Dataset: Transcription profiling of very low risk Wilms Tumors show distinctive gene expression, histologic, and clinical features

The goal of this study is to define biologically distinct subsets of Very Low Risk Wilms Tumors (VLRWT) using oligonucleotide arrays. Description: 52 tumors from the original case:cohort of 600 tumors from NWTS-5 met the criteria for VLRWT. Thirteen tumors were excluded for quality control reasons, resulting in 39 tumors for analysis. Global gene expression analysis was performed on these 39 tumors. A total of 4,000 probesets representing the greatest variability according to coefficient of variation was utilized for hierarchical clustering, and three clusters were identified. Two subsets within VLRWT are identified that have pathogenetic and molecular differences and apparent differences in risk for relapse. If these predictors can be prospectively validated, this would enable future clinical stratification and broadening the definition of VLRWT. Experiment Overall Design: Global gene expression analysis was performed on 39 tumors that met the criteria of VLRWT and passed quality control parameters in order to define biologically distinct subsets. Experiment Overall Design: Hierarchical clustering identified three tumor clusters (C1, C2 and C3). The top differentially expressed genes were identified by first filtering out probesets with a maximum expression of less than 6.5 in all 39 tumors. Using the remaining 14,452 probesets, the expression of each cluster was compared with the expression in the remaining tumors, and those genes with a p-value <0.00001 and positive or negative fold-change (FC) of greater than 2.5 were identified. This resulted in 161 probesets from the comparison of C1 with C2+C3, 43 probesets from the comparison of C2 with C1+C3, and 71 probesets from the comparison of C3 with C1+C2. The false discovery rates were 0.02%, 0.06% and 0.05% for C1, C2, and C3, respectively. These three lists were combined, resulting in 239 probesets (161 genes) which are provided in Supplemental Table 1, linked below.

Species:

human

Samples:

39

Source:

E-GEOD-14767

PubMed:

19903788

Updated:

Dec.12, 2014

Registered:

Jun.19, 2014