A polygenic risk score for breast cancer in U.S. Latinas and Latin-American women

Published on Apr 12, 2019in bioRxiv
· DOI :10.1101/598730
Yiwey Shieh8
Estimated H-index: 8
(University of California, Berkeley),
Laura Fejerman17
Estimated H-index: 17
(University of California, Berkeley)
+ 20 AuthorsSusan L. Neuhausen66
Estimated H-index: 66
(Beckman Research Institute)
Background: Over 180 single nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility have been identified; these SNPs can be combined into polygenic risk scores (PRS) to predict breast cancer risk. Since most SNPs were identified in predominantly European populations, little is known about the performance of PRS in non-Europeans. We tested the performance of a 180-SNP PRS in Latinas, a large ethnic group with variable levels of Indigenous American, European, and African ancestry. Methods: We conducted a pooled case-control analysis of U.S. Latinas and Latin-American women (4,658 cases, 7,629 controls). We constructed a 180-SNP PRS consisting of SNPs associated with breast cancer risk (p < 5 x 10-8). We evaluated the association between the PRS and breast cancer risk using multivariable logistic regression and assessed discrimination using area under the receiver operating characteristic curve (AUROC). We also assessed PRS performance across quartiles of Indigenous American genetic ancestry. Results: Of 180 SNPs tested, 140 showed directionally consistent associations compared with European populations, and 43 were nominally significant (p < 0.05). The PRS was associated with breast cancer risk, with an odds ratio (OR) per standard deviation increment of 1.58 (95% CI 1.52-1.64) and AUCROC of 0.63 (95% CI 0.62 to 0.64). The discrimination of the PRS was similar between the top and bottom quartiles of Indigenous American ancestry. Conclusions: The 180-SNP PRS predicts breast cancer risk in Latinas, with similar performance as reported for Europeans. The performance of the PRS did not vary substantially according to Indigenous American ancestry.
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