Identification of differentially methylated regions in rare diseases from a single-patient perspective

Abstract

Background DNA methylation (5-mC) is being widely recognized as an alternative in the detection of sequence variants in the diagnosis of some rare neurodevelopmental and imprinting disorders. Identification of alterations in DNA methylation plays an important role in the diagnosis and understanding of the etiology of those disorders. Canonical pipelines for the detection of differentially methylated regions (DMRs) usually rely on inter-group (e.g., case versus control) comparisons. However, these tools might perform suboptimally in the context of rare diseases and multilocus imprinting disturbances due to small cohort sizes and inter-patient heterogeneity. Therefore, there is a need to provide a simple but statistically robust pipeline for scientists and clinicians to perform differential methylation analyses at the single patient level as well as to evaluate how parameter fine-tuning may affect differentially methylated region detection. Result We implemented an improved statistical method to detect differentially methylated regions in correlated datasets based on the Z-score and empirical Brown aggregation methods from a single-patient perspective. To accurately assess the predictive power of our method, we generated semi-simulated data using a public control population of 521 samples and investigated how the size of the control population, methylation difference, and region size affect DMR detection. In addition, we validated the detection of methylation events in patients suffering from rare multi-locus imprinting disturbance and evaluated how this method could complement existing tools in the context of clinical diagnosis. Conclusion In this study, we present a robust statistical method to perform differential methylation analysis at the single patient level and describe its optimal parameters to increase DMRs identification performance. Finally, we show its diagnostic utility when applied to rare disorders.

PCBS: an R package for fast and accurate analysis of bisulfite sequencing data

“…Introduction DNA methylation plays important roles in a variety of basic biological functions such as gene splicing, transcription, and chromosomal stability, as well as in numerous disease states including cancer, autoimmune, and neurodevelopmental diseases (Jones 2012, Robertson 2005, Grolaux et al 2022). Whole Genome Bisulfite Sequencing (WGBS) is one of the most powerful tools for assessing methylation states genome-wide.…”