Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial.

ABSTRACT: Gene expression data obtained in large studies hold great promises for discovering disease signatures or subtypes through data analysis. It is also prone to technical variation, whose removal is essential to avoid spurious discoveries. Because this variation is not always known and can be confounded with biological signals, its removal is a challenging task. Here we provide a step-wise procedure and comprehensive analysis of the MINDACT microarray dataset. The MINDACT trial enrolled 6693 breast cancer patients and prospectively validated the gene expression signature MammaPrint for outcome prediction. The study also yielded a full-transcriptome microarray for each tumor. We show for the first time in such a large dataset how technical variation can be removed while retaining expected biolo

SUBMITTER: Jacob L 

PROVIDER: S-EPMC7385160 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature