Dataset for "Scalable screening of ternary-code DNA methylation dynamics associated with human traits."

Methylation Screening Array (MSA) Dataset Repository This repository contains comprehensive annotation files, design specifications, and test datasets for the Illumina Infinium Methylation Screening Array (MSA), a novel 48-sample BeadChip platform designed for ultra-high throughput, cost-effective screening of trait-associated DNA methylation in large human populations. The MSA enables scalable screening of ternary-code DNA methylation (5mC, 5hmC, and unmodified cytosine) with ~270,000 carefully curated methylation sites enriched for trait associations (~5.6 trait associations per site vs. ~2.2 in EPICv2) and cell-identity signatures (~3.7 cell signatures per site vs. ~2.3 in EPICv2). Repository Contents 1. MSA Array Probe Addresses, Ordering and Controls (hg38) Complete manifest of probe addresses mapped to human genome reference hg38 Probe ordering information for data processing workflows Control probe specifications for quality assessment 2. Test Dataset: MSA SigDF Objects 9 MSA SigDF objects from 3 different cell lines Provided for testing and validation purposes Compatible with the SeSAMe R/Bioconductor package (version 3.22+) 3. Probe Design Files Probe design files: Technical specifications for each MSA probe including sequence information, genomic coordinates, and design parameters Probe-trait association file: Comprehensive annotation linking probes to human traits, diseases, and phenotypes (Figure 1C in the publication) 4. Legacy KYCG Knowledgebases MSA probe masking by SNP effects Mapping issues and quality flags (hg38 reference) Additional performance evaluations and validation metrics Related Resources Goldberg et al. (2025). "Scalable screening of ternary-code DNA methylation dynamics associated with human traits." Cell Genomics. Infinium Annotation Website Infinium Methylation Screening Array Product Page Illumina Methylation Screening Array Webinar GSE264438: Human cell line and primary tissue methylome profiles (N=676) SeSAMe for Data Analysis