Whole exome sequencing and replication for breast cancer among Hispanic/Latino women identifies FANCM as a susceptibility gene for estrogen-receptor-negative breast cancer

INTRODUCTION: Breast cancer (BC) is one of the most common cancers globally. Genetic testing can facilitate screening and risk-reducing recommendations, and inform use of targeted treatments. However, genes included in testing panels are from studies of European-ancestry participants. We sequenced Hispanic/Latina (H/L) women to identify BC susceptibility genes. METHODS: We conducted a pooled BC case-control analysis in H/L women from the San Francisco Bay area, Los Angeles County, and Mexico (4,178 cases and 4,344 controls). Whole exome sequencing was conducted on 1,043 cases and 1,188 controls and a targeted 857-gene panel on the remaining samples. Using ancestry-adjusted SKAT-O analyses, we tested the association of loss of function (LoF) variants with overall, estrogen receptor (ER)-positive, and ER-negative BC risk. We calculated odds ratios (OR) for BC using ancestry-adjusted logistic regression models. We also tested the association of single variants with BC risk. RESULTS: We saw a strong association of LoF variants in FANCM with ER-negative BC (p=4.1×10(−7), OR [CI]: 6.7 [2.9–15.6]) and a nominal association with overall BC risk. Among known susceptibility genes, BRCA1 (p=2.3×10(−10), OR [CI]: 24.9 [6.1–102.5]), BRCA2 (p=8.4×10(−10), OR [CI]: 7.0 [3.5–14.0]), and PALB2 (p=1.8×10(−8), OR [CI]: 6.5 [3.2–13.1]) were strongly associated with BC. There were nominally significant associations with CHEK2, RAD51D, and TP53. CONCLUSION: In H/L women, LoF variants in FANCM were strongly associated with ER-negative breast cancer risk. It previously was proposed as a possible susceptibility gene for ER-negative BC, but is not routinely tested in clinical practice. Our results demonstrate that FANCM should be added to BC gene panels.