{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["GenomeWideSNP_6-BirdseedV2"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00010000508"],"sample_count":["12"],"description":["EGA dataset EGAD00010000508"],"repository":["EGA"],"title":["Title not provided"],"pubmed_abstract":["Bladder cancer (or urothelial cell carcinoma [UCC]) is characterized by field disease (malignant alterations in surrounding mucosa) and frequent recurrences. Whole-genome, exome, and transcriptome sequencing of 38 tumors, including four metachronous tumor pairs and 20 superficial tumors, identified an APOBEC mutational signature in one-third. This was biased toward the sense strand, correlated with mean expression level, and clustered near breakpoints. A>G mutations were up to eight times more frequent on the sense strand (p<0.002) in [ACG]AT contexts. The patient-specific APOBEC signature was negatively correlated to repair-gene expression and was not related to clinicopathological parameters. Mutations in gene families and single genes were related to tumor stage, and expression of chromatin modifiers correlated with survival. Evolutionary and subclonal analyses of early/late tumor pairs showed a unitary origin, and discrete tumor clones contained mutated cancer genes. The ancestral clones contained Pik3ca/Kdm6a mutations and may reflect the field-disease mutations shared among later tumors."],"pubmed_title":["Mutational context and diverse clonal development in early and late bladder cancer."],"pubmed_authors":["Nordentoft Iver I, Lamy Philippe P, Birkenkamp-Demtröder Karin K, Shumansky Karey K, Vang Søren S, Hornshøj Henrik H, Juul Malene M, Villesen Palle P, Hedegaard Jakob J, Roth Andrew A, Thorsen Kasper K, Høyer Søren S, Borre Michael M, Reinert Thomas T, Fristrup Niels N, Dyrskjøt Lars L, Shah Sohrab S, Pedersen Jakob Skou JS, Ørntoft Torben F TF"],"name_synonyms":["average."],"pubmed_title_synonyms":["lod, cancer of bladder, Cancer of Bladder, DmelCG2684, cancer of the bladder, Bladder, Bladder Tumor, Bladder Cancers, single-organism developmental process, cancer of the urinary bladder, Neoplasms, postnatal development, Malignant Tumor of Urinary Bladder, postnatal growth, Urinary Bladder Neoplasm, Bladder Tumors, Cancer of the Bladder, growth and development, bladder cancer, NTef2, Tumor, Lds, early, Fs(3)Sz11, development, tumor of the bladder, Bladder Cancer, Urinary Bladder Cancer, Horka, Bladder., CG2684, Neoplasm, Fs(3)Horka, DmF2, cancer of urinary bladder, BLC, Bladder Neoplasms, Fs(3)Hor, growth, Urinary Bladder, urinary bladder cancer, Bladder Neoplasm, Cancer, Tumors"],"description_synonyms":["preventive measures, CG11478, Dmel_CG6393, DmelCG42257, Controlling, cg11478, preventive therapy, microarray., reference sample, control, 65K, prophylaxis, CG6393, CG42257, Dmel_CG30327, snp, CG30327, prevention and control, Controlled, prevention"],"pubmed_abstract_synonyms":["bB128O4.1, other disease, whole exome, cytoplasmic chromatin, Materials, Bladder Tumor, cancer of the urinary bladder, Transcriptome Profile, Muscularis Mucosae, Neoplasms, Benign Neoplasm, Gene Expression Profile, Gene, PI3K, tumour stage, bladder cancer, Profiles, APOBEC, Tumor, Malignant, Muscularis, Mutations, p110-alpha, organ field, diseases, Urinary Bladder Cancer, disease or disorder, carcinoma of transitional epithelial cell, diseases and disorders, p110alpha, field, DmF2, BLC, Fs(3)Hor, insulin potentiating fragments of growth hormone, Chromatins, Bladder Neoplasm, lod, AcG, human disease, DmelCG2684, Gene Expressions, Genetic, Genomes, Malignancy, Tissues, developmental field, Profile, Tissue, Cancer of the Bladder, apoB mRNA editing enzyme complex, clumped, NTef2, transitional carcinoma, region of mucosa, Expressions, mucous membrane, Signatures, transitional cell neoplasm, Lamina, non-neoplastic, Neoplasias, MCAP, mucosa of organ, high frequency, ACG, clustered, transitional epithelial cell carcinoma, Expression Signature, malignant neoplasm, time of survival, Propria, Clients, chromosome scaffold, mucosa of organ part, Transcriptomes, disorder, Homo sapiens disease, Malignancies, carcinoma, Expression, MCM, MCMTC, Cancer, Tumors, nuclear chromatin, Cancer of Bladder, Mucosa, Transcriptome, cancer of the bladder, Bladder Cancers, Malignant Neoplasm, 6330412C24Rik, malignant, transitional cell carcinoma, Expression Profiles, Urinary Bladder Neoplasm, disorders, Bladder Tumors, p110, future organ, medical condition, UTX, Utx, urothelial cell carcinoma, transitional cell tumor, Cistrons, Client, urothelial, KABUK2, Fs(3)Sz11, Gene Expression, tumor of the bladder, Mucosal, Benign, survival, MT, carcinoma of urothelial cell, CWS5, mucosal region, Mucosae, Expression Signatures, ZIZ2, Gene Expression Signatures, Diseases, Neoplasm, condition, Genetic Materials, Gene Expression Signature, Lamina Propria, Bladder Neoplasms, utx, Expression Profile, uty, Genetic Material, Transcriptome Profiles, cancer of bladder, Mucosal Tissue, Membranes, primary cancer, Bladder, frequent, death rate, tunica mucosa, Malignant Tumor of Urinary Bladder, organ mucosa, Exomes, Benign Neoplasms, Mucous, patient, INSDC_feature:gene, whole genome, Cancers, Membrane, Lds, malignant tumor, early, Malignant Neoplasms, disease, caPI3K, CLOVE, Patient, Bladder Cancer, Material, Mucous Membranes, Gene Expression Profiles, Horka, xtutx, CG2684, Fs(3)Horka, Cistron, tutx, Signature, cancer of urinary bladder, other neoplasm, Zizimin-2, Activated Cdc42-associated guanine nucleotide exchange factor, Neoplasia, Urinary Bladder, Mucosal Tissues, bA386N14.2, urinary bladder cancer, Malignant Neoplasms."],"additional_accession":[]},"is_claimable":false,"name":"Matched_normal_Affymetrix - samples","description":"Matched control samples using SNP 6.0 Array","dates":{"updated":"2017-07-26 15:39:26"},"accession":"EGAD00010000508","cross_references":{"TAXONOMY":["9606"],"pubmed":["24835989"],"EGA":["EGAC00001000145","EGAS00001000641"]}}