scTWAS: a powerful statistical framework for single-cell transcriptome-wide association studies.

Despite the low abundance of Mic.15, the association signal of PPP1R37 was highly significant ( p -value = 2.9 × 10 −18 ), suggesting that AD-associated variants may regulate PPP1R37 specifically in the inflammatory microglial subtype.

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We note that although APOE has previously been identified as a AD TWAS gene in microglia 83 , we did not highlight it in our scTWAS results because it did not pass Stage 1 screening, despite nominally significant Stage 2 associations in proliferate, surveilling, and reacting microglia (nominal p -values < 0.05).

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