A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells
In order to call a specific locus as being associated with a potential cis-regulatory variant, we used a χ2 -test to select the expression SNPs showing greater than a 60:40 allelic imbalance as well as having relatively higher read counts. (A) After making such confidence calls (‘mapping’) for each SNP, the reproducibility of ASE ratio measurements increased to R2 = 0.9802. (B) We prepared two sequencing libraries from the same pool of total RNA (technical replicates). In order to estimate the error rate in ASE calling/mapping overall, we compared the ASE ratio in these replicate libraries using a χ2 -test. We found that 1.6% of the statistically significant ASE calls were due to the sample processing and/or measurement error.