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Prospective Evaluation of a Breast Cancer Risk Model Integrating Classical Risk Factors and Polygenic Risk in 15 Cohorts from Six Countries

By Amber N. Wilcox, Parichoy Pal Choudhury, Chi Gao, Anika Hüsing, Mikael Eriksson, Min Shi, Christopher Scott, Brian D. Carter, Kara Martin, Elaine Harkness, Mark N. Brook, Thomas U. Ahearn, Nasim Mavaddat, Antonis C. Antoniou, Jenny Chang-Claude, Jacques Simard, Michael E. Jones, Nick Orr, Minouk J. Schoemaker, Anthony J. Swerdlow, Sarah Sampson, William G. Newman, Elke M van Veen, D. Gareth R. Evans, Robert J. MacInnis, Graham G Giles, Melissa Southey, Roger L. Milne, Susan M. Gapstur, Mia M. Gaudet, Stacey J Winham, Kathy Brandt, Aaron Norman, Celine M. Vachon, Dale P Sandler, Clarice R. Weinberg, Kamila Czene, Marike Gabrielson, Per Hall, Carla H van Gils, Kay-Tee Khaw, Myrto Barrdahl, Rudolf Kaaks, Paul M Ridker, Julie E Buring, Dan I Chasman, Douglas F. Easton, Marjanka K. Schmidt, Peter Kraft, Montserrat Garcia-Closas, Nilanjan Chatterjee

Posted 05 Nov 2019
medRxiv DOI: 10.1101/19011171

PURPOSERisk-stratified breast cancer prevention requires accurate identification of women at sufficiently different levels of risk. We conducted a comprehensive evaluation of a model integrating classical risk factors and a recently developed 313-variant polygenic risk score (PRS) to predict breast cancer risk. METHODSFifteen prospective cohorts from six countries with 237,632 women (7,529 incident breast cancer patients) of European ancestry aged 19-75 years at baseline were included. Calibration of five-year risk was assessed by comparing predicted and observed proportions of cases overall and within risk categories. Risk stratification for women of European ancestry aged 50-70 years in those countries was evaluated by the proportion of women and future breast cancer cases crossing clinically-relevant risk thresholds. RESULTSThe model integrating classical risk factors and PRS accurately predicted five-year risk. For women younger than 50 years, median (range) expected-to-observed ratio across the cohorts was 0.94 (0.72 to 1.01) overall and 0.9 (0.7 to 1.4) at the highest risk decile. For women 50 years or older, these ratios were 1.04 (0.73 to 1.31) and 1.2 (0.7 to 1.6), respectively. The proportion of women in the general population identified above the 3% five-year risk threshold (used for recommending risk-reducing medications in the US) ranged from 7.0% in Germany ([~]841,000 of 12 million) to 17.7% in the US ([~]5.3 of 30 million). At this threshold, 14.7% of US women were re-classified by the addition of PRS to classical risk factors, identifying 12.2% additional future breast cancer cases. CONCLUSIONEvaluation across multiple prospective cohorts demonstrates that integrating a 313-SNP PRS into a risk model substantially improves its ability to stratify women of European ancestry for applying current breast cancer prevention guidelines.

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