Finding potential cis-regulatory loci using allele-specific chromatin accessibility as weights in a kernel-based variance component test.

ABSTRACT: We present a novel approach to detect potential cis-acting regulatory loci that combines the functional potential, an empirical DNase-seq based estimate of the allele-specificity of DNase-I hypersensitivity sites, with kernel-based variance component association analyses against expression phenotypes. To test our method we used public ENCODE whole genome DNase-I sequencing data, from a single sample, to estimate the functional potentials of the subset of 10,552 noncoding heterozygous single-nucleotide polymorphisms (SNPs) that were also present in the Genetic Analysis Workshop 19 (GAW19) family-based data set. We then built two covariance kernels, one nonweighted and one weighted by the functional potentials, and conducted kernel-based variance component association analyses against

SUBMITTER: Peralta JM 

PROVIDER: S-EPMC5133489 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature