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A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells

Figure 3

Noise and reproducibility in padlock-based ASE measurements.

(A) The ASE ratio measurement from the PGP1 fibroblast cDNA (1,021 SNPs) was plotted as a function of the total number of mapped reads (reference + alternative alleles), demonstrating a relationship between the ASE ratio variance and the read count. (B) Twelve random SNPs were examined in PGP1 fibroblasts and lymphocytes using quantitative Sanger sequencing, in which the height of each sequencing trace was used to calculate the allelic ratio in the cDNA. These values were then compared against the ASE ratio determined using padlock probes. (C) The correlation among the ASE ratios with less than 100 observations remained high (R2 = 0.799) in technical replicates (PGP1 EB7b and EB7c). (D) Among the ASE ratios with more than 100 observations, the correlation improved to R2 = 0.905.

Figure 3