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, in the context of rare diseases and ii-locus imprinting disturbances, these tools might perform suboptimal 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: In this paper, we describe 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 assessed how the size of the control population, the effect size and region size affect DMRs detection. In addition, we have validated the detection of methylation events in patients suffering from rare multi-locus imprinting disturbance and discuss how this method could complement existing tools in the context of clinical diagnosis. Conclusion: We present a robust statistical method to perform differential methylation analysis at the single patient level and evaluated its optimal parameters to increase DMRs identification performance and show its diagnostic utility when applied to rare disorders.