{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2000;"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001001627"],"sample_count":["4"],"description":["EGA dataset EGAD00001001627"],"repository":["EGA"],"title":["GBM-ZEB1: RNA sequencing of parental tumors used for cell line generation"],"pubmed_abstract":["Promoter methylation status of O-6-methylguanine-DNA methyltransferase (MGMT), a DNA repair enzyme, is a critical biomarker in glioblastoma (GBM), as treatment decisions and clinical trial inclusion rely on its accurate assessment. However, interpretation of results is complicated by poor interassay reproducibility as well as a weak correlation between methylation status and expression levels of MGMT. This study systematically investigates the influence of tumor purity on tissue subjected to MGMT analysis. A quantitative, allele-specific real-time PCR (qAS-PCR) assay was developed to determine genotype and mutant allele frequency of telomerase promoter (pTERT) mutations as a direct measure of tumor purity. We studied tumor purity, pTERT mutation by Sanger sequencing, MGMT methylation by pyrosequencing, IDH1 mutation status, and clinical parameters in a cohort of high-grade gliomas (<i>n</i> = 97). The qAS-PCR reliably predicted pTERT genotype and tumor purity compared with independent methods. Tumor purity positively and significantly correlated with the extent of methylation in MGMT methylated GBMs. Extent of MGMT methylation differed significantly with respect to pTERT mutation hotspot (C228T vs. C250T). Interestingly, frontal lobe tumors showed greater tumor purity than those in other locations. Above all, tumor purity was identified as an independent prognostic factor in GBM. In conclusion, we determined mutual associations of tumor purity with MGMT methylation and pTERT mutations and found that the extent of MGMT methylation reflects tumor purity. In turn, tumor purity is prognostic in IDH1 wild-type GBM.<b>Implications:</b> Tumor purity is an independent prognostic marker in glioblastoma and is associated with the extent of MGMT methylation. <i>Mol Cancer Res; 15(5); 532-40. ©2017 AACR</i>."],"pubmed_title":["Prognostic Relevance of Tumor Purity and Interaction with MGMT Methylation in Glioblastoma."],"pubmed_authors":["Schulze Heuling Eva E, Knab Felix F, Radke Josefine J, Eskilsson Eskil E, Martinez-Ledesma Emmanuel E, Koch Arend A, Czabanka Marcus M, Dieterich Christoph C, Verhaak Roel G RG, Harms Christoph C, Euskirchen Philipp P"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"pubmed_title_synonyms":["grade IV adult astrocytic tumour, Malignant Neoplasm, O6-alkylguanine-DNA alkyltransferase, Neoplasms, Benign Neoplasm, Tumor, methylated-DNA-protein-cysteine S-methyltransferase activity, Giant Cell, Grade IV, Malignant, Astrocytomas, DNA-6-O-methylguanine:protein-L-cysteine S-methyltransferase activity, DNA-6-O-methylguanine - [protein]-L-cysteine S-methyltransferase activity, adult glioblastoma multiforme, Benign, 6-O-methylguanine-DNA methyltransferase activity, primary glioblastoma multiforme, Neoplasm, DNA-6-O-methylguanine:[protein]-L-cysteine S-methyltransferase activity, glioblastoma, methylation, Giant Cell Glioblastomas, 6-O-methylguanine-DNA methyltransferase, DNA-6-O-methylguanine - protein-L-cysteine S-methyltransferase activity, glioblastoma multiforme, O-6-methylguanine-DNA-alkyltransferase, Glioblastoma, grade IV adult astrocytic tumor, O-6-methylguanine-DNA-alkyltransferase activity, Malignancy, spongioblastoma multiforme, Glioblastomas, GBM, Benign Neoplasms, Cancers, Giant Cell Glioblastoma, Astrocytoma, Malignant Neoplasms, Neoplasias, Glioblastoma Multiforme, 2.1.1.63, MGMT, Agat, Grade IV Astrocytomas, grade IV adult Astrocytic tumor, AGT, Malignancies, Grade IV Astrocytoma, Grade IV., other neoplasm, Methylations, Neoplasia, Cancer, Tumors, AI267024"],"description_synonyms":["RNA, Bru, dTAF[[II]]230, TAF[[II]]250, d230, Malignant Neoplasm, Data Set, RNA Sequence Determination, Raw, taxonomy, RNA Sequence Determinations, Sequence Determination, Neoplasms, RNA Sequence, Benign Neoplasm, Systematics, TAF200, Gene, l(3)84Ab, dTAFII250, BG:DS00004.13, Tumor, TAFII-250, TAF250/230, Malignant, EfW1, Cell, Determinations, dTAF230, Classifications, dmTAF[[II]]230, Taxonomies, hierarchies, TAFII250, Benign, hierarchy, MT, dmTAF1, Taf230, systematics, p230, Neoplasm, TAF[[II]]250/230, TFIID, Del(8)44H, Analysis, TAF250, Svc, Taf[[II]]250, Taf200, Taxonomy, primary cancer, Col4a-1, dTAF[[II]]250, TAF[[II]]230, Gene Expressions, TFIID TAF250, Analyses, Malignancy, Determination, cel, cell, Benign Neoplasms, Taf1p, TAF[II]250, Cancers, CG17603, Sequence Determinations, Expressions, TAF[[II]], malignant tumor, Sequencing, Malignant Neoplasms, Neoplasias, dTAF250, DmelCG17603, TAF1., RNA Sequence Analyses, Taf250, malignant neoplasm, SR3-5, RNA Sequence Analysis, RNA Sequencing, Malignancies, Expression, TAF, Neoplasia, TAF230, Sequence Analyses, Cancer, Tumors"],"pubmed_abstract_synonyms":["extent, Real Time PCR, Surrogate Endpoints, O6-alkylguanine-DNA alkyltransferase, Nucleotide Sequencing, odd(Oz), Laboratory, Grade (high/low), Physical, A4, Genetic Hotspot, INCLUSION, Tumor, Lobus Frontalis, Status, DNA-6-O-methylguanine:protein-L-cysteine S-methyltransferase activity, Methylated-DNA—Protein-Cysteine Methyltransferase, Mutations, Personal, Compared, Biological, Method, Telomerase Catalytic, Associations, Equilibrium, Correlated, B1, ten-m, l(2)SH1330, DNA-6-O-methylguanine:[protein]-L-cysteine S-methyltransferase activity, correlation, Polymerase Chain, Frontal, Id-1, Deep Sequencing, PICD, treatment, Correlation, Methylated MGMT Promoter, gamma sarcoglycan, independent, Histopathology Grade, l(3)rP126, Subunit, Illumina Sequencing, Idpc, Intervention Study, Tissue, Weights, Comparison, procedures, Giant Cell Glioblastoma, BcDNA:AT25108, Alkylguanine DNA Alkyltransferase, Astrocytoma, Prognosis Marker, Poor, Malignant Germ Cell International Collaborative Risk Classification, Independence, scientific observation, grade IV adult Astrocytic tumor, IDPC, Methylated MGMT Gene Promoter, Tumors, Ten-mc, Brodmann's, RES, Quantitative Real-Time, Anchored Polymerase Chain Reaction, Tumor Grade, Viral, completeness, Low Income, assessment, CG5723, AACR, Real-Time PCR, Telomerase Reverse, Observation Result, Giant Cell, Procedure, Frontal Eye Fields, predicted, MaGIC Risk, DNA-6-O-methylguanine - [protein]-L-cysteine S-methyltransferase activity, l(2)br3, Benign, Marker, TERT C228T, 6-O-methylguanine-DNA methyltransferase activity, Interpretation, Next-Generation, Molecular Marker of Prognosis, Telomerase Reverse Transcriptase c.1-146C>T, sarcoglycan, simple tissue, EC 2.1.1.63, Mutant, Turn, PCR, 6-O-methylguanine-DNA methyltransferase, Complicated, Physical Assessment, Idh-1, TUMCECE, Glioblastoma, Moving from wheelchair to bed and return independent, O-6-methylguanine-DNA-alkyltransferase activity, End Points, IMDC Poor Risk Group, IDH1 Mutation, histological_grade, Benign Neoplasms, Immunologic, Methodological, Laboratory Marker, DNA repair enzyme, Supplementary, Present, polymerase chain reaction, Malignant Neoplasms, High Throughput Sequencing, Poor CALGB Criteria, MGMT, Area 8, Supplementary Eye Fields, 35kD dystrophin-associated glycoprotein, AGT, 2017, DNA, Interpretation of Laboratory Test, 1 295 250 C>T, Allele Frequencies, Lobe, Clinical Batch, TERT:c.1-146C>T, Respect, 5301, Clinical Marker, Neoplasms, number, Telomerase Reverse Transcriptase c.1-124C>T, Polymerase Chain Reactions, High-Throughput DNA, Prognostic Factors, DNA repair protein, Determine, DmelCG4482, Next-Generation Sequencing, Cytosolic Gene Mutation, Odz, physical_exam, Deep, Repair Enzymes, Brodmann's Area 8, Soluble Gene Mutation, glioblastoma, MAM, gamma-SG, Giant Cell Glioblastomas, PHYSICAL EXAMINATION, Sanger sequencing, Technique, TERT NM_198253.2:c.1-146C>T, odz, In, Clinical, MGMT Gene Methylation, frontal cortex, Frontal Eye Field, Pyrosequencing, Methylated-DNA Protein-Cysteine Methyltransferase, l(3)rJ307, Grading, Sequencing, Genotypes, TERT:c.1-124C>T, Study, Neoplasias, l(3)05301, Glioblastoma Multiforme, Enzyme, Tumor_Grade, Isocitrate Dehydrogenase (NADP(+)) 1, Grade IV Astrocytoma, Expression, Anchored PCR, Tumor Cells/Total Cells, Independent for Wheelchair Transfer, Methylations, Supplementary Eye Field, Biologic, Cancer, measuring, grade IV adult astrocytic tumour, Malignant Neoplasm, 35 kDa dystrophin-associated glycoprotein, DNA-6-O-Methylguanine[protein]-L-Cysteine S-Methyltransferase, CG4482, Serum Markers, Inclusion Bodies, Factor, SGCG, Immune Marker, Conclusion, Ten79E, adult glioblastoma multiforme, Cortex, MT, Inclusion Body, pyrosequencing, Surrogate End Point, C250T, chemical analysis, Neoplasm, clinical, INSDC_feature:regulatory, Next Generation Sequencing, Biologic Markers, glioblastoma multiforme, Methylated MGMT, primary cancer, CT16449, DMDA1, Surrogate, Endpoints, Glioblastomas, Accuracy, Directly, American Association of Cancer Research., O-6-Methylguanine-DNA-Alkyltransferase, Cancers, Independent for Transfer Between Wheelchair and Bed, Prognostic Marker, malignant tumor, TERT NM_198253.2:c.1-124C>T, Methylguanine-DNA Methyltransferase, br3, Genogroups, Eye Fields, Specific, Kinetic Polymerase Chain Reaction, High Throughput Nucleotide Sequencing, Independent, ten(m), NIP, Reproducibility, DNA Repair, physical exam, Neoplasia, High-Throughput Nucleotide, CG11452, Immune Markers, Quantitative Real Time Polymerase Chain Reaction, MGC130048, O-6-Methylguanine-DNA Methyltransferase Gene Promoter Methylation, Biological Markers, Viral Marker, determination, Physical Exam, Massively-Parallel, Direct, clinical data, Biochemical, Endpoint, nip, Measure, Serum, Astrocytomas, Quantitative, Laboratory Markers, Techniques, DmelCG5723, High-Throughput RNA Sequencing, AI314845, grade, Mutual, Influence, HISTOLOGY_GRADE, IMDC Poor, gene expression, Quantitative Real-Time PCR, INTP, Frontal Cortex, Prognoses, INTERPRETATION, Identification, Determination, l(3)rL201, Inverse Polymerase Chain Reaction, ten-m/odz, 35Bb, General Examination, ten[m], IDH1 Gene Mutation, Frontal Cortices, inclusion criteria, Brodmann Area 8, grading, Immune, Markers, High Throughput RNA Sequencing, Methodological Studies, malignant neoplasm, Viral Markers, Reaction, Telomerase Reverse Transcriptase Catalytic Subunit, Hotspot, disease management, Therapies, Real-Time, Great, gamma-sarcoglycan, Allele, Malignancies, Positive, Frequency, Genetic Equilibrium, PHYSICAL EXAM, 1 295 228 C>T, High-Throughput RNA, Therapy, Determined, Surrogate Endpoint, IDH, SG-gamma, High-Throughput DNA Sequencing, IDP, Biochemical Markers, l(3)05309, Biologic Marker, results, Telomerase, IDCD, tumor grade, Gene Expression, Poverty, Ion Torrent Sequencing, l35Bb, Frequencies, primary glioblastoma multiforme, Massively-Parallel Sequencing, Tumor_Purity, NM_198253.2:c.1-124C>T, Ion Torrent, Quantitative Real Time PCR, Assessed, Clinical Data, DNA-6-O-methylguanine - protein-L-cysteine S-methyltransferase activity, Inclusion, Gene Frequencies, Factors, Nested Polymerase Chain Reaction, spongioblastoma multiforme, Prognostic, conclusion, Dignity, Brodmanns Area 8, GBM, Presence, gamma (35kDa dystrophin-associated glycoprotein), Methylated-DNA--Protein-Cysteine Methyltransferase, Methodological Study, Treatments, l(2)SH2 1330, Identified, Real Time Polymerase Chain Reaction, TERT C250T, Agat, DMDA, Histopathologic Grade, Grade IV Astrocytomas, Expressed, Biochemical Marker, Tumor Purity, Assess, Measures and Weights, BG:DS01219.1, Physical Examination, IMDC Poor Risk, Prognostic Factor, Inclusion Criteria, Allelomorphs, High Throughput DNA Sequencing, SGCG_HUMAN, Procedures, Independent for Transfer, Clinical Markers, mol, NM_198253.2:c.1-146C>T, Real-Time PCRs, Benign Neoplasm, Correlative, Gene, Ten[m], Grade IV, Inverse, Compare, Malignant, presence, Illumina, TYPE, Surrogate End Points, Protein Turn, DAGA4, Surrogate Markers, Inverse PCR, Allele Frequency, Repair Enzyme, 35DAG, Studies, Massively Parallel Sequencing, HEL-216, AI788952, SCG3, l(2)br23, Biomarker, study, hotspot, Ion Proton Sequencing, grade IV adult astrocytic tumor, Genetic, PRESENT, O-6-Methylguanine-DNA Alkyltransferase, Malignancy, Inclusions, Biological Marker, weak, Measures, Eye Field, E030024J03Rik, Methylguanine-DNA Methyltransferase Gene Promoter Methylation, Quantitative Real-Time PCRs, dye terminator sequencing, Tumor Cell to Total Cell Ratio Measurement, Allelomorph, Reverse Transcriptase, Immunologic Markers, Catalytic Subunit, Found, odz/ten-m, Telomerase Catalytic Subunit, Personal Respect, histological grade, High-Throughput, RNA Sequencing, Immunologic Marker, AI267024, Telomerase Reverse Transcriptase, Methylated-DNA-Protein-Cysteine Methyltransferase, Include, physical examination, Critical, Quantitative Real-Time Polymerase Chain Reaction, l(2)35Bb, End Point, O-6-Methylguanine-DNA Methyltransferase, methylated-DNA-protein-cysteine S-methyltransferase activity, LGMD2C, Enzymes, count in organism, TERT 1 295 228 C>T, Clinical Lot, Genogroup, Grade, Brodmann, DNA Sequencing, MGMT Gene Promoter Methylation, HEL-S-26, PCRs, Isocitrate Dehydrogenase 1 (NADP+), methylation, techniques, MGMT Methylation, O-6-methylguanine-DNA-alkyltransferase, Anchored, Serum Marker, Assessment, Reactions, Nested, Scales, C228T, CG15268, Surrogate Marker, DNA Repair Enzyme, Accurate, Specified, O6-Alkylguanine DNA Alkyltransferase, 2.1.1.63, Therapeutic, High-Throughput Sequencing, Transcriptase, Histologic Grade, SCARMD2, International Metastatic Renal Cell Carcinoma Database Consortium (IMDC) Criteria - Poor-Risk Group, Nested PCR, Treatment, assay, Ion Proton, Greater, Frontal Lobes, l(3)00844, tumor_grade, methodology"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-CHARITE-28-09-2015-14:05:54:879-543 - samples","description":"This dataset contains RNA sequencing raw data from four parental tumors that were used for classification of gene expression subtypes (Verhaak, Cancer Cell 2010) using ssGSEA.","dates":{"updated":"2017-07-26 15:39:26"},"accession":"EGAD00001001627","cross_references":{"TAXONOMY":["9606"],"pubmed":["28148826"],"EGA":["EGAC00001000354","EGAS00001001167"]}}