Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole Exome Sequencing of Signet Ring/Plasmacytoid Variant Bladder Cancer

ABSTRACT:

In this study, six plasmacytoid bladder cancers were analyzed by whole exome sequencing. The results show loss of the CDH1 gene in every sample and correlate with E-cadherin loss of expression by immunohistochemistry. A separate validation cohort of plasmacytoid samples showed loss of E-cadherin expression by CDH1 mutation or promoter hypermethylation.

PROVIDER: phs001064 | dbGaP |

SECONDARY ACCESSION(S): PRJNA310265PRJNA310264

REPOSITORIES: dbGaP

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	GapExchange_phs001064.v1.p1.xml	Xml
	dbGaPEx2.1.5.xsd	Other
	Study_Report.phs001064.PC_SRC_Bladder.v1.p1.MULTI.pdf	Pdf
	manifest_phs001064.PC_SRC_Bladder.v1.p1.c2.DS-BLADDERCA.pdf	Pdf
	datadict_v2.xsl	Other

Items per page:

1 - 5 of 15

Similar Datasets

E-MTAB-1940

Project description:Expression profile of non-muscle invasive (superficial) bladder carcinoma

2025-01-23 | E-MTAB-1940 | ExpressionAtlas

E-MTAB-2610

Project description:Expression profiling in four human bladder cancer cell lines

2025-01-23 | E-MTAB-2610 | ExpressionAtlas

E-GEOD-56037

Project description:Effect of increased FOXA1 on gene expression in bladder cancer cells

2025-01-24 | E-GEOD-56037 | ExpressionAtlas

E-MTAB-2930

Project description:Chronic cystitis microarray comparing C3H/HeN and C57BL/6 bladder gene expression

2014-09-15 | E-MTAB-2930 | ExpressionAtlas

Identification of nine genomic regions of amplification in bladder cancer, correlation with stage, and potential prognositic and therapeutic value

Project description:We sought to test the hypothesis that ascertainment of genome-wide copy number alterations in bladder cancer may have value for clinical management. We performed a genome wide analysis of 164 bladder cancer samples and 27 bladder cancer cell lines to identify genetic changes associated with disease characteristics. Multiplex inversion probe (MIP) analysis, a newly developed genomic technique, was used to study 80 bladder cancers to identify mutations and copy number changes. Selected amplification events were then analyzed in a validation cohort of 84 bladder cancers by multiplex ligation-dependent probe assay (MLPA). In the MIP analysis, 44 regions of significant copy number change were identified using GISTIC. Nine gene-containing regions of amplification were selected for validation in the second cohort by MLPA. Amplification events at these 9 genomic regions were found to correlate strongly with stage, being seen in only 2 of 23 (9%) Ta grade 1 or 1-2 cancers, in contrast to 31 of 61 (51%) Ta grade 3 and T2 grade 2 cancers, p < 0.001. These observations suggest that analysis of genomic amplification of these 9 regions might serve as a guide for clinical decision making, in terms of management decisions following transurethral resection of bladder cancers. This approach is facilitated by the capability of each of the MIP and MLPA methods to analyze formalin-fixed paraffin-embedded DNA, as done here. Furthermore several of the amplified genes identified here (ERBB2, MDM2, CCND1) render the bladder cancers potentially sensitive to targeted therapy. Copy number profiling was completed for 80 urothelial carcinoma samples using the Affymetrix OncoScan(TM) FFPE Express platform.

2013-04-29 | E-GEOD-44323 | biostudies-arrayexpress

E-MTAB-4133

Project description:Gene expression changes in mouse hematopoietic stem cell enriched populations following the loss of Meis1 expression

2016-01-04 | E-MTAB-4133 | ExpressionAtlas

Correlation of gene expression with bladder capacity in interstitial cystitis/bladder pain syndrome

Project description:Interstitial cystitis (IC) and bladder pain syndrome are terms used to describe a heterogenous chronic pelvic and bladder pain disorder of unknown etiology. The goal of this pilot study was to determine if gene expression profiling of bladder biopsy tissue from patients experiencing symptoms could be used to separate the patients based on some clinical parameter.

2014-05-13 | GSE57560 | GEO

Identification of nine genomic regions of amplification in bladder cancer, correlation with stage, and potential prognositic and therapeutic value

2013-04-29 | GSE44323 | GEO

De-obstruction of bladder outlet in humans reverses organ remodeling

Project description:Bladder outlet obstruction (BOO) causes lower urinary tract symptoms and objectifiable urodynamic changes in bladder function. We carried out an integrated transcriptome and proteome analysis of bladder samples from male patients with BOO before and 3 months after de-obstruction surgery (transurethral resection of the prostate, TURP). mRNA and protein profiles were correlated with urodynamic findings, specifically voiding detrusor pressure (PdetQmax) before TURP. Patients with high PdetQmax showed less advanced remodeling and inflammatory changes than those with lower values. We oberved significant dysregulation of gene expression, which was reversed by de-obstruction in both patients’ groups. We propose a series of biomarker genes, indicative of BOO, and possibly contributing to the bladder changes. Our data sheds light on the stages of progressive obstruction-induced bladder decompensation, and might add selecting the operation point to avoid the loss of contractility.

2024-05-21 | PXD044777 | Pride

E-GEOD-16972

Project description:COPD-Specific Gene Expression Signatures of Alveolar Macrophages as well as Peripheral Blood Monocytes Overlap and Correlate with Lung Function

2025-01-24 | E-GEOD-16972 | ExpressionAtlas