On the reproducibility of TCGA ovarian cancer microRNA profiles.
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. Corrections for false discovery and microRNA abundance had minimal impact on this discrepancy. Further investigation is warranted.
Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America.
Ying-Wooi
YW
Wan
Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, United States of America ; College of Pharmacy, University of Houston, Houston, Texas, United States of America.
Claire M
CM
Mach
Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America ; Neurological Research Institute, Texas Children's Hospital, Houston, Texas, United States of America ; Department of Statistics and Electrical & Computer Engineering, Rice University, Houston, Texas, United States of America.
Genevera I
GI
Allen
Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, United States of America ; Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America ; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America.
Matthew L
ML
Anderson
Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America ; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America ; Computational and Integrative Biomedical Research (CIBR) Center, Baylor College of Medicine, Houston, Texas, United States of America ; Neurological Research Institute, Texas Children's Hospital, Houston, Texas, United States of America.
Zhandong
Z
Liu
D005260:Female; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D010051:Ovarian Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000401:mortality*; D016016:Proportional Hazards Models; D015203:Reproducibility of Results; D059467:Transcriptome
D035683:MicroRNAs