Table 2.
Summary of the SBS mutation data and results of the AA signature analysis
| Case ID | Total SBS |
SBS per Mbp |
A > T SBS |
A > T per Mbp |
% A > T | % CAG context |
SB A > T | SB p value |
SB FDR q value |
Contribution to Sig 1A/1B (Age) |
Contribution to Sig 22 (AA) |
AA signature |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EN-01 | 600 | 9.4 | 224 | 3.5 | 37.3 | 23.0 | 1.6 (128/78) | 0.00064 | 0.010 | 228 (38%) | 372 (62%) | Yes |
| EN-02 | 375 | 5.9 | 57 | 0.9 | 15.2 | 11.4 | 2.8 (39/14) | 0.00098 | 0.013 | 256 (68%) | 119 (32%) | Yes1 |
| EN-03 | 355 | 5.5 | 17 | 0.3 | 4.8 | 7.0 | 2.5 (10/4) | 0.181 | 0.746 | 355 (100%) | 0 (0%) | – |
| EN-04 | 249 | 3.9 | 124 | 1.9 | 49.8 | 22.3 | 2.7 (82/30) | 0 | 0 | 0 (0%) | 249 (100%) | Yes |
| EN-05 | 286 | 4.5 | 28 | 0.4 | 9.8 | 8.2 | 1.3 (14/11) | 0.689 | 1 | 231 (81%) | 55 (19%) | – |
| EN-06 | 977 | 15.3 | 201 | 3.1 | 20.6 | 35.0 | 2.6 (140/53) | 0 | 0 | 623 (64%) | 354 (36%) | Yes |
| EN-07 | 443 | 6.9 | 76 | 1.2 | 17.2 | 23.7 | 1.8 (46/26) | 0.025 | 0.231 | 325 (73%) | 118 (27%) | Yes |
| EN-08 | 159 | 2.5 | 13 | 0.2 | 8.2 | 0.0 | 1.8 (7/4) | 0.546 | 1 | 159 (100%) | 0 (0%) | – |
| Ctrl-01 | 199 | 3.1 | 15 | 0.2 | 7.5 | 0.0 | 0.6 (5/8) | 0.579 | 1 | 185 (93%) | 14 (7%) | – |
| Ctrl-02 | 388 | 6.1 | 25 | 0.4 | 6.4 | 7.5 | 0.9 (12/13) | 1 | 1 | 376 (97%) | 12 (3%) | – |
A > T: A:T > T:A transversion; SB A > T: strand bias expressed as the ratio of A:T > T:A transversions on the nontranscribed versus transcribed strand (the number of respective transversions is shown in brackets). % CAG context: percentage of A:T > T:A transversions in the most frequent context reported for the AA signature. SB p value and false discovery rate (FDR) q value = measures of significance of the strand bias, see Materials and Methods. Contribution to Sig (Sig = non-negative matrix factorization-determined mutational signature) is shown as the number of SBS and the corresponding percentage (in parentheses) of the total SBS number per sample. AA signature—sample positivity for AA signature considering the simultaneous occurrence of ≥50 SBS and ≥15% A > T, ≥20% CAG context and its significance (SB p and/or q value) and mutation load contribution to Sig 22 (AA).
Lower percentage of A > T and CAG context but supported by NMF.
Abbreviation: SBS: single base substitutions.