Extended Data Fig. 4: Signatures of mutations in PNE, dysplasia and cancer samples. | Nature

Extended Data Fig. 4: Signatures of mutations in PNE, dysplasia and cancer samples.

From: Age-related remodelling of oesophageal epithelia by mutated cancer drivers

Extended Data Fig. 4

a, Number (middle) and relative frequency (bottom) of mutations allocated to signatures A–D in the individual samples. Information about pathology, lifestyle ESCC risks, cohort and age of the subject is indicated (top). b, Number of mutations allocated to indicated mutational signatures is plotted against the age of the subject for PNE samples from low-risk (blue) and high-risk (red) individuals. Numbers of samples from low-risk and high-risk individuals are 34 and 19 (0.2-mm2 sampling), 19 and 12 (0.8-mm2 sampling), and 40 and 33 (4-mm2 sampling), respectively. Regression lines for samples from low-risk individuals are indicated with R2. P values for significance between samples from high-risk and low-risk individuals are also provided (one-sided Mann–Whitney U-test). c, Mean (± 95% confidence interval) of standardized residuals of the number of mutations allocated to each signature in samples from high-risk individuals against the linear regression model in samples from low-risk individuals is plotted for 0.2-mm2, 0.8-mm2 and 4-mm2 samples and for combined samples in a random-effects model. P value in the random-effects model is indicated, together with the weight from each sample size during the model fitting (two-sided Wald test) (Methods). d, Mean (±s.d.) number of mutations allocated to signature 16 in oesophagus (ESCC) (n = 90) (left), hepatic (LIHC) (n = 361) (middle) and stomach (STAD) (n = 239) (right) cancers from TCGA, are plotted according to the status of the ALDH2 risk allele. P values for significance between samples from risk-positive and risk-negative individuals are also provided (two-sided Mann–Whitney U-test). e, Frequency of mutations allocated to signature C in Japanese ESCC samples is plotted according to the status of alcohol drinking and smoking. According the history of heavy drinking and smoking, the subjects were divided into four groups; drinking- and smoking-negative (n = 18); drinking-negative and smoking-positive (n = 3); drinking-positive and smoking-negative (n = 40); and drinking- and smoking-positive (n = 96), as indicated in the panel. Box plots represent the median, first quartile and third quartile, with whiskers extending to the furthest value within 1.5× interquartile range; points show outliers.

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