Development and testing of a polygenic risk score for breast cancer aggressiveness

Author:

Shieh YiweyORCID,Roger JacquelynORCID,Yau ChristinaORCID,Wolf Denise M.,Hirst Gillian L.ORCID,Swigart Lamorna BrownORCID,Huntsman Scott,Hu DongleiORCID,Nierenberg Jovia L.,Middha PoojaORCID,Heise Rachel S.ORCID,Shi Yushu,Kachuri Linda,Zhu QianqianORCID,Yao SongORCID,Ambrosone Christine B.ORCID,Kwan Marilyn L.ORCID,Caan Bette J.,Witte John S.ORCID,Kushi Lawrence H.ORCID,‘T Veer Laura vanORCID,Esserman Laura J.ORCID,Ziv EladORCID

Abstract

AbstractAggressive breast cancers portend a poor prognosis, but current polygenic risk scores (PRSs) for breast cancer do not reliably predict aggressive cancers. Aggressiveness can be effectively recapitulated using tumor gene expression profiling. Thus, we sought to develop a PRS for the risk of recurrence score weighted on proliferation (ROR-P), an established prognostic signature. Using 2363 breast cancers with tumor gene expression data and single nucleotide polymorphism (SNP) genotypes, we examined the associations between ROR-P and known breast cancer susceptibility SNPs using linear regression models. We constructed PRSs based on varying p-value thresholds and selected the optimal PRS based on model r2 in 5-fold cross-validation. We then used Cox proportional hazards regression to test the ROR-P PRS’s association with breast cancer-specific survival in two independent cohorts totaling 10,196 breast cancers and 785 events. In meta-analysis of these cohorts, higher ROR-P PRS was associated with worse survival, HR per SD = 1.13 (95% CI 1.06–1.21, p = 4.0 × 10–4). The ROR-P PRS had a similar magnitude of effect on survival as a comparator PRS for estrogen receptor (ER)-negative versus positive cancer risk (PRSER-/ER+). Furthermore, its effect was minimally attenuated when adjusted for PRSER-/ER+, suggesting that the ROR-P PRS provides additional prognostic information beyond ER status. In summary, we used integrated analysis of germline SNP and tumor gene expression data to construct a PRS associated with aggressive tumor biology and worse survival. These findings could potentially enhance risk stratification for breast cancer screening and prevention.

Funder

U.S. Department of Health & Human Services | NIH | National Cancer Institute

Publisher

Springer Science and Business Media LLC

Subject

Cancer Research,Oncology

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