Expression- and splicing-based multi-tissue transcriptome-wide association studies identified multiple genes for breast cancer by estrogen-receptor status

Table 2 Genes significantly associated with estrogen receptor (ER)-negative breast cancer that have not been identified in previous TWAS of breast cancer

Loci	Gene Name	Min. 11 Tissue ACAT p-value^a	Min. Breast p-value^b	TWAS-significant Approaches^c	Max. PIP (gene)^d	Max. PIP (intron)^e
1q32.1, L3	LGR6	8.52E-08	1.22E-08	splice	NA	1
1q32.1, L4	PIK3C2B	< 5.50E-17	1.46E-24	express	1	NA
2p23.2	WDR43	6.54E-13	7.81E-13	express\|splice	1	1
2q33.1	CLK1	1.34E-08	6.97E-01	express\|splice	1	0.45
2q33.1	FAM126B	6.89E-08	2.02E-04	express\|splice	0.26	0.36
2q33.1	NDUFB3	2.36E-08	NA	express	0.64	NA
5q11.2, L2	PELO	2.36E-06	2.76E-05	splice	NA	0.87
5q33.3	EBF1	7.34E-07	NA	splice	NA	0.92
6p21.32	RPS18	1.49E-07	1.15E-07	express	0.98	NA
6p21.32	B3GALT4	3.38E-08	8.46E-09	express	0.9	NA
8p23.3	RPL23AP53	2.16E-06	6.86E-07	splice	NA	0.97
9p21.3	CDKN2B	1.58E-06	1.94E-01	express	0.97	NA
11q22.3	ACAT1	2.53E-06	1.99E-06	splice	NA	0.96
11q22.3	C11orf65	1.50E-06	4.92E-04	express	1	NA
16q12.2, L1	FTO	7.19E-08	NA	splice	NA	0.99
17p13.1	TP53	2.34E-06	9.92E-07	express	0.87	NA
19p13.11, L1	USE1	6.75E-09	4.03E-02	splice	NA	0
19p13.11, L1	OCEL1	3.16E-10	4.30E-10	express\|splice	0.15	0
19p13.11, L1	NR2F6	1.40E-10	2.33E-11	express	0.08	NA
19p13.11, L1	USHBP1	6.11E-16	5.55E-17	splice	NA	0
19p13.11, L1	DDA1	2.96E-14	7.13E-01	express\|splice	1	0
19p13.11, L1	ANO8	1.02E-13	4.86E-08	express\|splice	0	1
19p13.11, L1	GTPBP3	1.52E-11	1.86E-11	splice	NA	0.33
19q13.31	ZNF45	3.53E-08	3.80E-08	splice	NA	1

Abbreviations:
TWAS, transcriptome-wide association study; ER-, estrogen receptor-negative.
^a The minimum joint-tissue TWAS p-value between either the expression-based or splicing-based approach.
^b The minimum TWAS p-value in breast tissue between either the expression-based approach or splicing-based approach.
^c “Express” indicates the listed gene was identified using only the expression-based TWAS approach in either only breast tissue or jointly across all tissues. “splice” indicates the listed gene was identified using only the splicing-based TWAS approach in either only breast tissue or jointly across all tissues. “express|splice” indicates the listed gene was identified in either expression-based or splicing-based approaches in either breast tissue or jointly across all tissues.
^d The maximum PIP for a given gene across 11 tissues.
^e The maximum PIP of introns in a given gene across 11 tissues.

ISSN: 1465-542X