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


ABSTRACT: 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.

SUBMITTER: Brandt M 

PROVIDER: S-EPMC7488413 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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

Brandt Margot M   Gokden Alper A   Ziosi Marcello M   Lappalainen Tuuli T  

Genome medicine 20200911 1


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 abilit  ...[more]

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