On the Reproducibility of TCGA Ovarian Cancer MicroRNA Profiles

TL;DR

This study examines the reproducibility of microRNA expression data from TCGA ovarian cancer samples, revealing significant discrepancies between microarray and sequencing platforms and highlighting challenges in data consistency.

Contribution

The paper systematically compares miRNA profiles from two different platforms in ovarian cancer, uncovering platform-specific differences and emphasizing the need for improved reproducibility.

Findings

Only 1 miRNA is consistently associated with survival across platforms.

Poor correlation between microarray and sequencing miRNA levels.

Platform differences impact reproducibility of miRNA survival associations.

Abstract

Dysregulated microRNA (miRNA) expression is a well-established feature of human cancer. However, the role of specific miRNAs in determining cancer outcomes remains unclear. Using Level 3 expression data from the Cancer Genome Atlas (TCGA), we identified 61 miRNAs that are associated with overall survival in 469 ovarian cancers profiled by microarray (p<0.01). We also identified 12 miRNAs that are associated with survival when miRNAs were profiled in the same specimens using Next Generation Sequencing (miRNA-Seq) (p<0.01). Surprisingly, only 1 miRNA transcript is associated with ovarian cancer survival in both datasets. Our analyses indicate that this discrepancy is due to the fact that miRNA levels reported by the two platforms correlate poorly, even after correcting for potential issues inherent to signal detection algorithms. Further investigation is warranted.