{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2000;ILLUMINA"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001002718"],"sample_count":["71"],"description":["EGA dataset EGAD00001002718"],"repository":["EGA"],"title":["mapped Bam files from whole transcriptome RNA-seq"],"pubmed_abstract":["Greater knowledge concerning tumor heterogeneity and clonality is needed to determine the impact of targeted treatment in the setting of bladder cancer. In this study, we performed whole-exome, transcriptome, and deep-focused sequencing of metachronous tumors from 29 patients initially diagnosed with early-stage bladder tumors (14 with nonprogressive disease and 15 with progressive disease). Tumors from patients with progressive disease showed a higher variance of the intrapatient mutational spectrum and a higher frequency of APOBEC-related mutations. Allele-specific expression was also higher in these patients, particularly in tumor suppressor genes. Phylogenetic analysis revealed a common origin of the metachronous tumors, with a higher proportion of clonal mutations in the ancestral branch; however, 19 potential therapeutic targets were identified as both ancestral and tumor-specific alterations. Few subclones were present based on PyClone analysis. Our results illuminate tumor evolution and identify candidate therapeutic targets in bladder cancer. Cancer Res; 76(19); 5894-906. ©2016 AACR."],"pubmed_title":["Paired Exome Analysis Reveals Clonal Evolution and Potential Therapeutic Targets in Urothelial Carcinoma."],"pubmed_authors":["Lamy Philippe P, Nordentoft Iver I, Birkenkamp-Demtröder Karin K, Thomsen Mathilde Borg Houlberg MB, Villesen Palle P, Vang Søren S, Hedegaard Jakob J, Borre Michael M, Jensen Jørgen Bjerggaard JB, Høyer Søren S, Pedersen Jakob Skou JS, Ørntoft Torben F TF, Dyrskjøt Lars L"],"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":["Somatic, whole exome, Uroepithelial carcinoma, Clonal, determination, chemical analysis, transitional cell carcinoma of the urinary tract., Exomes, transitional cell carcinoma of the urothelial tract, urothelial carcinoma, assay, Evolution, transitional cell car. -uroth., Somatic Evolution"],"description_synonyms":["Forms, other disease, Ribonucleic, tumor of urinary bladder, BamF, bim, Bladder Tumor, biml, tumor of bladder, BamC, Complete Exome, Neoplasms, developmental stage, 5-dihydroxy-1, bam, Benign Neoplasm, RNA-seq., tumour of bladder, Tumor, Malignant, Neodymate(5-), 3-benzenedisulfonato(4-)-O4, fs(3)neo61, bladder tumours, CG10422, bladder tumors, diseases, Urinary Bladder Cancer, Gene Products, disease or disorder, tumour of the urinary bladder, Whole Transcriptome Shotgun Sequencing, neoplasm of the bladder, diseases and disorders, bim-beta7, Whole Transcriptome, Transcriptome Sequencing, DmF2, neoplasm of bladder, DmelCG10422, Fs(3)Hor, Non Polyadenylated, RNA Gene Products, Bladder Neoplasm, lod, study, WES, DmelCG2684, human disease, Complete, Exome Sequencings, Malignancy, HCAP, bim-beta6, O5)-, Complete Exome Sequencing, Whole Transcriptome Sequencing, Cancer of the Bladder, urinary bladder tumour, urinary bladder neoplasm (disease), neoplasm of urinary bladder, NTef2, ASM, CDLS3, BMH, urinary bladder tumours, Sequencing, non-neoplastic, Non-Polyadenylated RNA, Neoplasias, Whole Exome, bladder tumor, Clients, Whole, disorder, Homo sapiens disease, stage, Malignancies, CSPG6, bladder tumour, Cancer, Tumors, Cancer of Bladder, RNA, Bladder Cancers, Malignant Neoplasm, Complete Exome Sequencings, ribose nucleic acid, tumor of the urinary bladder, bis(4, Exome, Urinary Bladder Neoplasm, disorders, ribonucleic acids, Bladder Tumors, RNA-seq, ham, RNS, BOD, medical condition, urinary bladder neoplasms, Client, Fs(3)Sz11, whole transcriptome, urinary bladder neoplasm, tumor of the bladder, read, Exome Sequencing, Benign, yeast nucleic acid, Ribonukleinsaeure, Diseases, neodymium pyrocatechin disulphonate, Neoplasm, tumour of urinary bladder, condition, pentosenucleic acids, Ribonucleic acids, bod, Bladder Neoplasms, ASMASE, bimel, (T-4)-, ribonucleic acid, Acid, NPD, Complete Transcriptome, Complete Transcriptome Sequencing, Bladder, neoplasm of the urinary bladder, Non Polyadenylated RNA, Malignant Tumor of Urinary Bladder, Non-Polyadenylated, urinary bladder tumor, Benign Neoplasms, tumour of the bladder, Cancers, Ribonucleic Acid, alpha, Lds, bladder neoplasm, early, Malignant Neoplasms, disease, BIM, Patient, Bladder Cancer, Horka, Bam-C, BAM, Whole Exome Sequencing, Bam, CG2684, Fs(3)Horka, SMC3L1, Transcriptome Sequencings, Neoplasia, Urinary Bladder, urinary bladder tumors"],"pubmed_abstract_synonyms":["whole exome, other disease, tumor of urinary bladder, Materials, Bladder Tumor, tumor suppressor, tumor of bladder, determination, cancer of the urinary bladder, Transcriptome Profile, Neoplasms, developmental stage, Benign Neoplasm, Gene Expression Profile, Gene, bladder cancer, Profiles, APOBEC, tumour of bladder, Tumor, Malignant, Ximpact, bladder tumours, Mutations, cell cycle regulator, bladder tumors, diseases, Urinary Bladder Cancer, disease or disorder, tumour of the urinary bladder, neoplasm of the bladder, diseases and disorders, DmF2, neoplasm of bladder, BLC, Fs(3)Hor, Bladder Neoplasm, imprinted and ancient gene protein, lod, treatment, study, proportion, DmelCG2684, human disease, Genetic, lateral shoot, Malignancy, occurrence, proportionality to, Profile, prevalence, Cancer of the Bladder, urinary bladder tumour, apoB mRNA editing enzyme complex, urinary bladder neoplasm (disease), neoplasm of urinary bladder, NTef2, Signatures, urinary bladder tumours, non-neoplastic, Neoplasias, Expression Signature, malignant neoplasm, Clients, bladder tumor, heterogeneity, disease management, Therapies, Transcriptomes, disorder, Homo sapiens disease, Malignancies, stage, bladder tumour, axillary shoot, incidence, Cancer, Tumors, Therapy, Cancer of Bladder, Transcriptome, Malignant Neoplasm, cancer of the bladder, Bladder Cancers, tumor of the urinary bladder, frequency, Expression Profiles, Urinary Bladder Neoplasm, disorders, Bladder Tumors, medical condition, urinary bladder neoplasms, Cistrons, Client, impact-a, results, Fs(3)Sz11, Gene Expression, urinary bladder neoplasm, tumor of the bladder, Benign, MT, Expression Signatures, Gene Expression Signatures, chemical analysis, Diseases, Neoplasm, tumour of urinary bladder, imprinted and ancient gene protein homolog, IMPACT, condition, Genetic Materials, Gene Expression Signature, Bladder Neoplasms, Expression Profile, outbreaks, Genetic Material, Transcriptome Profiles, cancer of bladder, Epistemology, primary cancer, Bladder, neoplasm of the urinary bladder, Malignant Tumor of Urinary Bladder, proportionality, Exomes, urinary bladder tumor, Benign Neoplasms, common, rate, Cancers, tumour of the bladder, Lds, surveillance, Treatments, morbidity, malignant tumor, bladder neoplasm, endemics, early, Malignant Neoplasms, disease, Therapeutic, Patient, Bladder Cancer, Material, Gene Expression Profiles, Horka, CG2684, quotient, Fs(3)Horka, Treatment, epidemics, Cistron, assay, Signature, cancer of urinary bladder, other neoplasm, E430016J11Rik, Neoplasia, RWDD5, Urinary Bladder, urinary bladder cancer, urinary bladder tumors, Malignant Neoplasms."],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-MOMA-28-09-2016-13:04:50:567-495 - samples","description":"In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors).\nData provided here consist of 71 mapped Bam files form whole transcriptome RNA-seq.","dates":{"updated":"2017-07-26 15:39:28"},"accession":"EGAD00001002718","cross_references":{"TAXONOMY":["9606"],"pubmed":["27488526"],"EGA":["EGAC00001000145","EGAS00001001686"]}}