{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2000;, Illumina HiSeq 2500;, Illumina Genome Analyzer IIx;"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001000734"],"sample_count":["88"],"description":["EGA dataset EGAD00001000734"],"repository":["EGA"],"title":["Kidney Cancer Heterogeneity and Evolution Revealed by Multi-Region Exome Sequencing"],"pubmed_abstract":["Clear cell renal carcinomas (ccRCCs) can display intratumor heterogeneity (ITH). We applied multiregion exome sequencing (M-seq) to resolve the genetic architecture and evolutionary histories of ten ccRCCs. Ultra-deep sequencing identified ITH in all cases. We found that 73-75% of identified ccRCC driver aberrations were subclonal, confounding estimates of driver mutation prevalence. ITH increased with the number of biopsies analyzed, without evidence of saturation in most tumors. Chromosome 3p loss and VHL aberrations were the only ubiquitous events. The proportion of C>T transitions at CpG sites increased during tumor progression. M-seq permits the temporal resolution of ccRCC evolution and refines mutational signatures occurring during tumor development."],"pubmed_title":["Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing."],"pubmed_authors":["Gerlinger Marco M, Horswell Stuart S, Larkin James J, Rowan Andrew J AJ, Salm Max P MP, Varela Ignacio I, Fisher Rosalie R, McGranahan Nicholas N, Matthews Nicholas N, Santos Claudio R CR, Martinez Pierre P, Phillimore Benjamin B, Begum Sharmin S, Rabinowitz Adam A, Spencer-Dene Bradley B, Gulati Sakshi S, Bates Paul A PA, Stamp Gordon G, Pickering Lisa L, Gore Martin M, Nicol David L DL, Hazell Steven S, Futreal P Andrew PA, Stewart Aengus A, Swanton Charles C"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"description_synonyms":["High-Throughput RNA, High Throughput DNA Sequencing, Ion Proton Sequencing, Edg, Nucleotide Sequencing, Illumina Sequencing, Massively-Parallel, Exomes, High-Throughput DNA Sequencing, High-Throughput DNA, Pyrosequencing, Sequencing, Illumina, Next-Generation Sequencing, other neoplasm., High Throughput Sequencing, High-Throughput RNA Sequencing, Ion Torrent Sequencing, High Throughput RNA Sequencing, High-Throughput Sequencing, Deep, DNA Sequencing, Massively-Parallel Sequencing, Next-Generation, High-Throughput, RNA Sequencing, High Throughput Nucleotide Sequencing, Ion Torrent, Massively Parallel Sequencing, ORW1, END, Ion Proton, HHT1, High-Throughput Nucleotide, Next Generation Sequencing, Deep Sequencing"],"pubmed_title_synonyms":["Adenocarcinoma, Carcinomas, Carcinoma, Adenocarcinoma Of, Hypernephromas, Collecting Duct, Clear Cell Renal Carcinoma., Renal Cell, Renal Carcinoma, Kidney, Chromophil Renal Cell Carcinoma, Collecting Duct Carcinoma, Collecting Duct Carcinomas, Renal Cell Cancers, Renal Cell Carcinomas, Renal, Renal Cell Adenocarcinoma, Clear Cells, Renal Adenocarcinoma, Renal Adenocarcinomas, Adenocarcinoma Of Kidney, Tumor, Nephroid, Papillary Renal Cell Carcinoma, Renal Cell Carcinoma, Adenocarcinomas, Renal Cell Cancer, Papillary, Chromophobe Renal Cell Carcinoma, Collecting Duct Carcinoma of the Kidney, Hypernephroid, Clear Cell Renal Cell Carcinoma, Adenocarcinoma Of Kidneys, Renal Cell Adenocarcinomas, Collecting Duct Carcinoma (Kidney), Collecting Duct (Kidney), Sarcomatoid Renal Cell Carcinoma, Hypernephroid Carcinomas, Renal Collecting Duct Carcinoma, Nephroid Carcinomas, Renal Carcinomas, Hypernephroid Carcinoma, Collecting Duct Carcinomas (Kidney), Hypernephroma, Nephroid Carcinoma, Grawitz Tumor, Grawitz, Cancer"],"pubmed_abstract_synonyms":["dmVHL, clear cell renal cell adenocarcinoma, postnatal development., single-organism developmental process, Complete Exome, Period Prevalence, Neoplasms, number, Benign Neoplasm, Period Prevalences, Dvhl, growth and development, Tumor, Malignant, supernumerary, CCRCC, temporal, Mutations, Point Prevalence, RCA1, Point Prevalences, Whole Transcriptome, Transcriptome Sequencing, DVhl, increased, WES, proportion, Complete, Exome Sequencings, Biopsies, Malignancy, Prevalences, occurrence, proportionality to, Complete Exome Sequencing, Whole Transcriptome Sequencing, Modifiers of, prevalence, HRCA1, chromatid, Clear Cells, Sequencing, Von Hippel Lindau disease, pVHL, genetic, Neoplasias, clear cell renal cell carcinoma, Whole Exome, d-VHL, Whole, heterogeneity, Malignancies, VHL syndrome, constitutitional genetic, incidence, Cancer, Tumors, Prevalence, d-vhl, Complete Exome Sequencings, Malignant Neoplasm, frequency, Exome, familial, Von Hippel-Lindau Disease, CG13221, development, Exome Sequencing, prophase chromosome, Benign, Von Hippel-Lindau syndrome, Period, DmelCG13221, Neoplasm, BcDNA:RH61560, outbreaks, VHL1, Complete Transcriptome, Complete Transcriptome Sequencing, increased number, interphase chromosome, proportionality, postnatal growth, Benign Neoplasms, rate, Cancers, dVHL, surveillance, VHL, morbidity, endemics, Malignant Neoplasms, present in greater numbers in organism, Vhlh, Chromosome, Point, cardinality, Whole Exome Sequencing, quotient, epidemics, inherited genetic, other neoplasm, Transcriptome Sequencings, hereditary, growth, vhl, Neoplasia, accessory"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-CRUK-LRI-04-02-2014-11:46:00:265-3 - samples","description":"Paired end Illumina sequencing of whole exomes of multiple tumour regions.","dates":{"updated":"2021-05-07 14:10:03"},"accession":"EGAD00001000734","cross_references":{"TAXONOMY":["9606"],"pubmed":["24487277"],"EGA":["EGAC00001001907","EGAS00001000667"]}}