A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells
(A) We examined 1,124 genes in PGP1 fibroblast cDNA shared between Illumina's BeadChip Ref-8 V3 and our padlock probe set. To normalize for the probe-specific differences in capture, the cDNA capture reads were divided by the number of reads obtained from the genomic DNA. For those genes that were targeted by padlock probes more than once, we averaged the number of normalized reads from each probe. We generated a plot of the relative gene expression from BeadChip versus the normalized average capture counts, demonstrating only a weak correlation between the level of gene expression and the frequency of padlock capture. (B) We then examined the distribution of the gene expression level detected on BeadChip (green) versus those captured by padlock probes (red). Of the 18,630 genes, approximately 50% did not reach the detection criteria (p-value <0.01) on BeadChip. On the other hand, 14% of all digital RNA allelotyping calls were made using these ‘undetectable’ rare transcripts.