Genome-wide association study identifies common variants associated with breast cancer in South African Black women

Mahtaab Hayat (), Wenlong C. Chen, Chantal Babb de Villiers, Sang Hyuck Lee, Charles Curtis, Rob Newton, Tim Waterboer, Freddy Sitas, Debbie Bradshaw, Mazvita Muchengeti, Elvira Singh, Cathryn M. Lewis, Michele Ramsay, Christopher G. Mathew and Jean-Tristan Brandenburg ()
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Mahtaab Hayat: University of the Witwatersrand
Wenlong C. Chen: University of the Witwatersrand
Chantal Babb de Villiers: University of the Witwatersrand
Sang Hyuck Lee: King’s College London
Charles Curtis: King’s College London
Rob Newton: MRC/UVRI and LSHTM Uganda Research Unit
Tim Waterboer: German Cancer Research Center (DKFZ)
Freddy Sitas: South African Medical Research Council
Debbie Bradshaw: South African Medical Research Council
Mazvita Muchengeti: National Health Laboratory Service
Elvira Singh: National Health Laboratory Service
Cathryn M. Lewis: King’s College London
Michele Ramsay: University of the Witwatersrand
Christopher G. Mathew: University of the Witwatersrand
Jean-Tristan Brandenburg: University of the Witwatersrand

Nature Communications, 2025, vol. 16, issue 1, 1-11

Abstract: Abstract Genome-wide association studies (GWAS) have characterized the contribution of common variants to breast cancer (BC) risk in populations of European ancestry, however GWAS have not been reported in resident African populations. This GWAS included 2485 resident African BC cases and 1101 population matched controls. Two risk loci were identified, located between UNC13C and RAB27A on chromosome 15 (rs7181788, p = 1.01 × 10−08) and in USP22 on chromosome 17 (rs899342, p = 4.62 × 10−08). Several genome-wide significant signals were also detected in hormone receptor subtype analysis. The novel loci did not replicate in BC GWAS data from populations of West Africa ancestry suggesting genetic heterogeneity in different African populations, but further validation of these findings is needed. A European ancestry derived polygenic risk model for BC explained only 0.79% of variance in our data. Larger studies in pan-African populations are needed to further define the genetic contribution to BC risk.

Date: 2025
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DOI: 10.1038/s41467-025-58789-0

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