Table 3.

Significant Genes Identified by BGW-TWAS using IGAP GWAS Summary Statistics of AD

Gene	CHR	Position	TWAS p Value
			BGW-TWAS	BVSR cis-eQTL	PrediXcan	TIGAR
GPX1a	3	49,394,608	2.45 × 10−98	2.45 × 10−98	–	3.15 × 10−1
FAM86DP	3	75,484,261	1.55 × 10−13	4.81 × 10−1	5.38 × 10−1	9.63 × 10−1
BTN3A2a	6	26,378,546	$1.59\times {10}^{-26}$	$1.56\times {10}^{-26}$	$3.17\times {10}^{-1}$	$5.04\times {10}^{-1}$
ZNF192a	6	28,124,089	$1.26\times {10}^{-32}$	$1.25\times {10}^{-32}$	$8.56\times {10}^{-2}$	$2.07\times {10}^{-1}$
AL022393.7a	6	28,144,452	$3.25\times {10}^{-178}$	$2.24\times {10}^{-178}$	$1.50\times {10}^{-1}$	$8.36\times {10}^{-2}$
HLA-DRB1a,b	6	32,557,625	$1.02\times {10}^{-12}$	$8.99\times {10}^{-13}$	$2.06\times {10}^{-6}$	–
AEBP1	7	44,154,161	$5.55\times {10}^{-220}$	$8.62\times {10}^{-1}$	$6.69\times {10}^{-1}$	$4.19\times {10}^{-1}$
BUB3	10	124,924,886	$6.64\times {10}^{-18}$	$1.05\times {10}^{-2}$	–	$4.76\times {10}^{-1}$
FBXO3	11	33,796,089	$1.48\times {10}^{-9}$	$6.88\times {10}^{-1}$	–	$1.13\times {10}^{-1}$
CEACAM19a,b,c	19	45,187,631	$4.7\times {10}^{-13}$	$2.54\times {10}^{-13}$	$3.60\times {10}^{-12}$	$2.83\times {10}^{-16}$
APOC1a	19	45,422,606	$8.9\times {10}^{-11}$	$1.11\times {10}^{-10}$	$3.18\times {10}^{-6}$	$7.2\times {10}^{-3}$
ZC3H12B	X	64,727,767	$2.08\times {10}^{-37}$	–	–	–
CXorf56	X	118,699,397	$6.02\times {10}^{-07}$	–	–	–

TWAS p values by alternative methods, i.e., using BVSR cis-eQTL estimates only, PrediXcan, and TIGAR are also provided. p values for genes that were missed by TWAS were indicated as “–.” ZC3H12B that was identified by BGW-TWAS using individual-level GWAS data from ROS/MAP and MCADGS was also identified by BGW-TWAS using IGAP summary-level GWAS statistics. CEACAM19 from chromosome 19 was identified by all TWAS methods, and HLA-DRB1 from chromosome 6 is a known GWAS risk locus.

^aGenes that were also identified as significant by using BVSR cis-eQTL estimates.

^bGenes that were also identified by PrediXcan.

^cGenes that were also identified by TIGAR.