Background: Although change in the birth cohort effect on cancer mortality rates is known to be highly associated with the decreasing rates of age-standardized cancer mortality rates in Japan, the differences in the trends of cohort effect for representative cancer types among the prefectures remain unknown. This study aimed to investigate the differences in the decreasing rate of cohort effects among the prefectures for representative cancer types using age-period-cohort (APC) analysis. Methods: Data on stomach, colorectal, liver, and lung cancer mortality for each prefecture and the population data from 1999 to 2018 were obtained from the Vital Statistics in Japan. Mortality data for individuals aged 50 to 79 years grouped in 5-year increments were used, and corresponding birth cohorts born 1920–1924 through 1964–1978 were used for analysis. We estimated the effects of age, period, and cohort on each type of mortality rate for each prefecture by sex. Then, we calculated the decreasing rates of cohort effects for each prefecture. We also calculated the mortality rate ratio of each prefecture compared with all of Japan for cohorts using the estimates. Results: As a result of APC analysis, we found that the decreasing rates of period effects were small and that there was a little difference in the decreasing rates among prefectures for all types of cancer among both sexes. On the other hand, there was a large difference in the decreasing rates of cohort effects for stomach and liver cancer mortality rates among prefectures, particularly for men. For men, the decreasing rates of cohort effects in cohorts born between 1920–1924 and 1964–1978 varied among prefectures, ranging from 4.1 to 84.0% for stomach cancer and from 20.2 to 92.4% for liver cancers, respectively. On the other hand, the differences in the decreasing rates of cohort effects among prefectures for colorectal and lung cancer were relatively smaller. Conclusions: The decreasing rates of cohort effects for stomach and liver cancer varied widely among prefectures. It is possible that this will influence cancer mortality rates in each prefecture in the future.
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