The spectrum of TP53 mutations in Rwandan patients with gastric cancer

Genes and Environment

Table 4 Frequency of the mutation spectrum of TP53 in Rwandan patients with gastric cancer compared with the previous TP53 mutational studies in non-Rwandan patients with gastric cancer

Mutation	Present study (n = 29)	Previous TP53 mutational studies for gastric cancer patients
	Present study (n = 29)	Natsume et al. [33]^a (n = 272)		TCGA dataset [52]^b (n = 226)		Wang et al. [43]^c (n = 58)
	n (%)	n (%)	p ^d	n (%)	p^d	n (%)	p ^d
Mutation spectrum
A:T > C:G	2 (6.9)	15 (5.5)	0.503	5 (2.2)	0.183	2 (3.4)	0.598
A:T > G:C	1 (3.4)	26 (9.6)	0.238	27 (11.9)	0.796	6 (10.3)	0.725
A:T > T:A	1 (3.4)	10 (3.7)	0.325	7 (3.1)	1	2 (3.4)	1
G:C > A:T at CpG	10 (34.5)	88 (32.4)	0.482	71 (31.4)	0.833	21 (36.2)	1
G:C > A:T at non-CpG	4 (13.8)	55 (20.2)	0.29	41 (18.1)	0.22	8 (13.8)	0.261
G:C > C:G	1 (3.4)	9 (3.3)	0.643	12 (5.3)	1	6 (10.3)	0.416
G:C > T:A	7 (24.1)	22 (8.1)	0.013**	19 (8.4)	0.017**	2 (3.4)	0.006**
deletion	3 (10.3)	34 (12.5)	0.51	35 (15.5)	0.588	8 (13.8)	0.745
deletion-insertion	NA	3 (1.1)	NA	NA	NA	NA	NA
insertion	NA	10 (3.7)	NA	8 (3.5)	NA	3 (5.2)	NA
fusion	NA	NA	NA	1 (0.4)	NA	NA	NA
Mutation type
Missense	19 (65.5)	172 (63.2)	0.808	167 (73.9)	0.397	33 (56.9)	0.4395
Nonsense	5 (17.2)	42 (15.4)	0.8	NA	NA	10 (17.2)	1
Silent	1 (3.4)	10 (3.7)	0.95	NA	NA	NA	NA
Splice-site	1 (3.4)	1 (0.4)	0.052	19 (8.4)	0.42	4 (6.9)	0.515

NA: Not applicable
^aData collected from our previous work [33], the work consisted of 272 TP53 mutations identified in 689 gastric cancer patients from China (n = 133), Eastern Europe (n = 288), and Japan (n = 268)
^bThe Cancer Genome Atlas (TCGA) data on TP53 mutation in stomach adenocarcinoma accessed through cBioPortal for Cancer Genomics [52]. In the database, 213 stomach adenocarcinoma cases with TP53 mutation are registered. The mutation-positive cases consisted of Black or African American (n = 8), Asians (n = 45), Whites (n = 135), and 25 cases without information on race. The total number of TP53 mutations was 226
^cDataset from whole genome sequencing of 100 gastric cancers of patients from Hong Kong, in a study by the University of Hong Kong and Pfizer, accessible in cBioPortal for Cancer Genomics but also published in Nat Genet 2014 [43]. In this study 58 TP53 mutations were seen in 55 patients with TP53 mutation(s)
^dThe Fischer’s exact test between each study and the present study was performed
**indicate the significant difference (less than 0.05) in the p-value of Fischer’s exact test. The statistical significance was observed even after the Benjamin–Hochberg procedure with a maximum FDR of d = 0.05 for multiple comparisons [the adjusted p-values: 0.034 for this study vs. study by Natsume et al. [33], 0.034 for this study vs. TCGA study [52], and 0.033 for this study vs. study by Wang et al. [43]]

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