Integrated analysis of cell-free DNA for the early detection of cancer in people with Li-Fraumeni Syndrome

Despite advances in cancer therapeutics, early detection is often the best prognostic indicator for survival ( [1][1] ). People with Li-Fraumeni syndrome harbor a germline pathogenic variant in the tumor suppressor gene TP53 ( [2][2] ) and face a near 100% lifetime risk of developing a wide spectrum of, often multiple, cancers ( [3][3] ). TP53 mutation carriers routinely undergo intensive surveillance protocols which, although associated with significantly improved survival, are burdensome to both the patient and the health care system ( [4][4] ). Liquid biopsy, the analysis of cell-free DNA fragments in bodily fluids, has become an attractive tool for a range of clinical applications, including early cancer detection, because of its ability to provide real-time holistic insight into the cellular milieu ( [5][5] ). Here, we assess the efficacy of a multi-modal liquid biopsy assay that integrates a targeted gene panel, shallow whole genome, and cell-free methylated DNA immunoprecipitation sequencing for the early detection of cancer in a cohort of Li-Fraumeni syndrome patients: 196 blood samples from 89 patients, of which 26 were pediatric and 63 were adults. Our integrated analysis was able to detect a cancer-associated signal in 79.4% of samples from patients with active cancer, a 37.5% – 58.8% improvement over each individual analysis. Through analysis of patient plasma at cancer negative timepoints, we were able to detect cancer-associated signals up to 16 months prior to occurrence of cancer as detected by conventional clinical modalities in 17.6% of TP53 mutation carriers. This study provides a framework for the integration of liquid biopsy into current surveillance methods for patients with Li-Fraumeni syndrome. ### Competing Interest Statement The authors declare the following financial or non-financial competing interest: TJP reports personal fees from AstraZeneca, Canadian Pension Plan Investment Board, Chrysalis Biomedical Advisors, Illumina, Merck, and PACT Pharma and grants from Roche/Genentech outside the submitted work. ### Funding Statement This study was funded by The Terry Fox Research Institute (grant number #1081) and Canadian Institutes for Health Research. This study was a collaboration with the CHARM consortium and is performed under the auspice of the LIBERATE study. Additional funding support was made possible by the Princess Margaret Cancer Foundation and the Ontario Institute for Cancer Research. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This study was approved by the University Health Network institutional review board (REB# 19-6239) I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present work are contained in the manuscript [1]: #ref-1 [2]: #ref-2 [3]: #ref-3 [4]: #ref-4 [5]: #ref-5