Table 4 Replications of previous TWAS-identified breast cancer-associated genes in African-ancestry participants at a nominal significant level of P < 0.05 with consistent direction
Gene | Current study | Previous TWAS (EUR/ASN) | |||||
|---|---|---|---|---|---|---|---|
Z score | P value | Breast cancer subtypea | Modelb | Z Score | P Value | Breast cancer subtypea | |
ABHD8 | 2.4 | 9.0 × 10−3 | Overall | Exp-TWAS | 4.8 | 2.1 × 10−6 | Overall |
ALS2CR12 | 1.9 | 2.9 × 10−2 | Overall | spTWAS | 8.4 | 5.5 × 10−17 | Overall |
ATG10 | −1.9 | 2.7 × 10−2 | ER-Pos | APA-WAS | −6.7 | 2.5 × 10−11 | Overall |
CASP8 | −2.4 | 7.9 × 10−3 | Overall | Exp-TWAS | −8.5 | 2.0 × 10−17 | Overall |
CMB9-22P13.1 | 2.2 | 1.4 × 10−2 | ER-Neg | Exp-TWAS | 5.6 | 1.7 × 10−8 | Overall |
CPNE1 | −2.4 | 9.2 × 10−3 | Overall | Exp-TWAS | −4.7 | 2.9 × 10−6 | Overall |
GSTM1 | −2.0 | 2.5 × 10−2 | Overall | spTWAS | −4.8 | 1.4 × 10−6 | Overall |
GTF2IP1 | −1.8 | 3.4 × 10−2 | Overall | Exp-TWAS | −4.8 | 1.3 × 10−6 | Overall |
GTF2IRD2 | 1.9 | 3.1 × 10−2 | Overall | Exp-TWAS | 5.2 | 1.8 × 10−7 | Overall |
HLA-F | 1.7 | 4.2 × 10−2 | Overall | APA-WAS | 4.8 | 2.1 × 10−6 | Overall |
KLHDC7A | −1.7 | 4.7 × 10−2 | Overall | Exp-TWAS | −6.3 | 2.4 × 10−10 | Overall |
LINC00886 | −1.7 | 4.2 × 10−2 | ER-Neg | Exp-TWAS | −5.0 | 5.9 × 10−7 | Overall |
LRRC25 | 1.9 | 2.8 × 10−2 | Overall | Exp-TWAS | 9.5 | 2.8 × 10−21 | Overall |
LRRC37A2 | −1.8 | 3.7 × 10−2 | ER-Neg | Exp-TWAS | −5.7 | 1.5 × 10−8 | Overall |
MAN2C1 | −3.3 | 4.7 × 10−4 | Overall | Exp-TWAS | −5.9 | 2.8 × 10−9 | Overall |
METTL15P1 | −2.4 | 8.8 × 10−3 | ER-Neg | Exp-TWAS | −5.1 | 2.8 × 10−7 | Overall |
MLEC | 2.1 | 1.6 × 10−2 | ER-Neg | spTWAS | 5.6 | 2.6 × 10−8 | Overall |
NAGLU | −1.8 | 4.0 × 10−2 | Overall | spTWAS | −5.3 | 1.3 × 10−7 | Overall |
NCF1 | 1.8 | 4.0 × 10−2 | ER-Pos | APA-WAS | 4.9 | 9.4 × 10−7 | Overall |
PEX14 | 2.3 | 1.2 × 10−2 | Overall | Exp-TWAS | 4.9 | 1.2 × 10−6 | Overall |
PLEKHM1 | −1.7 | 4.9 × 10−2 | ER-Neg | spTWAS | −5.9 | 4.1 × 10−9 | Overall |
PRSS45 | −2.0 | 2.1 × 10−2 | ER-Neg | spTWAS | −5.4 | 6.3 × 10−8 | Overall |
RCCD1 | −2.6 | 4.7 × 10−3 | Overall | Exp-TWAS | −10.9 | 1.6 × 10−27 | Overall |
RPS23 | 2.1 | 1.6 × 10−2 | Overall | Exp-TWAS | 6.1 | 1.4 × 10−9 | Overall |
SEMA4A | 1.7 | 4.2 × 10−2 | TNBC | spTWAS | 6.3 | 4.2 × 10−10 | Overall |
SEPT14P8 | −1.9 | 2.8 × 10−2 | ER-Pos | Exp-TWAS | −6.0 | 2.0 × 10−9 | ER-Neg |
SGCE | 1.7 | 4.1 × 10−2 | ER-Pos | APA-WAS | 5.7 | 9.3 × 10−9 | Overall |
STXBP4 | 1.9 | 3.1 × 10−2 | Overall | spTWAS | 10.0 | 2.2 × 10−23 | Overall |
THBS3 | 2.0 | 2.5 × 10−2 | ER-Pos | Exp-TWAS | 5.3 | 1.3 × 10−7 | Overall |
