MethylDetectR: a software for methylation-based health profiling

Abstract

DNA methylation is an important biological process that involves the reversible addition of chemical tags called methyl groups to DNA and affects whether genes are active or inactive. Individual methylation profiles are determined by both genetic and environmental influences. Inter-individual variation in DNA methylation profiles can be exploited to estimate or predict a wide variety of human characteristics and disease risk profiles. Indeed, a number of methylation-based predictors of human traits have been developed and linked to important health outcomes. However, there is an unmet need to communicate the applicability and limitations of state-of-the-art methylation-based predictors to the wider community. To address this need, we have created a secure, web-based interactive platform called ‘MethylDetectR’ which automates the calculation of estimated values or scores for a variety of human traits using blood methylation data. These traits include age, lifestyle traits and high-density lipoprotein cholesterol. Methylation-based predictors often return scores on arbitrary scales. To provide meaning to these scores, users can interactively view how estimated trait scores for a given individual compare against other individuals in the sample. Users can optionally upload binary phenotypes and investigate how estimated traits vary according to case vs. control status for these phenotypes. Users can also view how different methylation-based predictors correlate with one another, and with phenotypic values for corresponding traits in a large reference sample (n = 4,450; Generation Scotland). The ‘MethylDetectR’ platform allows for the fast and secure calculation of DNA methylation-derived estimates for several human traits. This platform also helps to show the correlations between methylation-based scores and corresponding traits at the level of a sample, report estimated health profiles at an individual level, demonstrate how scores relate to important binary outcomes of interest and highlight the current limitations of molecular health predictors.