Table 3:
Summary of the 11 AD PWAS-significant genes with evidence for being consistent with a causal role in AD.
| Discovery | Confirmatory | Evidence for causality | TWAS | Novel | ||||
|---|---|---|---|---|---|---|---|---|
| Gene | Chr | PWAS | PWAS | COLOC | SMR | significant | gene | |
| 1 | CTSH | 15 | significant | replicated | yes | yes | suggestive | yes |
| 2 | DOC2A | 16 | significant | replicated | yes | yes | n/a | yes |
| 3 | ICA1L | 2 | significant | replicated | yes | yes | no | yes |
| 4 | LACTB | 15 | significant | replicated | yes | yes | suggestive | no |
| 5 | SNX32 | 11 | significant | replicated | yes | yes | yes | yes |
| 6 | ACE | 17 | significant | replicated | yes | no | yes | yes |
| 7 | RTFDC1 | 20 | significant | replicated | yes | no | suggestive | no |
| 8 | CARHSP1 | 16 | significant | replicated | no | yes | yes | yes |
| 9 | STX6 | 1 | significant | replicated | no | yes | yes | yes |
| 10 | STX4* | 16 | significant | − | yes | yes | yes | no |
| 11 | PLEKHA1* | 10 | significant | − | yes | yes | n/a | yes |
(*)
Asterisk denotes proteins not found in the confirmation PWAS. n/a refers to genes that did not have significant heritability estimates to be included in the TWAS of AD. Full results for TWAS is in Supplementary tables 17-18. “suggestive” in “TWAS significant” column refers to genes with 0.05 <TWAS nominal p <0.1. Novel gene refers to genes not within 1Mb window of SNPs with p < 5E-08 identified in Jansen et. al. AD GWAS1.