RT Journal Article
SR Electronic
T1 Identification of Novel Common Breast Cancer Risk Variants in Latinas at the 6q25 Locus
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 343806
DO 10.1101/343806
A1 Joshua Hoffman
A1 Laura Fejerman
A1 Donglei Hu
A1 Scott Huntsman
A1 Min Li
A1 Esther John
A1 Gabriela Torres Mejia
A1 Larry Kushi
A1 Yuan Chun Ding
A1 Jeffrey Weitzel
A1 Susan L. Neuhausen
A1 Paul Lott
A1 COLUMBUS Consortium
A1 Magdalena Echeverry
A1 Luis Carvajal Carmona
A1 Esteban Burchard
A1 Celeste Eng
A1 Wei Zheng
A1 Jirong Long
A1 Olufunmilayo Olopade
A1 Dezheng Huo
A1 Christopher Haiman
A1 Elad Ziv
YR 2018
UL http://biorxiv.org/content/early/2018/06/11/343806.abstract
AB Background: Breast cancer is a partially heritable trait and over 180 common genetic variants have been associated with breast cancer in genome wide association studies (GWAS). We have previously performed breast cancer GWAS in Latinas and identified a strongly protective single nucleotide polymorphism (SNP) at 6q25 with the protective minor allele originating from Indigenous American ancestry. Here we report on additional GWAS and replication in Latinas.Methods: We performed GWAS in 2385 cases and 7342 controls who were either U.S. Latinas or Mexican women. We replicated 2412 cases and 1620 controls of U.S Latina, Mexican, and Colombian women. In addition, we replicated the top novel variants in study of African American and African women and in one study of Chinese women. In each dataset we used logistic regression models to test the association between SNPs and breast cancer risk and corrected for genetic ancestry using either principal components or genetic ancestry inferred from ancestry informative markers using a model based approach.Results: We identified 3 SNPs (p=1.9×10-8 - 2.8×10-8) at 6q25 locus not in linkage disequilibrium (LD) with variants previously reported at this locus. These SNPs were in high LD with each other, with the top SNP, rs3778609, associated with breast cancer with an odds ratio (OR) and 95% confidence interval (95% CI) of 0.75 (0.68-0.83). In a replication in women of Latin American origin, we also observed a consistent effect (OR: 0.88; 95% CI: 0.78-0.99; p=0.037). Since the minor allele was common in East Asians and African American but not European ancestry populations, we replicated in a meta-analysis of those populations and also observed a consistent effect (OR 0.94; 95% CI: 0.91 – 0.97; p=0.013).Conclusion: The effect size of this variant is relatively large compared to other common variants associated with breast cancer and adds to evidence about the importance of the 6q25 locus for breast cancer susceptibility. Our finding also highlights the utility of performing additional searches for genetic variants for breast cancer in non-European populations.GWASGenome wide association studySNPSingle nucleotide polymorphismORodds ratioCIconfidence intervalPCAPrincipal components analysisPCPrincipal componentEREstrogen receptor