"Gap hunting" to characterize clustered probe signals in Illumina methylation array data.

ABSTRACT:

Background

The Illumina 450k array has been widely used in epigenetic association studies. Current quality-control (QC) pipelines typically remove certain sets of probes, such as those containing a SNP or with multiple mapping locations. An additional set of potentially problematic probes are those with DNA methylation distributions characterized by two or more distinct clusters separated by gaps. Data-driven identification of such probes may offer additional insights for downstream analyses.

Results

We developed a procedure, termed "gap hunting," to identify probes showing clustered distributions. Among 590 peripheral blood samples from the Study to Explore Early Development, we identified 11,007 "gap probes." The vast majority (9199) are likely attributed to an underlying

SUBMITTER: Andrews SV 

PROVIDER: S-EPMC5142147 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature