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.
CITATION STYLE
Brandt, M., Gokden, A., Ziosi, M., & Lappalainen, T. (2020). A polyclonal allelic expression assay for detecting regulatory effects of transcript variants. Genome Medicine, 12(1). https://doi.org/10.1186/s13073-020-00777-8
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