Sequencing regions assoc with breast cancer risk in European and African American

Kraft, Peter

Abstract

Genome-wide association studies (GWAS) have identified over 14 independent common marker alleles associated with risk of breast cancer. However, the causal variants responsible for these associations have yet to be identified, and the regions surrounding these marker alleles have not been thoroughly screened for additional common or rare variants that affect cancer risk. Moreover, few of these marker alleles generalize to African American women. To address these knowledge gaps, we propose to sequence regions surrounding validated breast cancer risk markers (including a large region on chromosome 8q24 that contains multiple independent alleles associated with several other cancers) in 1,430 breast cancer cases and 2,289 breast cancer controls of European ancestry from the Nurses Health Study and Nurses Health Study 2 and approximately 500 African American cases and 1,000 African American controls from the Multi-ethnic Cohort. All subjects have GWAS data available, and all have detailed prospective longitudinal data on breast cancer risk factors. Cases have clinically-validated information on tumor subtypes. The resulting data will help identify sets of potential common causal alleles in each population;assess whether these regions are enriched for rare variants that are disproportionately found among cases (or controls);and assess whether this enrichment varies by ethnicity, breast cancer subtype, family history of breast cancer or known risk factors for breast cancer. The data will also help empirically evaluate the efficiency of different sequencing designs, including: sampling a subset of cases based on tumor characteristics;sampling subsets of cases and controls at high and respectively low risk as determined by standard risk factors, including age and menopausal status;and sampling subsets at high and low risk as determined by the collection of known risk SNPs. Together, this multiethnic sample contains a wide spectrum of genetic diversity and will provide excellent power for discovery of rare variants in these regions that may be missed by the 1000 Genomes Project. We will be able to replicate findings from this sequencing effort and investigate their functional significance through other current and planned collaborative studies of breast cancer, including the Breast and Prostate Cancer Cohort Consortium and the African American Breast Cancer GWAS Consortium.

Public Health Relevance

Several genetic regions have recently been found to be associated with risk of breast cancer in women of European ancestry, but the precise causal variant in these regions remains unknown. We propose to comprehensively measure the genetic sequence in those regions in over 5,000 women of European and African American ancestry. This will help will help generalize these associations to African American women, and identify variants for future functional studies, helping us better understand the biology of breast cancer.