Critical Analysis of Strand-Biased Somatic Mutation Signatures in TP53 versus Ig Genes, in Genome-Wide Data and the Etiology of Cancer

Table 5

Somatic point mutation patterns in the TP53 coding region in “All Colorectum Cancers,” “All Stomach Cancers,” and “All Skin Cancers.”

(a) All Colorectum Cancers

Original base	Mutant base
	A	T	C	G	Total		Statistics
A (22%)^†	—	2.0	0.8	4.6	7.4	A≫T	1.0x	NS
T (21%)	1.9	—	3.7	2.0	7.7	A>G versus T>C	1.2x	NS
C (29%)	2.1	27.1	—	2.2	31.4	G≫C	1.7x	𝑃<0.001
G (28%)	43.5	7.5	2.6	—	53.6	G>A versus C>T	1.6x	𝑃<0.001
						G>T versus C>A	3.7x	𝑃<0.001
						G>C versus C>G	1.2x	NS

(b) All Stomach Cancers

Original base	Mutant base
	A	T	C	G	Total		Statistics
A (22%)^†	—	2.3	1.9	7.3	11.5	A≫T	1.2x	NS
T (21%)	3.8	—	4.0	2.3	10.0	A>G versus T>C	1.8x	𝑃<0.05
C (29%)	3.6	27.5	—	3.9	35.00	G≫C	1.2x	𝑃<0.05
G (28%)	32.5	7.7	3.3	—	43.4	G>A versus C>T	1.2x	NS
						G>T versus C>A	2.2x	𝑃<0.05
						G>C versus C>G	0.9x	NS

(c) All Skin Cancers

Original base	Mutant base
	A	T	C	G	Total		Statistics
A (22%)^†	—	3.3	1.4	5.2	9.9	A≫T	0.9x	NS
T (21%)	2.4	—	6.2	3.0	11.7	A>G versus T>C	0.8x	NS
C (29%)	3.2	39.8	—	2.8	45.8	C≫G	1.4x	𝑃<0.01
G (28%)	21.2	7.0	4.6	—	32.7	C>T versus G>A	1.9x	𝑃<0.001
						G>T versus C>A	2.2x	𝑃<0.05
						G>C versus C>G	1.6x	NS

Values in (a) represent the percentage of the total of 1553 somatic point mutations scored in category “All Colorectum Cancers” (R15); values in (b) represent the percentage of the total of 844 somatic point mutations scored in category “All Stomach Cancers” (R15); values in (c) represent the % of the total of 789 somatic point mutations scored in category “All Skin 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 328 occur at CpG sites and 93 occur at non-CpG sites. For G-to-A 489 occur CpG and 186 occur at non-CpG sites. In (b) for C-to-T 145 occur at CpG sites and 87 occur at non-CpG sites. For G-to-A 180 occur at CpG sites and 90 occur at non-CpG sites. In (c). for C-to-T 97 occur at CpG and 217 occur at non-CpG sites. For G-to-A 44 occur at CpG and 123 occur at non-CpG sites.