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

Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor.

Paper Id
COSP28310
Authors
Xu X,Hou Y,Yin X,Bao L,Tang A,Song L,Li F,Tsang S,Wu K,Wu H,He W,Zeng L,Xing M,Wu R,Jiang H,Liu X,Cao D,Guo G,Hu X,Gui Y,Li Z,Xie W,Sun X,Shi M,Cai Z,Wang B,Zhong M,Li J,Lu Z,Gu N,Zhang X,Goodman L,Bolund L,Wang J,Yang H,Kristiansen K,Dean M,Li Y and Wang J
Affiliation
BGI-Shenzhen, Shenzhen, China.
Journal
Cell 2012;148(5):886-95
ISSN:1097-4172
PUBMED:22385958
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer and has very few mutations that are shared between different patients. To better understand the intratumoral genetics underlying mutations of ccRCC, we carried out single-cell exome sequencing on a ccRCC tumor and its adjacent kidney tissue. Our data indicate that this tumor was unlikely to have resulted from mutations in VHL and PBRM1. Quantitative population genetic analysis indicates that the tumor did not contain any significant clonal subpopulations and also showed that mutations that had different allele frequencies within the population also had different mutation spectrums. Analyses of these data allowed us to delineate a detailed intratumoral genetic landscape at a single-cell level. Our pilot study demonstrates that ccRCC may be more genetically complex than previously thought and provides information that can lead to new ways to investigate individual tumors, with the aim of developing more effective cellular targeted therapies.
Paper Status
Curated
Genes Analysed
210
Mutated Samples
18
Total No. of Samples
18
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