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

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 1,448 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. Batch effects and resulting bias are not an error of an individual study but an inherent feature of TMA-based protein biomarker studies. They always need to be considered during study design and addressed analytically in studies using more than one TMA. ### Competing Interest Statement P.W. Kantoff reports the following disclosures for the last 24-month period: he has investment interest in Context Therapeutics LLC, DRGT, Placon, and Seer Biosciences; he is a company board member for Context Therapeutics LLC; he is a consultant/scientific advisory board member for Bavarian Nordic Immunotherapeutics, DRGT, GE Healthcare, Janssen, OncoCellMDX, Progenity, Seer Biosciences, and Tarveda Therapeutics; and he serves on data safety monitoring boards for Genentech/Roche and Merck. G. Parmigiani reports the following disclosures for the last 24-month period: he had investment interest in CRA Health; he is a co-founder and company board member of Phaeno Biotechnology; he is a consultant / scientific advisory board member for Konica-Minolta, Delfi Diagnostics and Foundation Medicine; he serves on a data safety monitoring board for Geisinger. None of these activities are related to the content of this article.