Polygenic score distribution differences across European ancestry populations: implications for breast cancer risk prediction

Yiangou, Kristia; Mavaddat, Nasim; Dennis, Joe; Zanti, Maria; Wang, Qin; Bolla, Manjeet K.; Abubakar, Mustapha; Ahearn, Thomas U.; Andrulis, Irene L.; Anton-Culver, Hoda; Antonenkova, Natalia N.; Arndt, Volker; Aronson, Kristan J.; Augustinsson, Annelie; Baten, Adinda; Behrens, Sabine; Bermisheva, Marina; de Gonzalez, Amy Berrington; Białkowska, Katarzyna; Boddicker, Nicholas; Bodelon, Clara; Bogdanova, Natalia V.; Bojesen, Stig E.; Brantley, Kristen D.; Brauch, Hiltrud; Brenner, Hermann; Camp, Nicola J.; Canzian, Federico; Castelao, Jose E.; Cessna, Melissa H.; Chang-Claude, Jenny; Chenevix-Trench, Georgia; Chung, Wendy K.; Colonna, Sarah V.; Couch, Fergus J.; Cox, Angela; Cross, Simon S.; Czene, Kamila; Daly, Mary B.; Devilee, Peter; Dörk, Thilo; Dunning, Alison M.; Eccles, Diana M.; Eliassen, A. Heather; Engel, Christoph; Eriksson, Mikael; Evans, D. Gareth; Fasching, Peter A.; Fletcher, Olivia; Flyger, Henrik; Fritschi, Lin; Gago-Dominguez, Manuela; Gentry-Maharaj, Aleksandra; González-Neira, Anna; Guénel, Pascal; Hahnen, Eric; Haiman, Christopher A.; Hamann, Ute; Hartikainen, Jaana M.; Ho, Vikki; Hodge, James; Hollestelle, Antoinette; Honisch, Ellen; Hooning, Maartje J.; Hoppe, Reiner; Hopper, John L.; Howell, Sacha; Howell, Anthony; Jakovchevska, Simona; Jakubowska, Anna; Jernström, Helena; Johnson, Nichola; Kaaks, Rudolf; Khusnutdinova, Elza K.; Kitahara, Cari M.; Koutros, Stella; Kristensen, Vessela N.; Lacey, James V.; Lambrechts, Diether; Lejbkowicz, Flavio; Lindblom, Annika; Lush, Michael; Mannermaa, Arto; Mavroudis, Dimitrios; Menon, Usha; Murphy, Rachel A.; Nevanlinna, Heli; Obi, Nadia; Offit, Kenneth; Park-Simon, Tjoung-Won; Patel, Alpa V.; Peng, Cheng; Peterlongo, Paolo; Pita, Guillermo; Plaseska-Karanfilska, Dijana; Pylkäs, Katri; Radice, Paolo; Rashid, Muhammad U.; Rennert, Gad; Roberts, Eleanor; Rodriguez, Juan; Romero, Atocha; Rosenberg, Efraim H.; Saloustros, Emmanouil; Sandler, Dale P.; Sawyer, Elinor J.; Schmutzler, Rita K.; Scott, Christopher G.; Shu, Xiao-Ou; Southey, Melissa C.; Stone, Jennifer; Taylor, Jack A.; Teras, Lauren R.; van de Beek, Irma; Willett, Walter; Winqvist, Robert; Zheng, Wei; Vachon, Celine M.; Schmidt, Marjanka K.; Hall, Per; MacInnis, Robert J.; Milne, Roger L.; Pharoah, Paul D. P.; Simard, Jacques; Antoniou, Antonis C.; Easton, Douglas F.; Michailidou, Kyriaki

doi:10.1186/s13058-024-01947-x

Table 1 Mean standardized PRS₃₁₃ by country in controls of the pooled BCAC dataset

From: Polygenic score distribution differences across European ancestry populations: implications for breast cancer risk prediction

Country	Number of controls	Mean PRS₃₁₃^a	Mean PRS adjusted for array and 6 PCs^b	PRS adjusted for 6 PCs, fitted values^c	Empirical Bayes Posterior Mean^d
Australia	4049	− 0.005	0.01	− 0.005	− 0.003
Belarus	342	0.07	0.071	0.016	0.064
Belgium	1823	− 0.006	− 0.007	0.010	− 0.002
Canada	2277	0.018	0.019	0.013	0.02
Denmark	5241	− 0.013	0.012	− 0.031	− 0.012
Finland	2083	0.031	0.008	0.010	0.032
France	1372	0.0003	− 0.008	0.008	0.004
Germany	8563	0.011	0.004	0.013	0.011
Greece	607	0.232	0.043	0.208	0.199
Ireland	719	− 0.118	− 0.015	− 0.112	− 0.092
Israel	724	0.047	0.001	0.062	0.047
Italy	1554	0.115	− 0.007	0.131	0.11
Netherlands	4407	0.021	0.043	− 0.019	0.022
Norway	217	0.077	0.094	− 0.027	0.066
Poland	2554	0.013	0.025	0.010	0.015
Republic of North Macedonia	92	0.25	0.134	0.140	0.129
Russia	120	0.18	0.166	0.044	0.11
Spain	2098	0.057	− 0.006	0.057	0.056
Sweden	16,680	− 0.015	0.005	− 0.017	− 0.014
UK	16,854	− 0.01	0.019	− 0.023	− 0.01
USA	21,696	0.029	0.033	0.013	0.029

This table presents the mean PRS by country when adjusted for array type, 6 PCs and array type, using fitted values adjusted for 6 PCs and array type, and when using an empirical Bayes approach adjusted for array type
^aMean PRS₃₁₃ after adjustment for array type
^bMean PRS after adjustment for 6 PCs. Since PC adjustment explains much of the variation, these values are typically close to 0
^cMean PRS₃₁₃ by country based on averaging the predicted PRS of each individual; estimated using linear predictor of PRS versus 6 PCs and the command predict () in R
^dCountry-specific estimates, means β, using the empirical Bayes approach, adjusted for array type

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ISSN: 1465-542X

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