Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus

BACKGROUND: Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk. METHOD: We performed a fine-scale mapping study of a 700 kb region including 441 genotyped and more than 1300 imputed genetic variants in 48,155 cases and 43,612 controls of European descent, 6269 cases and 6624 controls of East Asian descent and 1116 cases and 932 controls of African descent in the Breast Cancer Association Consortium (BCAC; http://bcac.ccge.medschl.cam.ac.uk/ ), and in 15,252 BRCA1 mutation carriers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Stepwise regression analyses were performed to identify independent association signals. Data from the Encyclopedia of DNA Elements project (ENCODE) and the Cancer Genome Atlas (TCGA) were used for functional annotation. RESULTS: Analysis of data from European descendants found evidence for four independent association signals at 12p11, represented by rs7297051 (odds ratio (OR) = 1.09, 95 % confidence interval (CI) = 1.06-1.12; P = 3 × 10(-9)), rs805510 (OR = 1.08, 95 % CI = 1.04-1.12, P = 2 × 10(-5)), and rs1871152 (OR = 1.04, 95 % CI = 1.02-1.06; P = 2 × 10(-4)) identified in the general populations, and rs113824616 (P = 7 × 10(-5)) identified in the meta-analysis of BCAC ER-negative cases and BRCA1 mutation carriers. SNPs rs7297051, rs805510 and rs113824616 were also associated with breast cancer risk at P < 0.05 in East Asians, but none of the associations were statistically significant in African descendants. Multiple candidate functional variants are located in putative enhancer sequences. Chromatin interaction data suggested that PTHLH was the likely target gene of these enhancers. Of the six variants with the strongest evidence of potential functionality, rs11049453 was statistically significantly associated with the expression of PTHLH and its nearby gene CCDC91 at P < 0.05. CONCLUSION: This study identified four independent association signals at 12p11 and revealed potentially functional variants, providing additional insights into the underlying biological mechanism(s) for the association observed between variants at 12p11 and breast cancer risk

Risk Factors for Maternal Vitamin D Deficiency within the United Arab Emirates

Introduction: Vitamin D deficiency during pregnancy is a public health problem and it has been associated with negative pregnancy outcomes for both mothers and infants. Aim: To estimate the prevalence of vitamin D deficiency in pregnant women in the United Arab Emirates (UAE) and to identify the contribution of risk factors to the 25(OH)D levels. Methods: It is a cross-sectional study in which vitamin D levels of 1088 adult pregnant women were assessed. Information on vitamin D intake was available in a sub-sample of 266 women. Results: The mean serum 25(OH)D was 26.2 nmol/L (95% CI 25.2-27.1 range 5-129.1 nmol/L) with 69% of women being vitamin D deficient (<30 nmol/L). In the bivariate analysis, showed that no predictors could have been indicated as no values exceeded significance (p<0.2). Stepwise multiple linear regression analysis could not be applied to identify predictors of vitamin D levels as no values exceeded p=0.2. Conclusion: Due to the high prevalence of vitamin deficiency in UAE, there is an urge for interventions focusing on supplementation, fortification and diet diversity for preventing health consequences during a critical period of development.