{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["N/A"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001005061"],"sample_count":["124"],"description":["EGA dataset EGAD00001005061"],"repository":["EGA"],"title":["Whole Genome Sequencing data for epigenetic subgroups of meningioma"],"pubmed_abstract":["DNA methylation patterns delineate clinically relevant subgroups of meningioma. We previously established the six meningioma methylation classes (MC) benign 1-3, intermediate A and B, and malignant. Here, we set out to identify subgroup-specific mutational patterns and gene regulation. Whole genome sequencing was performed on 62 samples across all MCs and WHO grades from 62 patients with matched blood control, including 40 sporadic meningiomas and 22 meningiomas arising after radiation (Mrad). RNA sequencing was added for 18 of these cases and chromatin-immunoprecipitation for histone H3 lysine 27 acetylation (H3K27ac) followed by sequencing (ChIP-seq) for 16 samples. Besides the known mutations in meningioma, structural variants were found as the mechanism of NF2 inactivation in a small subset (5%) of sporadic meningiomas, similar to previous reports for Mrad. Aberrations of DMD were found to be enriched in MCs with NF2 mutations, and DMD was among the most differentially upregulated genes in NF2 mutant compared to NF2 wild-type cases. The mutational signature AC3, which has been associated with defects in homologous recombination repair (HRR), was detected in both sporadic meningioma and Mrad, but widely distributed across the genome in sporadic cases and enriched near genomic breakpoints in Mrad. Compared to the other MCs, the number of single nucleotide variants matching the AC3 pattern was significantly higher in the malignant MC, which also exhibited higher genomic instability, determined by the numbers of both large segments affected by copy number alterations and breakpoints between large segments. ChIP-seq analysis for H3K27ac revealed a specific activation of genes regulated by the transcription factor FOXM1 in the malignant MC. This analysis also revealed a super enhancer near the HOXD gene cluster in this MC, which, together with general upregulation of HOX genes in the malignant MC, indicates a role of HOX genes in meningioma aggressiveness. This data elucidates the biological mechanisms rendering different epigenetic subgroups of meningiomas, and suggests leveraging HRR as a novel therapeutic target."],"pubmed_title":["Mutational patterns and regulatory networks in epigenetic subgroups of meningioma."],"pubmed_authors":["Paramasivam Nagarajan N, Hübschmann Daniel D, Toprak Umut H UH, Ishaque Naveed N, Neidert Marian M, Schrimpf Daniel D, Stichel Damian D, Reuss David D, Sievers Philipp P, Reinhardt Annekathrin A, Wefers Annika K AK, Jones David T W DTW, Gu Zuguang Z, Werner Johannes J, Uhrig Sebastian S, Wirsching Hans-Georg HG, Schick Matthias M, Bewerunge-Hudler Melanie M, Beck Katja K, Brehmer Stephanie S, Urbschat Steffi S, Seiz-Rosenhagen Marcel M, Hänggi Daniel D, Herold-Mende Christel C, Ketter Ralf R, Eils Roland R, Ram Zvi Z, Pfister Stefan M SM, Wick Wolfgang W, Weller Michael M, Grossmann Rachel R, von Deimling Andreas A, Schlesner Matthias M, Sahm Felix F"],"name_synonyms":["YT, ARACHE., ACEE, N-ACHE"],"description_synonyms":["BamF, bim, biml, Malignant Neoplasm, whole blood, BamC, Neoplasms, bam, Benign Neoplasm, Genome Sequencing, ham, BOD, Tumor, Malignant, fs(3)neo61, CG10422, Benign, Complete Genome, HiSeq X Ten., Neoplasm, bim-beta7, bod, DmelCG10422, bimel, Complete, Whole Genome, Malignancy, HCAP, bim-beta6, Complete Genome Sequencing, Benign Neoplasms, alpha, Cancers, CDLS3, BMH, Sequencing, Malignant Neoplasms, Neoplasias, BIM, Bam-C, Whole, BAM, Bam, SMC3L1, Malignancies, CSPG6, other neoplasm, Neoplasia, Cancer, Tumors"],"pubmed_title_synonyms":["Clear Cell, Parasagittal Meningioma, Intracranial Meningiomas, Sphenoid Wing Meningioma, Intraorbital, Hemangiopericytic, Wing Meningioma, intracranial meningioma, Angiomatous Meningiomas, Multiple Meningiomas, Multiple Meningioma, Cerebral Convexity Meningioma, supratentorial meningioma, Malignant, Microcystic, Sphenoid Wing Meningiomas, Sphenoid, Papillary Meningiomas, Angioblastic, Papillary Meningioma, Sphenoid Wing, Xanthomatous Meningioma, Secretory Meningiomas, Hemangioblastic Meningiomas, Olfactory Groove, Cerebral, Xanthomatous Meningiomas, Fibrous, Secretory Meningioma, Angioblastic Meningioma, Convexity Meningioma, primary meningeal tumor, Fibrous Meningiomas, primary meningeal tumour, Hemangioblastic, Posterior Fossa Meningioma, Clear Cell Meningioma, Transitional Meningiomas, Groove Meningiomas, Epigenomic, Meningotheliomatous, Angiomatous Meningioma, Olfactory, Hemangiopericytic Meningioma, Xanthomatous, Microcystic Meningioma, Meningiomatoses, Olfactory Groove Meningiomas, Secretory, Intraorbital Meningiomas, Meningioma, Posterior Fossa, Transitional, meningioma, meningothelial cell tumour, Cerebral Convexity., Spinal Meningiomas, Posterior Fossa Meningiomas, Benign Meningiomas, familial, Transitional Meningioma, meningothelial cell tumor, Angioblastic Meningiomas, Meningotheliomatous Meningioma, Clear Cell Meningiomas, Hemangioblastic Meningioma, Intraorbital Meningioma, Psammomatous Meningiomas, Benign, Intracranial Meningioma, Angiomatous, Parasagittal, Spinal Meningioma, Intraventricular Meningiomas, Meningotheliomatous Meningiomas, Olfactory Groove Meningioma, Malignant Meningiomas, MNGMA, Meningiomas, Epigenetic, Intraventricular Meningioma, Microcystic Meningiomas, Meningiomatosis, susceptibility to, Cerebral Convexity Meningiomas, Convexity Meningiomas, Cerebral Convexity, Hemangiopericytic Meningiomas, Papillary, Intracranial, Psammomatous Meningioma, Multiple, Wing Meningiomas, susceptibility to familial meningioma, Psammomatous, Fibrous Meningioma, Parasagittal Meningiomas, Spinal, Benign Meningioma, meningeal neoplasm, Epigenetics, Intraventricular, Malignant Meningioma"],"pubmed_abstract_synonyms":["Clear Cell, type 2, T-cell leukemia, BB238854, Materials, intracranial meningioma, RNA Sequence Determination, Lysine Hydrochloride, acetylglucosaminyltransferase-like protein, with congenital contractures and muscle atrophy, Sequence Determination, RNA Sequence, AGL4, mental retardation, A4, HMCS, Multiple Meningioma, DNA Methylations, Social Controls, prevention, Gene Clusters, Sphenoid, 5730420M11Rik, Mutations, Papillary Meningiomas, Multigene, hMCS, Lysine Acetate, Angioblastic, 2, TGT3, Analysis, myd, foxm1l, L Lysine, contractures of feet, gamma sarcoglycan, SET, Chromatin Immunoprecipitation Sequencing Chip, like-acetylglucosaminyltransferase, primary meningeal tumor, Analyses, Genomes, K, ChIP, Homologous, fkhl16, primary meningeal tumour, Chromatin Immuno Precipitation Paired End Tag, F10N7_150, Mbp-1, homologous recombinational repair, Sequence Determinations, Meningotheliomatous, Epigenomic, DmelCG4299, Social, set, oculomotor, Xanthomatous, LYS, Lysin, ACN, Role Concepts, ATAC-Seq, Histone H5, Histone H4, Histone H7, zinc ion regulated proximal promoter sequence-specific DNA binding, Precipitations, Nucleotide, Histone H1, TRANSCRIPTION FACTOR, Histone H3, RNA polymerase II distal enhancer sequence-specific binding, meningioma, meningothelial cell tumour, RNA polymerase II core promoter proximal region sequence-specific binding, preventive therapy, HRR, Benign Meningiomas, Cross Linking and Immunoprecipitation Followed by Deep Sequencing, acetylation, familial, Clear Cell Meningiomas, Dp71, Benign, Role Concept, mKIAA0609, Role, Intraventricular Meningiomas, sarcoglycan, Meningotheliomatous Meningiomas, sequence-specific distal enhancer binding RNA polymerase II transcription factor activity, MRXS4, activation, PIG29, nucleotides, Meningiomas, fg, AA408308, HLA-DR-associated protein II, DI-2, Severe dystrophinopathy, I-2Dm, F14P3_4, Convexity Meningiomas, INSDC_feature:gene, alpha, whole genome, Controls, DMD, Transcription factor, Genomic, Hemangiopericytic Meningiomas, I-2PP1, HFH-11B, Papillary, Psammomatous Meningioma, Multiple, MDC1D, hfh-11, TAF-IBETA, enr, Material, 2.8.1.9, 35kD dystrophin-associated glycoprotein, Parasagittal Meningiomas, copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, TAF-Ibeta, DNA, Epigenetics, ChIP-Exonuclease, metal ion regulated sequence-specific DNA binding, apraxia, Regulations, X-linked, Angiomatous Meningiomas, MPP-2, number, CLIP-Seq, DXS164, SEPALLATA 2, Cerebral Convexity Meningioma, supratentorial meningioma, Genomic Stability, Transcription Factor, HFH-11, LARGE1, X-linked recessive, zinc ion regulated core promoter proximal region sequence-specific DNA binding, Papillary Meningioma, Genomic Instabilities, Immune Precipitations, Lysine, MAM, gamma-SG, Immune Precipitation, Genome Instabilities, Histone H3.3, central type, Transcription, Complete, Whole Genome, Fibrous Meningiomas, MDDGB6, Complete Genome Sequencing, Hemangioblastic, Posterior Fossa Meningioma, Cross-Linking and Immunoprecipitation Followed by Deep Sequencing, 2pp2a, BMD, CG10574, Sequencing, Angiomatous Meningioma, AW554517, Hemangiopericytic Meningioma, 2PP2A, RNA polymerase II proximal promoter sequence-specific DNA binding, Whole, copper ion regulated proximal promoter sequence-specific DNA binding, dSET, dSet, and oculomotor apraxia, with congenital contractures and Low fingertip arches, Methylations, Secretory, Intraorbital Meningiomas, NF2, MCS, Sequence Analyses, Transitional, RNA, Fkh16, Gene Cluster, whole blood, 35 kDa dystrophin-associated glycoprotein, RNA Sequence Determinations, TRIDENT, Transitional Meningioma, Meningotheliomatous Meningioma, zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, homeobox 1, Factor, Histone, SGCG, Concept, Psammomatous Meningiomas, Reiterated Genes, Angiomatous, acoustic Schwannomas, Foxm1b, Parasagittal, I-2PP2A, Social Control, Acetate, Spinal Meningioma, Dm I-2, chemical analysis, RNA polymerase II transcription factor activity, Reiterated Gene, merlin, L-Lysine, Malignant Meningiomas, homology-directed repair, HNF-3, mdx, Rad51-dependent recombinational repair., DMDA1, ensemble, underdeveloped, Intraventricular Meningioma, pke, prophylaxis, MoCo sulfurase, Chromatin Immunoprecipitation, pseudohypertrophic progressive, metal ion regulated core promoter proximal region sequence-specific binding, ChIP-Seq, INS-1, Histone H1(s), F10N7.150, Assay for Transposase Accessible Chromatin Using Sequencing, Miles-Carpenter syndrome, Psammomatous, Genome Instability, like-glycosyltransferase, control, Families, Chromatin Immuno-Precipitation Paired-End Tag, Benign Meningioma, MRX85, regulation, Intraventricular, Instability, Enisyl, Rad51-dependent recombinational repair, Co-Immunoprecipitations, MGC130048, chromosomal crossover, Intracranial Meningiomas, Sphenoid Wing Meningioma, IPP2A2, Intraorbital, Hemangiopericytic, Wing Meningioma, determination, DXS206, muscular dystrophy, Mbp1, Genome Stability, Trident, Sphenoid Wing Meningiomas, Co Immunoprecipitation, Histone H2b, Histone H2a, Recombinations, interorganelle junction, BANF, Roles, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, Concepts, prevention and control, Formal Social Controls, Chromatins, ChIA-PET, Xanthomatous Meningiomas, Fibrous, Angioblastic Meningioma, Chromatin Immuno precipitation Sequencing, Convexity Meningioma, DNA methylation maintenance, reference sample, TAF-I, MCSL, Determination, Mpm2, Co-Immunoprecipitation, Clear Cell Meningioma, ZC4H2-Associated Rare Disorders (ZARD), Precipitation, hypoplasia, epsilon-diaminocaproic acid, Transitional Meningiomas, DXSmh7, MCSP, DXSmh9, DNA methylation, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity, Miles-Carpenter type, Chromatin Immunoprecipitation Paired-End Tag, preventive measures, IGAAD, Immune, DmelCG10574, chromosome scaffold, Chromatin Immunoprecipitation Sequencing-Chips, AGAMOUS-like 4, DXS239, gamma-sarcoglycan, Meningiomatoses, sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity, DXS230, Olfactory Groove Meningiomas, muscle atrophy, Meningioma, dys, nuclear chromatin, phapii, High Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, with congenital contractures and low fingertip arches, gyltl1b-b, SG-gamma, Genome Sequencing, StF-IT-1, syndromic 4, mpp2, Clusters, metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity, ChIP-PET, Determinations, neurofibromatosis central type, Intraorbital Meningioma, Complete Genome, Molybdenum cofactor sulfurtransferase, acoustic schwannomas bilateral, MDDGA6, lysine, Genetic Materials, Olfactory Groove Meningioma, Wieacker-Wolff syndrome, KIAA0609, MNGMA, Genetic Material, Dp427, acetylglucosaminyltransferase-like 1A, HFH11, F14P3.4, WRWF, Recombination, gyltl1b, Factors, Epigenetic, Microcystic Meningiomas, Meningiomatosis, susceptibility to, mdc1d, Control, CG4299, HDR, ChIP Exonuclease, DXS142, gamma (35kDa dystrophin-associated glycoprotein), LARGE_HUMAN, CMD3B, DXS268, DXS269, Intracranial, MPP2, type II, DXS270, DXS272, DMDA, Fibrous Meningioma, Patient, Cluster, X-linked intellectual disability, MOS, Cistron, meningeal neoplasm, foot contractures-muscle atrophy-oculomotor apraxia syndrome, Malignant Meningioma, Genomic Stabilities, i2pp2a, Regulation, MPHOSPH2, Methylation, metal ion regulated proximal promoter sequence-specific DNA binding, Parasagittal Meningioma, cytoplasmic chromatin, ChIP-Chip, acoustic neurinoma bilateral, SGCG_HUMAN, Chromatin Immuno-precipitation, Multiple Meningiomas, Gene, Assay for Transposase-Accessible Chromatin Using Sequencing, neurofibromatosis, Malignant, HSMCSGEN1, presence, Microcystic, TYPE, PHAPII, froggy, Gyltl1a, DAGA4, Wieacker Wolff syndrome, Stability, reduced, Sphenoid Wing, Instabilities, Xanthomatous Meningioma, Chromatin Immunoprecipitation Sequencing-Chip, 35DAG, neurofibromatosis type II, intellectual disability-developmental delay-contractures syndrome, Secretory Meningiomas, tiny, Hemangioblastic Meningiomas, Olfactory Groove, Cerebral, SCG3, acoustic neurinoma, Secretory Meningioma, Genetic, pattern, distribution, Chromatin Immunoprecipitation Paired End Tag, ipp2a2, Acetylations, LARGE, Groove Meningiomas, bilateral, inter-organelle junction, Duchenne type, BPFD#36, Olfactory, RNA Sequence Analyses, taf-ibeta, Clients, Microcystic Meningioma, RNA Sequencing, Rhp51-dependent recombinational repair, Wieacker syndrome, Family, Posterior Fossa, Controlled, Reiterated, small, Multigene Families, HITS-CLIP, Controlling, Spinal Meningiomas, Formal Social Control, Homologous Recombinations, Posterior Fossa Meningiomas, igaad, meningothelial cell tumor, ChIP Sequencing, Angioblastic Meningiomas, Cistrons, Client, ChIP-Exo, Hemangioblastic Meningioma, group, LGMD2C, Stabilities, transcription factor activity, WRWFXLR, count in organism, Intracranial Meningioma, I2PP2A, High-Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, methylation, Miles-CARPENTER X-linked mental retardation syndrome, metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, Genome Stabilities, KNOTTED1-like homeobox gene 5, WIN, Radiations, Genes, reciprocal DNA recombination, Cerebral Convexity Meningiomas, Chromatin Immuno-precipitation Sequencing, Cerebral Convexity, copper ion regulated core promoter proximal region sequence-specific binding, FOXM1B, FKHL16, dSET/TAF-Ibeta, Wing Meningiomas, susceptibility to familial meningioma, 2610030F17Rik, RNA Sequence Analysis, SCARMD2, cardinality, Spinal, H3(any), assay, AA407739, 6-diaminohexanoic acid, SCH, Genome, glycosyltransferase-like protein LARGE1"],"additional_accession":[]},"is_claimable":false,"name":"be40ebac-acee-4026-a661-4330bb0f657b - samples","description":"Bam files for 124 samples (62 tumor vs blood pairs); Whole Genome Sequencing performed on Illumina HiSeq X Ten","dates":{"updated":"2019-06-12 09:53:14"},"accession":"EGAD00001005061","cross_references":{"TAXONOMY":["9606"],"pubmed":["31069492"],"EGA":["EGAC00001000452","EGAS00001003481"]}}