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Fig. 1 | Genome Biology

Fig. 1

From: Systematic identification of regulatory variants associated with cancer risk

Fig. 1

The workflow to screen for regulatory SNPs associated with cancer risk. The genomic DNA from ten individuals was pooled and sonicated into fragments of ~ 500 bp. Regions containing 10,673 SNPs in LD with 996 GWAS-identified cancer risk SNPs were captured using a custom designed array. The captured fragments were inserted into a modified STARR-seq vector using Gibson assembly to generate a plasmid library, which was sequenced as the input library and then transfected into HEK293T cells. The RNAs were extracted from cells and sequenced as the output library. The regulatory activities were calculated based on the ratio of normalized fragment counts in the output library against the input library. The regulatory SNPs were detected by the changes in allelic ratios in the output library compared to those in the input library

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