decemedip: hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylome
MeDIP-seq is an enrichment-based DNA methylation profiling technique that measures abundance of methylated DNA. While this technique offers efficiency advantages over direct methylation profiling, it does not provide absolute quantification of DNAm necessary for cell type deconvolution. We introduce decemedip, a Bayesian hierarchical model for cell type deconvolution of methylated sequencing data that leverages reference atlases derived from direct methylation profiling. We demonstrate its accuracy and robustness through simulation studies and validation on cross-platform measurements, and highlight its utility in identifying tissue-specific and cancer-associated methylation signatures using MeDIP-seq profiling of patient-derived xenografts and cell-free DNA. decemedip is available at \url{https://github.com/nshen7/decemedip}. Overall design: The submitted samples were DNA from the LuCaP PDXs extracted using the DNeasy Blood and Tissue Kit (QIAGEN). Genomic DNA was sheared using a Covaris Sonicator E220, and AMPure XP beads (Beckman Coulter) were used to size select 150 to 250 bp DNA fragments. Library preparation was performed using the KAPA HyperPrep Kit (KAPA Biosystems) according to the manufacturer's protocol. We then performed end-repair, A-tailing, and ligation of NEBNext adaptors (NEBNext Multiplex Oligos for Illumina kit, New England BioLabs). Libraries were digested using the USER enzyme (New England BioLabs). Lamda DNA, consisting of unmethylated and in vitro methylated DNA, was added to prepared libraries to achieve a total amount of 100 ng DNA. Methylated and unmethylated Arabidopsis thaliana DNA (Diagenode) was added for quality control. MeDIP was performed using the MagMeDIP Kit (Diagenode anti-5-methylcytosine (5-mC) antibody, specifically the 33D3 clone) following the manufacturer's protocol. Samples were purified using the iPure Kit v2 (Diagenode). Success of the immunoprecipitation was confirmed using qPCR to detect recovery of the spiked-in Arabidopsis thaliana methylated and unmethylated DNA.