{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina OmniQuad 2.5 - CNVpartition"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00010000260"],"sample_count":["77"],"description":["EGA dataset EGAD00010000260"],"repository":["EGA"],"title":["Title not provided"],"pubmed_abstract":["<h4>Background</h4>Childhood CNS primitive neuro-ectodermal brain tumours (PNETs) are very aggressive brain tumours for which the molecular features and best treatment approaches are unknown. We assessed a large cohort of these rare tumours to identify molecular markers to enhance clinical management of this disease.<h4>Methods</h4>We obtained 142 primary hemispheric CNS PNET samples from 20 institutions in nine countries and examined transcriptional profiles for a subset of 51 samples and copy number profiles for a subset of 77 samples. We used clustering, gene, and pathway enrichment analyses to identify tumour subgroups and group-specific molecular markers, and applied immunohistochemical and gene-expression analyses to validate and assess the clinical significance of the subgroup markers.<h4>Findings</h4>We identified three molecular subgroups of CNS PNETs that were distinguished by primitive neural (group 1), oligoneural (group 2), and mesenchymal lineage (group 3) gene-expression signatures with differential expression of cell-lineage markers LIN28 and OLIG2. Patients with group 1 tumours were most often female (male:female ratio 0·61 for group 1 vs 1·25 for group 2 and 1·63 for group 3; p=0·043 [group 1 vs groups 2 and 3]), youngest (median age at diagnosis 2·9 years [95% CI 2·4-5·2] for group 1 vs 7·9 years [6·0-9·7] for group 2 and 5·9 years [4·9-7·8] for group 3; p=0·005), and had poorest survival (median survival 0·8 years [95% CI 0·5-1·2] in group 1, 1·8 years [1·4-2·3] in group 2 and 4·3 years [0·8-7·8] in group 3; p=0·019). Patients with group 3 tumours had the highest incidence of metastases at diagnosis (no distant metastasis:metastasis ratio 0·90 for group 3 vs 2·80 for group 1 and 5·67 for group 2; p=0·037).<h4>Interpretation</h4>LIN28 and OLIG2 are promising diagnostic and prognostic molecular markers for CNS PNET that warrant further assessment in prospective clinical trials.<h4>Funding</h4>Canadian Institute of Health Research, Brainchild/SickKids Foundation, and the Samantha Dickson Brain Tumour Trust."],"pubmed_title":["Markers of survival and metastatic potential in childhood CNS primitive neuro-ectodermal brain tumours: an integrative genomic analysis."],"pubmed_authors":["Picard Daniel D, Miller Suzanne S, Hawkins Cynthia E CE, Bouffet Eric E, Rogers Hazel A HA, Chan Tiffany S Y TS, Kim Seung-Ki SK, Ra Young-Shin YS, Fangusaro Jason J, Korshunov Andrey A, Toledano Helen H, Nakamura Hideo H, Hayden James T JT, Chan Jennifer J, Lafay-Cousin Lucie L, Hu Pingzhao P, Fan Xing X, Muraszko Karin M KM, Pomeroy Scott L SL, Lau Ching C CC, Ng Ho-Keung HK, Jones Chris C, Van Meter Timothy T, Clifford Steven C SC, Eberhart Charles C, Gajjar Amar A, Pfister Stefan M SM, Grundy Richard G RG, Huang Annie A"],"name_synonyms":["Genogroups, Genotypes., Genogroup"],"pubmed_title_synonyms":["the brain, poxn, Pox-n, DmelCG8246, suprasegmental structures, neuraxis, death rate, CNS, determination, Encephalon, PoxN, chemical analysis., Neuraxis, suprasegmental levels of nervous system, encephalon, metastatic, pox-n, P4, neuro, survival, time of survival, cerebrospinal axis, synganglion, assay, CG8246"],"description_synonyms":["Neuroepithelial Neoplasm, Primitive Neuroectodermal Tumors, Primitive Neuroepithelial, Ependymoblastoma, Primitive Neuroepithelial Tumors, Medulloepitheliomas, PNET, Neuroepithelial Neoplasms, neuroepithelioma, Neoplasms, Neuroepithelial Tumor, Primitive, Spongioblastomas, Primitive Neuroepithelial Tumor, Primitive., Cerebral Primitive Neuroectodermal Tumor, Tumor, Primitive Neuroepithelial Neoplasms, Primitive Neuroectodermal, Primitive Neuroectodermal Tumor, Neuroectodermal Tumor, Ependymoblastomas, Primitive Neuroepithelial Neoplasm, Medulloepithelioma, PNETs, Neuroepithelial Tumors, Neoplasm, Spongioblastoma, Tumors"],"pubmed_abstract_synonyms":["dmBest1, Materials, CNS primitive neuroectodermal tumor, Metastasis, Laboratory, acetylglucosaminyltransferase-like protein, central nervous system primitive neuroectodermal neoplasm, Incidences, Brain Neoplasms, cerebellar medulloblastoma, Person-time Rates, Proportion, Lin28, desmoplastic, pitslre, neoplasm metastasis, Tumor, Diagnosis, DmelCG6264, Primitive Neuroectodermal, p38a, dmTAF[[II]]230, LIN28, INTRACRANIAL NEOPL, Method, symptoms, Dp38, Analysis, AI604895, Research Activity, tumour of brain, myd, infratentorial primitive neuroectodermal tumour, Laboratory Research, p38A, Priorities, treatment, average, like-acetylglucosaminyltransferase, TFIID TAF250, Analyses, brain neoplasms, cel, Mbp-1, Brain Tumor, procedures, central nervous system primitive neuroectodermal tumour (WHO grade IV), suprasegmental levels of nervous system, set, Neuroectodermal Tumor, central nervous system primitive neuroectodermal tumor (WHO grade IV), Homo sapiens disease, central nervous system neuroectodermal tumor, Diagnose, DmMPK2, Tumors, screening, dTAF[[II]]230, suprasegmental structures, Intracranial Neoplasm, brain neoplasm, Lin-28, TAF200, Research Priorities, Primitive Neuroepithelial Tumor, Normalcy, Procedure, female, RACK17, Diagnoses, Tex17, Incidence Rates, Postmortem, PRKCBP2, RGD1566408, mKIAA0609, D-MPK2, Person-time Rate, TU15B, finances, Research and Development, fg, DmelCG5475, DmelCG4268, death rate, maleate, dbest1, signs, salaries, INSDC_feature:gene, Methodological, surveillance, Activities, MDC1D, neoplasm of the brain, enr, Taf250, Primitive Neuroepithelial Neoplasm, Material, AL024421, Neuroepithelial Tumors, Gta, financial management, primitive neuroectodermal tumor of central nervous system, Secondary Attack Rates, Spongioblastoma, other neoplasm, TAF230, poxn, Brain, D-p38 MAPK, Brain Tumors, Neoplasms, Neuroepithelial Tumor, number, PoxN, Normalcies, LARGE1, Rate, Recurrent Brain Tumors, dMPK2, disease or disorder, Screening, Attack Rates, Antemortem, Clinical Significance, Technique, Normalities, Pox-n, Primitive Neuroepithelial, Medulloepitheliomas, dTAF[[II]]250, Clinical, CNS, p38Ka, occurrence, cell, VMD2, MDDGB6, prevalence, Spongioblastomas, BMD, Diagnoses and Examinations, Study, dTAF250, Cumulative, NEOPL INTRACRANIAL., Person-time, Person time Rate, Development and Research, tumor metastasis, Bhlhb1, RP50, Dp38a, Antemortem Diagnoses, fees, Individual Health, findings, grupo, MDB, female human body, Metastases, disorders, central nervous system primitive neuroectodermal tumour, Secondary Attack, BG:DS00004.13, medulloblastoma with extensive nodularity, encephalon, Cell, OLIGO2, dTAF230, Cumulative Incidences, Metastase, Olg-2, medulloblastoma, cerebrospinal axis, Neoplasm, TAF[[II]]250/230, condition, Cluster Analyses, outbreaks, Taf[[II]]250, central primitive neuroectodermal tumor, brain neoplasm (disease), best, ensemble, male human body, P4, Incidence Proportion, infratentorial primitive neuroectodermal tumor, like-glycosyltransferase, epidemics, brain tumour, BEST, Antemortem Diagnosis, Primitive Neuroepithelial Tumors, Activity, Feature, central primitive neuroectodermal tumour, Mbp1, Neoplasm Metastases, D-p38, Foundation, p38 alpha, cancer metastasis, Primitive Neuroectodermal Tumor, Techniques, CPNET, diseases, Ependymoblastomas, CNS primitive neuroectodermal tumour, ARB, diseases and disorders, synganglion, Incidence Rate, (2Z)-but-2-enedioate, mpk2, RK17, male, central nervous system neuroectodermal tumour, Primitive Neuroectodermal Tumors, human disease, Oligo2, Clinical Importance, central nervous system primitive neuroectodermal tumor, neuro, Methodological Studies, Dmp38a, cdk11, neoplasm of brain, PNETs, Recurrent Brain Tumor, disease management, Therapies, CG4268, Research Priority, CG5475, Therapy, CG6264, localized primitive neuroectodermal tumor, gyltl1b-b, frequency, ERK2, Erk2, CSDD1, TAFII-250, NEOPL BRAIN, CNS PNET, TAF250/230, Significance, D-P38a, D-p38a, TAFII250, Screenings, MDDGA6, Examinations and Diagnoses, Diseases, Genetic Materials, P38, median, Individual, Postmortem Diagnosis, KIAA0609, Gat, bHLHe19, acetylglucosaminyltransferase-like 1A, Genetic Material, dBest1, Diagnoses and Examination, Clusterings, Postmortem Diagnoses, gyltl1b, Neuroepithelial Neoplasms, Encephalon, Relevance, mdc1d, Primitive, p38, tumor of the Brain, Features, CG17603, LARGE_HUMAN, Methodological Study, TAF[[II]], Treatments, morbidity, Primitive Neuroepithelial Neoplasms, ENSMUSG00000070700, Intracranial, CNS primitive neuroectodermal neoplasm, disease, Health, Cluster, Patient, brain tumor, SR3-5, Clustering, Cistron, LIN-28, Gruppe, the brain, Neuroepithelial Neoplasm, other disease, d230, Ependymoblastoma, PNET, Procedures, PITSLRE, lin-28A, Importance, Gene, dTAFII250, Cerebral Primitive Neuroectodermal Tumor, anon-WO0118547.380, EfW1, presence, froggy, Gyltl1a, Secondary Attack Rate, dp38a, dmTAF1, Taf230, Recurrent, Studies, Mass, CG8246, TAF250, primitive neuroectodermal tumour of central nervous system, tumor cell migration, Taf200, Genetic, tumour of the Brain, BHLHB1, Research, Taf1p, metastasis, LARGE, financing, central nervous system PNET, non-neoplastic, BPFD#36, funding, PRIMARY BRAIN NEOPL, grupos, time of survival, Clients, disorder, Characteristics, Incidence Proportions, TAF, incidence, tumor of brain, ZCCHC1, DmelCG8246, TAF[[II]]250, neuraxis, DMPK2, Males, Attack Rate, Cumulative Incidence, Incidence, l(3)84Ab, medical condition, Cistrons, Client, Examination and Diagnoses, group, pox-n, count in organism, Priority, Characteristic, survival, Mass Screenings, Medulloepithelioma, group 2, p230, Gm10299, group 3, Research Activities, TFIID, techniques, central primitive neuroectodermal neoplasm, Intracranial Neoplasms, Dbest, TAF[[II]]230, Normality, Desmoplastic, Rest, TAF[II]250, Neuraxis, localised primitive neuroectodermal tumour, endemics, dp38, Secondary, cost, DmelCG17603, Therapeutic, Attack, cardinality, Treatment, groupe, Females, glycosyltransferase-like protein LARGE1, methodology, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"Genotype - samples","description":"PNET genotyping","dates":{"updated":"2017-07-26 15:39:24"},"accession":"EGAD00010000260","cross_references":{"TAXONOMY":["9606"],"pubmed":["22691720"],"EGA":["EGAC01000000015","EGAS00000000116"]}}