Paired exome analysis in urothelial carcinoma

In this study we characterized genomic alterations in two to five metachronous 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), Ultra deep targeted sequencing (~6,809x mean read depth) and whole transcriptome RNA-seq was performed for all samples. In addition multiregional WES was performed on 8 adjacent regions from a single tumor.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

3 Datasets 2 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001002716	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) Data provided here consist of 122 Bam files for WES (83 Tumors and 39 blood)	Illumina HiSeq 2000	122
EGAD00001002717	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). Data provided here consist of 71 unmapped Bam files form whole transcriptome RNA-seq.	Illumina HiSeq 2000	71
EGAD00001002718	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). Data provided here consist of 71 mapped Bam files form whole transcriptome RNA-seq.	Illumina HiSeq 2000	71

Publications	Citations
Paired Exome Analysis Reveals Clonal Evolution and Potential Therapeutic Targets in Urothelial Carcinoma. Lamy P, Nordentoft I, Birkenkamp-Demtröder K, Thomsen MB, Villesen P, Vang S, Hedegaard J, Borre M, Jensen JB, Høyer S, Pedersen JS, Ørntoft TF, Dyrskjøt L. Cancer Res 76: 2016 5894-5906	53
Analysis of Several Common APOBEC-type Mutations in Bladder Tumors Suggests Links to Viral Infection. Rao N, Starrett GJ, Piaskowski ML, Butler KE, Golubeva Y, Yan W, Lawrence SM, Dean M, Garcia-Closas M, Baris D, Johnson A, Schwenn M, Malats N, Real FX, Kogevinas M, Rothman N, Silverman DT, Dyrskjøt L, Buck CB, Koutros S, Prokunina-Olsson L. Cancer Prev Res (Phila) 16: 2023 561-570	5