Ultra-deep duplex sequencing reveals unique features of somatic evolution in the normal tissues of a family with Li-Fraumeni syndrome

ABSTRACT Li-Fraumeni Syndrome (LFS) is caused by germline pathogenic variants in TP53 which predispose carriers to early onset cancer across multiple tissues. While genomically profiling those cancers has revealed factors contributing to their formation, little is understood about how LFS impacts clonal evolution in healthy tissues preceding cancer. Here, we use ultra-deep duplex sequencing (mean ∼15,000× depth) to investigate somatic mutation and selection in a family carrying the germline TP53 p.R181H pathogenic variant and a cohort of non-carrier controls. In blood samples, the germline variant was associated with more mutations in a panel designed to capture genomewide mutagenesis, and with reduced positive selection on somatic TP53 mutations, despite confounding by chemotherapy treatment in one individual. DNMT3A and TET2 mutations were positively selected and GATA2 mutations were negatively selected across the cohort, independent of the p.R181H status. Extensive multi-tissue sampling of 22 non-cancerous and 6 cancerous samples was also performed at autopsy in one individual with LFS who succumbed to esophageal cancer. Cross-tissue analysis revealed excess mutations in sun-exposed skin, esophagus and chronically-inflamed stomach tissue, and highly parallel emergence of mutations in the p.R248 hotspot of TP53 across most (18/28) tissue samples. Most somatic TP53 mutations in LFS that could be assessed for phase arose on the chromosomal copy lacking the p.R181H variant. Our study reveals how the germline p.R181H variant reshapes baseline somatic mutation and selection in normal tissues and highlights the importance of understanding early somatic evolution in LFS prior to cancer development and treatment. Competing Interest Statement THS, ZKN, JEH, CCV, EKS, and JJS are equity holders in TwinStrand Biosciences Inc. JEH, CCV, and JJS are named inventors on one or more patents owned by TwinStrand Biosciences Inc. EKS, JJS, and RAR are named inventors on one or more patents owned by the University of Washington and licensed to TwinStrand Biosciences Inc. and for which receive royalties. THS, ZKN, JEH, CCV, EKS, and JJS are previous employees of TwinStrand Biosciences Inc. RAR was a consultant and equity holder at TwinStrand Biosciences Inc. No disclosures were reported by the other authors. Footnotes ↵12 These authors jointly supervised this work.