1. A novel approach toward optimal workflow selection for DNA methylation biomarker discovery
- Author
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Naghme Nazer, Mohammad Hossein Sepehri, Hoda Mohammadzade, and Mahya Mehrmohamadi
- Subjects
DNA methylation marker discovery ,Simulation of DNA methylation array data ,Data analysis pipeline optimization ,Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract DNA methylation is a major epigenetic modification involved in many physiological processes. Normal methylation patterns are disrupted in many diseases and methylation-based biomarkers have shown promise in several contexts. Marker discovery typically involves the analysis of publicly available DNA methylation data from high-throughput assays. Numerous methods for identification of differentially methylated biomarkers have been developed, making the need for best practices guidelines and context-specific analyses workflows exceedingly high. To this end, here we propose TASA, a novel method for simulating methylation array data in various scenarios. We then comprehensively assess different data analysis workflows using real and simulated data and suggest optimal start-to-finish analysis workflows. Our study demonstrates that the choice of analysis pipeline for DNA methylation-based marker discovery is crucial and different across different contexts.
- Published
- 2024
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