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Table 3 Associations between APOBEC-mutational signature and germline APOBEC3A/B deletion

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

Cancer typea S ~ Dd S ~ D + Ee PS ~ Df PS ~ D + Eg
Beta P Beta P Beta P Beta P
bladder 0.430 1.7 × 10− 3 0.082 0.68 0.354 9.4 × 10− 3 0.000 0.99
breast −0.281 5.6 × 10− 3 −0.620 2.8 × 10− 6 − 0.287 4.8 × 10− 3 − 0.50 1.4 × 10− 4
cervical 0.281 0.19 0.017 0.96 0.278 0.20 −0.063 0.84
lungb −0.048 0.78 −0.282 0.07 −0.124 0.48 −0.449 0.03
lungc 0.511 0.13 0.077 0.88 0.385 0.25 −0.190 0.70
head and neck 0.160 0.42 −0.067 0.85 0.284 0.16 0.065 0.85
stomach −0.141 0.67 −0.319 0.42 −0.060 0.86 −0.074 0.85
pancreas −0.439 0.39 −0.571 0.29 −0.388 0.45 −0.498 0.36
thyroid 0.029 0.85 −0.238 0.19 0.025 0.87 −0.231 0.20
kidney 0.323 0.17 0.14 0.59 0.292 0.21 0.105 0.69
  1. a” Sample size for each cancer type: bladder (N = 286), breast (N = 734), cervical (N = 133), lung adenocarcinoma (N = 363), lung squamous carcinoma (N = 85), head and neck (N = 323), stomach (N = 66), pancreas (N = 90), thyroid (N = 333), kidney (N = 143). “b” and “c” refers to lung adenocarcinoma and lung squamous carcinoma, respectively. “d”: APOBEC-mutational signature ~ Germline APOBEC3A/B deletion; “e”: APOBEC-mutational signature ~ Germline APOBEC3A/B deletion + uc003awn + uc003awo + uc011aoc (Expression levels); “f”: Proportion of APOBEC-mutational signature ~ Germline APOBEC3A/B deletion; “g”: Proportion of APOBEC-mutational signature ~ Germline APOBEC3A/B deletion + uc003awn + uc003awo + uc011aoc (Expression levels); In association models: “S” refers to APOBEC-mutational signature; “D” refers to germline APOBEC3A/B deletion; “E” refers to isoform expression levels; “RS” refers to proportion APOBEC-mutational signature. The significance level at P = 0.005, corresponding to a threshold with a Bonferroni-correction of P = 0.05, given 10 tests