A polyclonal allelic expression assay for detecting regulatory effects of transcript variants.
CRISPR/Cas9 genome editing
Nonsense-mediated decay
Regulatory variation
Variant validation
eQTL
Journal
Genome medicine
ISSN: 1756-994X
Titre abrégé: Genome Med
Pays: England
ID NLM: 101475844
Informations de publication
Date de publication:
11 09 2020
11 09 2020
Historique:
received:
20
09
2019
accepted:
19
08
2020
entrez:
11
9
2020
pubmed:
12
9
2020
medline:
4
8
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 32912286
doi: 10.1186/s13073-020-00777-8
pii: 10.1186/s13073-020-00777-8
pmc: PMC7488413
doi:
Banques de données
figshare
['10.6084/m9.figshare.9883232']
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
79Subventions
Organisme : NIA NIH HHS
ID : R01 AG057422
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008224
Pays : United States
Organisme : NIH HHS
ID : R01MH106842
Pays : United States
Organisme : NIH HHS
ID : R01GM122924
Pays : United States
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