Normal-appearing mammary tissue from breast cancer patients can harbor significant genetic alterations. We analyzed DNA variants in both normal-looking tissue and tumors from 77 poor-prognosis patients, 49 patients without prognosis bias, and mammary gland samples from 15 non-cancerous individuals. Whole exome sequencing revealed a higher prevalence of pathogenic post-zygotic variants (29%) in poor-prognosis patients, affecting genes like AKT1, PIK3CA, PTEN, TBX3, and TP53, compared to 12.5% in those without prognosis criteria (p=0.0008578). Prevailing PIK3CA variants were recurrent across patients, while TP53 variants were present only in those with adverse prognoses. Duplex sequencing detected low-frequency pathogenic PIK3CA and TP53 variants in distant normal tissues of poor-prognosis patients. Disease recurrence significantly reduced survival rates, with poor prognosis patients experiencing higher mortality within 24 months (p=0.0088), further worsened by the presence of pathogenic post-zygotic variants. These findings highlight the importance of genetic monitoring even in normal-appearing mammary tissue.

J.P.D. is a cofounder and shareholder in Cray Innovation AB. J.M. is a co-founder and shareholder of Genegoggle sp. z o.o. The remaining authors have declared that no competing interests exist.

This work was supported by the Foundation for Polish Science under the International Research Agendas Program financed from the Smart Growth Operational Program 2014-2020 (Grant Agreement No. MAB/2018/6) to A.P. and J.P.D. Parts of the study were supported by The Swedish Cancer Society (No. 20 0889 PjF) and Swedish Medical Research Council (No. 2020-02010) to J.P.D., by The National Science Centre Poland Miniatura 4 (Project No. 2020/04/X/NZ2/02084) to K.C., and by the Austrian Science Fund FWF (P30867000) and the European Regional Development Fund (REGGEN ATCZ207) to I.T-B.

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