A Pilot Genome-wide Association Study of Breast Cancer Susceptibility Loci in Indonesia

Genome-wide association studies (GWASs) of the entire genome provide a systematic approach for revealingnovel genetic susceptibility loci for breast cancer. However, genetic association studies have hitherto been primarilyconducted in women of European ancestry. Therefofre we here performed a pilot GWAS with a single nucleotidepolymorphism (SNP) array 5.0 platform from Affymetrix® that contains 443,813 SNPs to search for new geneticrisk factors in 89 breast cancer cases and 46 healthy women of Indonesian ancestry. The case-control associationof the GWAS finding set was evaluated using PLINK. The strengths of allelic and genotypic associations wereassessed using logistic regression analysis and reported as odds ratios (ORs) and P values; P values less than1.00x10-8 and 5.00x10-5 were required for significant association and suggestive association, respectively. Afteranalyzing 292,887 SNPs, we recognized 11 chromosome loci that possessed suggestive associations with breastcancer risk. Of these, however, there were only four chromosome loci with identified genes: chromosome2p.12 with the CTNNA2 gene [Odds ratio (OR)=1.20, 95% confidence interval (CI)=1.13-1.33, P=1.08x10-7];chromosome 18p11.2 with the SOGA2 gene (OR=1.32, 95%CI=1.17–1.44, P=6.88x10-6); chromosome 5q14.1with the SSBP2 gene (OR=1.22, 95%CI=1.11–1.34, P=4.00x10-5); and chromosome 9q31.1 with the TEX10 gene(OR=1.24, 95%CI=1.12–1.35, P=4.68x10-5). This study identified 11 chromosome loci which exhibited suggestiveassociations with the risk of breast cancer among Indonesian women.