Critical Analysis of Strand-Biased Somatic Mutation Signatures in TP53 versus Ig Genes, in Genome-Wide Data and the Etiology of Cancer
Table 2
Somatic point mutation patterns in the TP53 coding region in “All Breast Cancers,” “All Bladder Cancers,” and “All Lung Cancers.”
(a) All Breast Cancers
Original
Mutant base
base
A
T
C
G
Total
Statistics
A (22%)†
—
2.6
1.9
11.0
15.5
AT
1.3x
T (21%)
3.1
—
4.8
3.9
11.8
A>G versus T>C
2.3x
C (29%)
2.8
20.4
—
3.6
26.8
GC
1.7x
G (28%)
31.0
9.3
5.5
—
45.9
G>A versus C>T
1.5x
G>T versus C>A
3.3x
G>C versus C>G
1.5x
(b) All Bladder Cancers
Original base
Mutant base
A
T
C
G
Total
Statistics
A (22%)†
—
3.1
1.4
9.6
14.1
AT
2.5x
T (21%)
1.8
—
1.7
2.2
5.7
A>G versus T>C
5.8x
C (29%)
2.9
18.9
—
5.2
27.0
GC
2.0x
G (28%)
34.4
9.5
9.3
—
53.3
G>A versus C>T
1.8x
G>T versus C>A
3.3x
G>C versus C>G
1.8x
(c) All Lung Cancers
Original base
Mutant base
A
T
C
G
Total
Statistics
A (22%)†
—
5.4
1.6
10.3
17.3
AT
2.5x
T (21%)
2.1
—
2.3
2.5
6.9
A>G versus T>C
4.5x
C (29%)
3.1
15.5
—
5.0
23.9
GC
2.2x
G (28%)
14.9
30.4
7.0
—
52.2
G>A versus C>T
1.0x
NS
G>T versus C>A
12.1x
G>C versus C>G
1.4x
Values in (a) represent the percentage of the total of 2279 somatic point mutations scored in category “All Breast Cancers” (R15); values in (b) represent the percentage of the total of 1215 somatic point mutations scored in category “All Bladder Cancers” (R15); values in (c) represent the percentage of the total of 2471 somatic point mutations scored in category “All Lung Cancers” (R15). †The percentage base composition in the TP53 coding region for codons 130–300 inclusive—the region which contains the vast majority of mutations spanning the DNA binding region. The Chi-Squared statistics (significance levels) are essentially unaltered if mutation frequencies are corrected for base composition. The breakdown of G-to-A and C-to-T mutations at CpG and non-CpG sites is as follows. In (a) for C-to-T mutations 199 occur at CpG sites and 267 occur at non-CpG sites. For G-to-A 320 occur CpG and 387 occur at non-CpG sites. In (b) for C-to-T 104 occur at CpG sites and 126 occur at non-CpG sites. For G-to-A 153 occur at CpG sites and 265 occur at non-CpG sites. In (c) for C-to-T 209 occur at CpG and 173 occur at non-CpG sites. For G-to-A 214 occur at CpG and 154 occur at non-CpG sites.
