A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells
(A) Padlock probes were used to capture approximately 19,000 SNPs from the genomic DNA. The number of mapped heterozygous reads (1.2 million) was then used to calculate the allelic ratio (reference:alternative) in 4,721 SNPs. The observed distribution of ASE ratios was symmetrically distributed around a mean of 0.51, suggesting little sequencing and/or mapping bias. (B) The heterozygous sequencing reads for both reference and alternative alleles were binned according to the observation counts. Their distribution probability was then plotted against the sequencing read counts, showing a nearly identical distribution pattern.