Figure 1.

GenIE overview. (A) Proportion of GWAS lead SNPs in different genomic regions; 69% fall in transcribed regions (introns/exons/splice sites/UTRs/ncRNAs). (B) Deletion profiles from Cas9 editing at MUL1 intronic SNP rs6700034 in hiPSCs, assayed in genomic DNA (gDNA, left) and complementary DNA (cDNA) generated from RNA (right). (top row) count of sequencing reads having a deletion at each nucleotide position relative to the cut site; (bottom row) profile of each unique Cas9-induced deletion. (C) Schematic of GenIE assay. Edited pools of cells contain a mixture of WT, edited point mutation (SNP) and a variety of deletion alleles (indel 1, 2, etc.), expression from each of which can be quantified by amplicon sequencing of cDNA and gDNA extracted from the same population of cells.