Integrative genomic analyses of APOBEC-mutational signature, expression and germline deletion of APOBEC3 genes, and immunogenicity in multiple cancer types

Table 1 Associations between APOBEC-mutational signature and isoform expression levels of APOBEC3A and APOBEC3B

Cancer type^a	uc003awn		uc011aoc		uc011awo
Cancer type^a	Beta	P	Beta	P	Beta	P
bladder	0.035	0.08	0.032	0.25	0.130	1.3 × 10^− 6
breast	0.085	1.3 × 10^− 7	0.159	5.3 × 10^− 11	0.053	6.5 × 10^− 3
cervical	0.105	3.2 × 10^− 5	0.035	0.27	0.076	0.04
lung^b	0.076	2.6 × 10^− 3	0.097	0.01	0.131	5.2 × 10^− 6
lung^c	0.021	0.57	−0.072	0.11	−0.037	0.55
head and neck	0.549	1.5 × 10^− 4	−0.013	0.52	0.086	2.3 × 10^− 3
stomach	−0.004	0.88	−0.050	0.40	0.144	8.9 × 10⁻⁷
pancreas	0.086	0.15	0.099	0.29	0.076	0.32
thyroid	0.070	0.03	0.043	0.56	0.059	0.12
kidney	0.024	0.52	−0.026	0.77	0.095	0.02

“^a” Sample size for each cancer type: bladder (N = 388), breast (N = 961), cervical (N = 185), lung adenocarcinoma (N = 475), lung squamous cell carcinoma (N = 178), head and neck (N = 498), stomach (N = 368), pancreas (N = 119), thyroid (N = 485) and kidney (N = 280). “^b” and “^c” refers to lung adenocarcinoma and lung squamous carcinoma, respectively. A multivariate regression analysis was constructed to include all six isoforms as independent variables and APOBEC-signature mutation as the dependent variable for each cancer type. Multivariate regression analysis was constructed to include all six isoforms as independent variables and APOBEC-signature mutation as the dependent variable for each cancer type. The significance level at P = 0.005, corresponding to a threshold with a Bonferroni-correction of P = 0.05, given 10 tests

ISSN: 1755-8794