Systematic evaluation of cell-type deconvolution pipelines for sequencing-based bulk DNA methylomes.

ABSTRACT: DNA methylation analysis by sequencing is becoming increasingly popular, yielding methylomes at single-base pair and single-molecule resolution. It has tremendous potential for cell-type heterogeneity analysis using intrinsic read-level information. Although diverse deconvolution methods were developed to infer cell-type composition based on bulk sequencing-based methylomes, systematic evaluation has not been performed yet. Here, we thoroughly benchmark six previously published methods: Bayesian epiallele detection, DXM, PRISM, csmFinder+coMethy, ClubCpG and MethylPurify, together with two array-based methods, MeDeCom and Houseman, as a comparison group. Sequencing-based deconvolution methods consist of two main steps, informative region selection and cell-type composition estimation, thus

SUBMITTER: Jeong Y 

PROVIDER: S-EPMC9294431 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature