Whole exome sequencing identifies FANCM as a susceptibility gene for estrogen-receptor-negative breast cancer in Hispanic/Latina women

Jovia L. Nierenberg, Aaron W. Adamson, Donglei Hu, Scott Huntsman, Carmina Patrick, Min Li, Linda Steele, Shu Tao, Yuan Chun Ding, Barry Tong, Yiwey Shieh, Laura Fejerman, Stephen B. Gruber, Christopher A. Haiman, Esther M. John, Lawrence H. Kushi, Gabriela Torres-Mejía, Charité Ricker, Jeffrey N. Weitzel, Elad Ziv () and Susan L. Neuhausen
Additional contact information
Jovia L. Nierenberg: San Francisco
Aaron W. Adamson: Beckman Research Institute of City of Hope
Donglei Hu: San Francisco
Scott Huntsman: San Francisco
Carmina Patrick: Beckman Research Institute of City of Hope
Min Li: San Francisco
Linda Steele: Beckman Research Institute of City of Hope
Shu Tao: Beckman Research Institute of City of Hope
Yuan Chun Ding: Beckman Research Institute of City of Hope
Barry Tong: San Francisco
Yiwey Shieh: Weill Cornell Medicine
Laura Fejerman: Davis
Stephen B. Gruber: City of Hope National Medical Center
Christopher A. Haiman: University of Southern California
Esther M. John: Stanford University School of Medicine
Lawrence H. Kushi: Kaiser Permanente Northern California
Gabriela Torres-Mejía: Instituto Nacional de Salud Pública
Charité Ricker: University of Southern California
Jeffrey N. Weitzel: The University of Kansas Comprehensive Cancer Center
Elad Ziv: San Francisco
Susan L. Neuhausen: Beckman Research Institute of City of Hope

Nature Communications, 2025, vol. 16, issue 1, 1-9

Abstract: Abstract Breast cancer (BC) is one of the most common cancers globally. Genetic testing facilitates screening and informs targeted risk-reduction and treatments. However, genes included in testing panels are from European-ancestry studies. We conducted a pooled case-control analysis in self-identified Hispanic/Latina women (4178 cases and 4344 controls), using whole exome sequencing and a targeted panel. We tested the association of loss of function (LoF) variants with overall, estrogen receptor (ER)-positive, and ER-negative BC risk. Using logistic regression, we found a strong association of LoF variants in FANCM with ER-negative BC (p = 4.1 × 10−7), odds ratio [confidence interval]: 6.7 [2.9–15.6]). Among known susceptibility genes, BRCA1, BRCA2, and PALB2 strongly associated with BC. FANCM was previously proposed as a possible susceptibility gene for ER-negative BC, but is not routinely tested clinically. Our results demonstrate that FANCM should be added to BC gene panels.

Date: 2025
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DOI: 10.1038/s41467-025-60564-0

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