A polyclonal allelic expression assay for detecting regulatory effects of transcript variants

Brandt, Margot; Gokden, Alper; Ziosi, Marcello; Lappalainen, Tuuli

We present an assay to experimentally test the regulatory effects of genetic variants within transcripts using CRISPR/Cas9 followed by targeted sequencing. We applied the assay to 32 premature stop-gained variants across the genome and in two Mendelian disease genes, 33 putative causal variants of eQTLs, and 62 control variants in HEK293T cells, replicating a subset of variants in HeLa cells. We detected significant effects in the expected direction (in 60% of variants), demonstrating the ability of the assay to capture regulatory effects of eQTL variants and nonsense-mediated decay triggered by premature stop-gained variants. The results suggest a utility for validating transcript-level effects of genetic variants.


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Genome Medicine

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Published Here
December 20, 2022


CRISPR/Cas9 genome editing, Variant validation, Regulatory variation, eQTL, Nonsense-mediated decay