PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data.

ABSTRACT:

Motivation

DNA methylation is an epigenetic change occurring in genomic CpG sequences that contribute to the regulation of gene transcription both in normal and malignant cells. Next-generation sequencing has been used to characterize DNA methylation status at the genome scale, but suffers from high sequencing cost in the case of whole-genome bisulfite sequencing, or from reduced resolution (inability to precisely define which of the CpGs are methylated) with capture-based techniques.

Results

Here we present a computational method that computes nucleotide-resolution methylation values from capture-based data by incorporating fragment length profiles into a model of methylation analysis. We demonstrate that it compares favorably with nucleotide-resolution bisulfite sequencing

SUBMITTER: Frankhouser DE 

PROVIDER: S-EPMC4253832 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature