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To compare the prevalences of refractive errors in Malay, Chinese and Indian children in Malaysia and Singapore.Children aged 7–9 years from three schools in the Singapore Cohort study of the Risk factors for Myopia (n = 1962) and similarly aged children from a random cluster sample in the metropolitan Kuala Lumpur area in the Malaysia Refractive Error Study in Children (n = 1752) were compared. Cycloplegic autorefraction was conducted in both countries.The prevalence of myopia (spherical equivalent of at least −0.5 diopters (D) in either eye) was higher in Singapore Malays (22.1%) than in Malays in Malaysia (9.2%; 95% confidence interval (CI) 11.2 to 14.7; p<0.001). Similarly, Singapore Chinese (40.1%) had higher prevalences than Malaysian Chinese (30.9%; 95% CI 1.5 to 16.9). Singapore Indians had a higher prevalence (34.1%) than Malaysian Indians (12.5%; 95% CI 17.4 to 25.9). The multivariate odds ratio of astigmatism (cylinder at least 0.75 D in either eye) in Singapore Malays compared with Malaysian Malays was 3.47 (95% CI 2.79 to 4.32). Ethnicity-specific hyperopia rates did not differ in Singapore and Malaysia.The ethnicity-specific prevalences of myopia in Singapore Malays, Chinese and Indians are higher than those in Malaysian Malays, Chinese and Indians. As Malays, Chinese and Indians in Malaysia have genetic make-up similar to that of Malays, Chinese and Indians in Singapore, environmental factors may contribute to the higher myopia rates.