Abstract
Pathogenic coding variants in BRCA1, BRCA2 and PALB2 confer hereditary breast/ovarian cancer risk, yet these regions comprise less than 10% of the genomic footprint of these genes, leaving most sequence unexplored. We investigated the contribution of non-coding variation to hereditary breast cancer by analyzing intronic variants and 5′ upstream regions of BRCA1, BRCA2 and PALB2 in the BEACCON case–control study of over 11,000 participants. Full-gene sequencing showed that 46.3% of cases carried at least one rare non-coding variant. This was associated with a modest increase in breast cancer risk (OR = 1.2, p < 0.0001), most likely reflecting the presence of a small proportion of pathogenic variants within a larger background of predominantly neutral variation. Stronger enrichment was observed for triple-negative disease, particularly for BRCA1 (OR = 1.5, p = 0.0001). Tumor sequencing of 42 high-priority variants identified 11 (26.2%) with wild-type allele loss and high homologous recombination deficiency. Functional CRISPR/Cas9 knock-in assays in MCF10A cells confirmed that two deep intronic variants created aberrant splice sites, disrupted splicing and impacted transcript expression.
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Data availability
The sequencing data generated in this study are not publicly available due to ethical and privacy restrictions but are available from the corresponding author upon reasonable request and with appropriate ethical approval.
Code availability
Python script used for data analysis available at https://github.com/Qihong0925/rare-non-coding-variants-in-BRCA1-BRCA2-and-PALB2-.git. The Seqliner code is available separately from the R script at http://bioinformatics.petermac.org/seqliner/. All other publicly available code used during whole genome sequence data processing and variant calling are available via the links mentioned within the methods.
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Acknowledgements
We thank all participants of the ViP and Lifepool studies for generously donating their DNA samples and clinical information. The work of D.C. was supported in part by funding from the Helen Lyons Foundation. This work was supported by the National Breast Cancer Foundation (IIRS-22-027; I.G.C. and P.A.J.).
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Q.Z. was responsible for formal data analysis, investigation, validation, and drafting of the original manuscript, and contributed to data curation, methodology, and visualization. In addition, Q.Z. undertook more than half of the tumor sample DNA collection and sequencing data processing, and was responsible for the design and construction of the mutant cell lines. M.Z. and N.L. contributed to primary data clean. E.M. was responsible for the collection of DNA from a subset of tumor samples. S.M. and L.D. coordinated patient contact for the collection of blood samples and performed subsequent sample processing. D.C. contributed to the review of data analysis results. D.C., A.B.S., and R.J.S. contributed to the study design. I.G.C. and P.A.J. were jointly responsible for project conceptualization, funding acquisition, supervision and methodology, with I.G.C. providing the resources for this work. D.C., A.B.S., I.G.C. and P.A.J. reviewed and edited the final manuscript.
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Zhao, Q., Li, N., Marinovic, E. et al. Investigating the contribution of rare non-coding variants in BRCA1, BRCA2 and PALB2 to hereditary breast cancer. npj Breast Cancer (2026). https://doi.org/10.1038/s41523-026-00942-z
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DOI: https://doi.org/10.1038/s41523-026-00942-z
