A unique pair of microarray datasets for microRNA profiling: data with careful design (Dataset A)

We set out to demonstrate the logistic feasibility of careful study design in microarray studies and the level of scientific benefits it can provide, in comparison with post-hoc data adjustment such as normalization, for preventing confounding handling effects and improving the accuracy and reproducibility of disease-relevant biomarker detection. Towards this end, we conducted a study of microRNA expression using endometroid endometrial cancer tumors (n=96) and serous ovarian cancer tumors (n=96) that were all primary, untreated, and collected in 2000-2012 at Memorial Sloan Kettering Cancer Center. The same set of tumor tissue samples were profiled twice using the Agilent microRNA microarrays with different study designs. In the first study, arrays were assigned to tumor samples using blocked randomization and they were processed by one experienced technician in one single run. In the second study, the arrays were assigned to the tumor samples in the order of their collection and they were handled by two technicians (the first of whom handled the first dataset) in five batches (with each batch on a separate date). This design mimicked typical practice. This dataset is from the first study. Tumor type: advanced serous ovarian cancer or endometrioid endometrial cancer.