Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci.

ABSTRACT:

Background

Genetic variation can alter transcriptional regulatory activity contributing to variation in complex traits and risk of disease, but identifying individual variants that affect regulatory activity has been challenging. Quantitative sequence-based experiments such as ChIP-seq and DNase-seq can detect sites of allelic imbalance where alleles contribute disproportionately to the overall signal suggesting allelic differences in regulatory activity.

Methods

We created an allelic imbalance detection pipeline, AA-ALIGNER, to remove reference mapping biases influencing allelic imbalance detection and evaluate accuracy of allelic imbalance predictions in the absence of complete genotype data. Using the sequence aligner, GSNAP, and varying amounts of genotype information to

SUBMITTER: Buchkovich ML 

PROVIDER: S-EPMC4515314 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature