Table 1.
Transcriptome-wide association study (TWAS) test statistics for thirteen significantly associated genes for Alzheimer's disease in monocytes
| Monocyte | Gene | Chromosome | Gene start | Gene end | K_TWAS.Z | M_TWAS.Z | K_TWAS.P | M_TWAS.P |
|---|---|---|---|---|---|---|---|---|
| CD14+ | LACTB2 | 8 | 71547553 | 71581409 | 4.305 | 0.861 | 1.67E−05 | 3.89E−01 |
| CD14+ | PTK2B** | 8 | 27168999 | 27316903 | 5.485 | 4.325 | 4.14E−08 | 1.52E−05 |
| CD14+ | MS4A4A | 11 | 60048014 | 60076445 | 6.683 | 3.200 | 2.33E−11 | 1.37E−03 |
| CD14+ | MS4A6A | 11 | 59939081 | 59952139 | 6.431 | 2.431 | 1.27E−10 | 1.51E−02 |
| CD14+ | MYBPC3 | 11 | 47352957 | 47374253 | 5.204 | 1.093 | 1.95E−07 | 2.74E−01 |
| CD14+ | SPI1 | 11 | 47376411 | 47400127 | 6.397 | 1.279 | 1.58E−10 | 2.01E−01 |
| CD14+ | STX3 | 11 | 59480929 | 59573354 | −4.898 | −2.302 | 9.66E−07 | 2.13E−02 |
| IFN | LACTB2 | 8 | 71547553 | 71581409 | 4.361 | 1.621 | 1.29E−05 | 1.05E−01 |
| IFN | SPI1 | 11 | 47376411 | 47400127 | 6.337 | 1.207 | 2.35E−10 | 2.27E−01 |
| IFN | APOE* | 19 | 45409011 | 45412650 | −2.495 | −6.039 | 1.26E−02 | 1.55E−09 |
| IFN | ZNF668* | 16 | 31072813 | 31073451 | 1.759 | 4.355 | 7.86E−02 | 1.33E−05 |
| LPS2 | BIN1 | 2 | 127805603 | 127864931 | −7.843 | −3.403 | 4.40E−15 | 6.66E−04 |
| LPS2 | PLIN2 | 9 | 19108373 | 19149288 | −4.356 | −1.918 | 1.33E−05 | 5.51E−02 |
| LPS2 | MS4A6E** | 11 | 60102304 | 60164069 | −7.879 | −4.314 | 3.31E−15 | 1.61E−05 |
| LPS2 | SPI1 | 11 | 47376411 | 47400127 | 6.218 | 1.327 | 5.04E−10 | 1.84E−01 |
| LPS2 | FNBP4 | 11 | 47738072 | 47788995 | 4.873 | 1.118 | 1.10E−06 | 2.63E−01 |
| LPS2 | APOE | 19 | 45409011 | 45412650 | 7.441 | 4.099 | 1.00E−13 | 4.16E−05 |
| LPS24 | BIN1 | 2 | 127805603 | 127864931 | −6.825 | −2.615 | 8.78E−12 | 8.92E−03 |
| LPS24 | PTK2B | 8 | 27168999 | 27316903 | −4.916 | −3.312 | 8.85E−07 | 9.28E−04 |
| LPS24 | LACTB2 | 8 | 71547553 | 71581409 | 4.274 | 2.262 | 1.92E−05 | 2.37E−02 |
| LPS24 | SPI1 | 11 | 47376411 | 47400127 | 6.333 | 1.219 | 2.41E−10 | 2.23E−01 |
| LPS24 | MS4A6E | 11 | 60102304 | 60164069 | −4.974 | −2.402 | 6.57E−07 | 1.63E−02 |
| LPS24 | PVR** | 19 | 45147098 | 45166850 | −6.691 | −5.495 | 2.21E−11 | 3.90E−08 |
| LPS24 | FOSB* | 19 | 45971253 | 45978437 | −1.571 | −4.737 | 1.16E−01 | 2.17E−06 |
Genes showing TWAS significant associations (P < 0.05 after Bonferroni correction for the number of genes for which TWAS was performed in each tissue). TWAS.P values shown are not corrected for multiple testing. K_TWAS.Z and M_TWAS.Z denote the gene-level TWAS Z-score using Kunkle 20198 and Marioni summary statistics,33 respectively. Genes without asterisks are TWAS significant using Kunkle summary statistics.
TWAS significant genes using Marioni summary statistics.
TWAS significant genes in both Kunkle and Marioni TWAS. TWAS significant genes that are novel candidate genes for Alzheimer’s disease are shown in bold.