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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