in a 5-workday routine workflow from the formalin-fixed paraffin-embedded sample to neuropathological report. This protocol was applied to 79 retrospective cases with established molecular aberrations for validation and 71 prospective cases for discovery of potential therapeutic targets. Concordance of NGS compared to established, single biomarker methods was 98.0 %, with discrepancies resulting from one case where a TERT promoter mutation was not called by NGS and three ATRX mutations not being detected by Sanger sequencing. Importantly, in samples with low tumor cell content, NGS was able to identify mutant alleles that were not detectable by traditional methods. Information derived from NGS data identified potential targets for experimental therapy in 37/47 (79 %) glioblastomas, 9/10 (90 %) pilocytic astrocytomas, and 5/14 (36 %) medulloblastomas in the prospective target discovery cohort. In conclusion, we present the settings for high-throughput, adaptive next-generation sequencing in routine neuropathology diagnostics. Such an approach will likely become highly valuable in the near future for treatment decision making, as more therapeutic targets emerge and genetic information enters the classification of brain tumors.
datePublished:2015-12-15T00:00:00Z
dateModified:2015-12-15T00:00:00Z
pageStart:903
pageEnd:910
sameAs:https://doi.org/10.1007/s00401-015-1519-8
keywords:
Medulloblastoma
Pilocytic Astrocytoma
FFPE Tissue
Copy Number Aberration
Diffuse Glioma
Pathology
Neurosciences
image:
https://media.springernature.com/lw1200/springer-static/image/art%3A10.1007%2Fs00401-015-1519-8/MediaObjects/401_2015_1519_Fig1_HTML.gif
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name:Department of Pediatric Oncology, Haematology and Immunology, Heidelberg University Hospital, and National Center for Tumor Diseases (NCT), Heidelberg, Germany
name:Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
name:Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
name:Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
name:Department of Neuropathology, Otto von Guericke University Magdeburg, Magdeburg, Germany
name:Center of Neuropathology, Ludwig-Maximilians-University, Munich, Germany
name:Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
name:Neurology Clinic, Heidelberg University Hospital, Heidelberg, Germany
name:Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
name:Department of Pediatric Oncology, Haematology and Immunology, Heidelberg University Hospital, and National Center for Tumor Diseases (NCT), Heidelberg, Germany
name:Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
name:Neurology Clinic, Heidelberg University Hospital, Heidelberg, Germany
name:Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
name:Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
name:Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
name:Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
name:Department of Pediatric Oncology, Haematology and Immunology, Heidelberg University Hospital, and National Center for Tumor Diseases (NCT), Heidelberg, Germany
name:Neurology Clinic, Heidelberg University Hospital, Heidelberg, Germany
name:Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
name:Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
name:Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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