Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes.

ABSTRACT:

Background

DNA methylation is an important epigenetic mark and dysregulation of DNA methylation is associated with many diseases including cancer. Advances in next-generation sequencing now allow unbiased methylome profiling of entire patient cohorts, greatly facilitating biomarker discovery and presenting new opportunities to understand the biological mechanisms by which changes in methylation contribute to disease. Enrichment-based sequencing assays such as MethylCap-seq are a cost effective solution for genome-wide determination of methylation status, but the technical reliability of methylation reconstruction from raw sequencing data has not been well characterized.

Methods

We analyze three MethylCap-seq data sets and perform two different analyses to assess data quality

SUBMITTER: Trimarchi MP 

PROVIDER: S-EPMC3535705 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature