title: A pilot genome-wide association study of breast cancer susceptibility loci in Indonesia.
abstract: Genome-wide association studies (GWASs) of the entire genome provide a systematic approach for revealing novel genetic susceptibility loci for breast cancer. However, genetic association studies have hitherto been primarily conducted in women of European ancestry. Therefofre we here performed a pilot GWAS with a single nucleotide polymorphism (SNP) array 5.0 platform from Affymetrix® that contains 443,813 SNPs to search for new genetic risk factors in 89 breast cancer cases and 46 healthy women of Indonesian ancestry. The case-control association of the GWAS finding set was evaluated using PLINK. The strengths of allelic and genotypic associations were assessed using logistic regression analysis and reported as odds ratios (ORs) and P values; P values less than 1.00x10(-8) and 5.00x10(-5) were required for significant association and suggestive association, respectively. After analyzing 292,887 SNPs, we recognized 11 chromosome loci that possessed suggestive associations with breast cancer risk. Of these, however, there were only four chromosome loci with identified genes: chromosome 2p.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 5q14.1 with 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 suggestive associations with the risk of breast cancer among Indonesian women.
authors.affiliation: Department of Oncology, MRCCC Siloam Hospital Semanggi, Jakarta, Indonesia E-mail : sj.haryono@gmail.com.
authors.forename: Samuel J
authors.initials: SJ
authors.lastname: Haryono
authors.forename: I Gusti Bagus
authors.initials: IG
authors.lastname: Datasena
authors.forename: Wahyu Budi
authors.initials: WB
authors.lastname: Santosa
authors.forename: Raymond
authors.initials: R
authors.lastname: Mulyarahardja
authors.forename: Kartika
authors.initials: K
authors.lastname: Sari
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics*; D001943:Breast Neoplasms / Q000453:epidemiology / Q000235:genetics* / Q000473:pathology; D016022:Case-Control Studies; D002877:Chromosomes, Human / Q000235:genetics*; D005260:Female; D005500:Follow-Up Studies; D056426:Genetic Loci; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D007214:Indonesia / Q000453:epidemiology; D008875:Middle Aged; D009367:Neoplasm Staging; D010865:Pilot Projects; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011379:Prognosis; D012306:Risk
chemical_list: D014408:Biomarkers, Tumor