MOTIVATION: Circulating-cell free DNA (cfDNA) is widely explored as a noninvasive biomarker for cancer screening and diagnosis. The ability to decode the cells of origin in cfDNA would provide biological insights into pathophysiological mechanisms, aiding in cancer characterization and directing clinical management and follow-up. RESULTS: We developed a DNA methylation signature-based deconvolution algorithm, MetDecode, for cancer tissue origin identification. We built a reference atlas exploiting de novo and published whole-genome methylation sequencing data for colorectal, breast, ovarian, and cervical cancer, and blood-cell-derived entities. MetDecode models the contributors absent in the atlas with methylation patterns learnt on-the-fly from the input cfDNA methylation profiles. In addition, our model accounts for the coverage of each marker region to alleviate potential sources of noise. In-silico experiments showed a limit of detection down to 2.88% of tumor tissue contribution in cfDNA. MetDecode produced Pearson correlation coefficients above 0.95 and outperformed other methods in simulations (P < 0.001; T-test; one-sided). In plasma cfDNA profiles from cancer patients, MetDecode assigned the correct tissue-of-origin in 84.2% of cases. In conclusion, MetDecode can unravel alterations in the cfDNA pool components by accurately estimating the contribution of multiple tissues, while supplied with an imperfect reference atlas. AVAILABILITY AND IMPLEMENTATION: MetDecode is available at https://github.com/JorisVermeeschLab/MetDecode.

Department of Gynaecologic Oncology Netherlands Cancer Institute Amsterdam 1066 CX The Netherlands

Department of Oncology GZA Ziekenhuis Antwerp 2610 Belgium

Department of Woman Child and Public Health Fondazione Policlinico Universitario Agostino Gemelli IRCCS Rome 00168 Italy

Digestive Oncology Unit University Hospital Gasthuisberg Leuven 3000 Belgium

Dynamical Systems Signal Processing and Data Analytics Department of Electrical Engineering KU Leuven Leuven 3001 Belgium

Gynaecological Oncology Department of Oncology KU Leuven Leuven 3000 Belgium

Gynaecology and Obstetrics University Hospitals KU Leuven Leuven 3000 Belgium

Laboratory for Cytogenetics and Genome Research Department of Human Genetics KU Leuven Leuven 3000 Belgium

Laboratory of Experimental Oncology Department of General Medical Oncology University Hospitals Leuven KU Leuven Leuven 3000 Belgium

Laboratory of Tumour Immunology and Immunotherapy Department of Oncology Leuven Cancer Institute KU Leuven Leuven 3000 Belgium

Multidisciplinary Breast Centre University Hospitals Leuven Leuven 3000 Belgium

Obstetrics and Gynaecology 1st Faculty of Medicine Charles University and General University Hospital Prague Prague Czech Republic

Translational Cell and Tissue Research Department of Pathology KU Leuven Leuven 3000 Belgium

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