This tab shows an overview of the selected study/paper [more details]
Reference

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder.

Paper Id
COSP26829
Authors
Gui Y,Guo G,Huang Y,Hu X,Tang A,Gao S,Wu R,Chen C,Li X,Zhou L,He M,Li Z,Sun X,Jia W,Chen J,Yang S,Zhou F,Zhao X,Wan S,Ye R,Liang C,Liu Z,Huang P,Liu C,Jiang H,Wang Y,Zheng H,Sun L,Liu X,Jiang Z,Feng D,Chen J,Wu S,Zou J,Zhang Z,Yang R,Zhao J,Xu C,Yin W,Guan Z,Ye J,Zhang H,Li J,Kristiansen K,Nickerson ML,Theodorescu D,Li Y,Zhang X,Li S,Wang J,Yang H,Wang J and Cai Z
Affiliation
Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China.
Journal
Nature genetics 2011;43(9):875-8
ISSN:1546-1718
PUBMED:21822268
Abstract
Transitional cell carcinoma (TCC) is the most common type of bladder cancer. Here we sequenced the exomes of nine individuals with TCC and screened all the somatically mutated genes in a prevalence set of 88 additional individuals with TCC with different tumor stages and grades. In our study, we discovered a variety of genes previously unknown to be mutated in TCC. Notably, we identified genetic aberrations of the chromatin remodeling genes (UTX, MLL-MLL3, CREBBP-EP300, NCOR1, ARID1A and CHD6) in 59% of our 97 subjects with TCC. Of these genes, we showed UTX to be altered substantially more frequently in tumors of low stages and grades, highlighting its potential role in the classification and diagnosis of bladder cancer. Our results provide an overview of the genetic basis of TCC and suggest that aberration of chromatin regulation might be a hallmark of bladder cancer.
Paper Status
Curated
Genes Analysed
465
Mutated Samples
91
Total No. of Samples
91
This tab shows genes with mutations in the selected study/paper [more details]
Genes Samples CDS Mutation AA Mutation
This tab shows genes without mutations in the selected study/paper [more details]
Non-Mutant Genes Gene Id (COSG)
This tab shows samples without mutations in the selected study/paper [more details]
Non-Mutant Samples Sample Id (COSS)
This tab shows mutated samples in the selected study/paper [more details]
Sample Name Mutation Count
This tab shows non coding variant in the selected study/paper [more details]
Sample ID Sample Name ID NCV Annotation Zygosity Chromosome Genome start Genome stop Genome version Strand WT seq Mut seq
This tab shows the copy number variation data for this study. Only variants (classified as gain or loss) are listed. [more details]
CNV Gene Sample Position Minor Allele Copy Number Average Ploidy

1. N/A represents cases where average ploidy value is not available( mostly ICGC samples). For some TCGA samples where minor allele information is not available the average ploidy value could not be calculated.

2. For TCGA samples, Ascat algorithm is used to calculate the average ploidy.

3. For CGP samples, Picnic algorithm is used to calculate the average ploidy.

Type
This tab shows a table of count of samples having gain or loss for all genes [more details]
Gene Gain Samples Loss Samples Samples Tested
This tab shows the fusion mutations observed in this sample [more details]
Gene Sample Name Id Sample(COSS) CDS Mutation Somatic status Zygosity Validated Type