Extent, impact, and mitigation of batch effects in tumor biomarker studies using tissue microarrays.

ABSTRACT: Tissue microarrays (TMAs) have been used in thousands of cancer biomarker studies. To what extent batch effects, measurement error in biomarker levels between slides, affects TMA-based studies has not been assessed systematically. We evaluated 20 protein biomarkers on 14 TMAs with prospectively collected tumor tissue from 1448 primary prostate cancers. In half of the biomarkers, more than 10% of biomarker variance was attributable to between-TMA differences (range, 1-48%). We implemented different methods to mitigate batch effects (R package batchtma), tested in plasmode simulation. Biomarker levels were more similar between mitigation approaches compared to uncorrected values. For some biomarkers, associations with clinical features changed substantially after addressing batch effects. Ba

SUBMITTER: Stopsack KH 

PROVIDER: S-EPMC8849344 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature