Table 3.

Transcriptome-wide association study of neuropathology-based AD traits

GWAS summary	Gene	Region	ACAT P	Leading tissues
Braak Stage	ST8SIA1 c	12p12.1	4.69 × 10–7	Brain_Cerebellar_Hemisphere, Brain_Cerebellum
	APOC1 a	19q13.32	1.18 × 10–18	Nucleus_accumbens_basal_ganglia
	APOE a	19q13.32	1.37 × 10–7	Brain_Caudate_basal_ganglia,
	TOMM40 a	19q12.32	8.33 × 10–34	Pituitary
	ANKRD36B c	2q11.2	3.38 × 10–6	Brain_Cortex Brain_Hippocampus Nucleus_accumbens_basal_ganglia Brain_Spinal_cord_cervical_c-1 Brain_Substantia_nigra
	MRPL38 c	17q25.1	2.34 × 10–12	Brain_Hypothalamus
	APOC4 a	19q13.31	2.67 × 10–21	Brain_Caudate_basal_ganglia, Brain_Hypothalamus Nucleus_accumbens_basal_ganglia
ncAD	TOMM40 a	19q13.32	5.43 × 10–16	Pituitary
NP score	SYT5 c	19q13.42	5.29 × 10–9	Brain_Cerebellar_Hemisphere
	APOE a	19q13.32	6.51 × 10–8	Brain_Caudate_basal_ganglia
	TOMM40a	19q13.32	1.88 × 10–31	Pituitary
	APEHc	3p21.31	1.03 × 10–8	Brain_Cerebellar_Hemisphere
	MRPL38c	17q25.1	1.97 × 10–6	Brain_Hypothalamus
	LINC02458 c	12q21.33	2.41 × 10–6	Brain_Frontal_Cortex_BA9
	CTXN2-AS1 c	15q21.1	1.60 × 10–15	Pituitary

Transcriptome-wide association study (TWAS) identifies 11 unique and 7 novel genes significantly associated with neuropathological features of AD in GTEx Brain tissues. GWAS: Genome-wide association study; TWAS: Transcriptome-wide association study; ACAT P: Aggregated Cauchy Association Test based combined TWAS p-value Bonferroni correction thresholds are p-value < 2.48 × 10–6 based on 20,205, 20,198, and 20,207 tests in Braak stage, ncAD case–control, and NP score combined JTI-ACAT TWAS analysis respectively. a: Genes have been identified as significant in previous clinical or neuropathology-based AD GWAS. b: Genes have been identified as significant in previous AD-related TWAS alone, c: Genes have not been identified as significant in previous AD GWAS or TWAS studies. * ncAD: neuropathology-confirmed AD