Fine-mapping within eQTL credible intervals by expression CROP-seq

Loading...
Thumbnail Image
Files
bpaa008.pdf(502.22 KB)
Published Version
bpaa008_supplementary_data.zip(2.16 MB)
Supplementary Data
Date
2020-03-28
Authors
Pan, Yidan
Tian, Ruoyu
Lee, Ciaran M.
Bao, Gang
Gibson, Greg
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford University Press
Research Projects
Organizational Units
Journal Issue
Abstract
The majority of genome-wide association study (GWAS)-identified SNPs are located in noncoding regions of genes and are likely to influence disease risk and phenotypes by affecting gene expression. Since credible intervals responsible for genome-wide associations typically consist of ≥100 variants with similar statistical support, experimental methods are needed to fine map causal variants. We report here a moderate-throughput approach to identifying regulatory GWAS variants, expression CROP-seq, which consists of multiplex CRISPR-Cas9 genome editing combined with single-cell RNAseq to measure perturbation in transcript abundance. Mutations were induced in the HL60/S4 myeloid cell line nearby 57 SNPs in three genes, two of which, rs2251039 and rs35675666, significantly altered CISD1 and PARK7 expression, respectively, with strong replication and validation in single-cell clones. The sites overlap with chromatin accessibility peaks and define causal variants for inflammatory bowel disease at the two loci. This relatively inexpensive approach should be scalable for broad surveys and is also implementable for the fine mapping of individual genes.
Description
Keywords
Regulatory GWAS variants , Expression CROP-seq , CRISPR-Cas9 , Genome editing , Single-cell RNAseq
Citation
Pan, Y., Tian, R., Lee, C., Bao, G. and Gibson, G. (2020) 'Fine-mapping within eQTL credible intervals by expression CROP-seq', Biology Methods and Protocols, 5(1), bpaa008 (8pp). doi: 10.1093/biomethods/bpaa008