Analysis of the loci where the gold-standard gene was missed looks pretty grim: eQTLs find other i.e. misleading genes, while CRISPRi often lacks power. "Wow they both suck, but in totally different ways" was my first reaction to this plot.
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The analysis of gold-standard genes in these GWAS loci shows how much you'd miss using only one approach, and how startlingly orthogonal the discoveries are. The patterns are highly variable between the loci. It depends on your downstream application if you prefer higher sensitivity vs specificity.
Overall, this provides important insights in cis-target gene discovery from eQTLs and CRISPRi. I think we're ultimately going to need both tools, as both have fundamental weaknesses: eQTL's bias against constrained genes, and difficulty of applying CRISPR to diverse cell types.
Neither approach does a stellar job, but I'm an optimist: Our works points to future potential, with larger and more diverse studies. The genes detected in these 1st gen CRISPRi work look pretty similar to eQTL data from 15 years ago (I was there). There is much to discover!
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