An artificial intelligence-based model for prediction of clonal hematopoiesis variants in cell-free DNA samples Article Swipe

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Gustavo Arango-Argoty , Marzieh Haghighi , Gerald J. Sun , Elizabeth Choe , Aleksandra Markovets , J. Carl Barrett , Zhongwu Lai , Etai Jacob ·

YOU? · · 2025 · Open Access · · DOI: https://doi.org/10.1038/s41698-025-00921-w

Circulating tumor DNA is a critical biomarker in cancer diagnostics, but its accurate interpretation requires careful consideration of clonal hematopoiesis (CH), which can contribute to variants in cell-free DNA and potentially obscure true tumor-derived signals. Accurate detection of somatic variants of CH origin in plasma samples remains challenging in the absence of matched white blood cells sequencing. Here we present an open-source machine learning framework (MetaCH) which classifies variants in cfDNA from plasma-only samples as CH or tumor origin, surpassing state-of-the-art classification rates.

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Biology

Computational Biology

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Somatic cell Haematopoiesis Biology Cell-free fetal DNA Computational biology Biomarker DNA DNA sequencing Genetics Stem cell Gene Prenatal diagnosis Fetus Pregnancy

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Type: article
Language: en
Landing Page: https://doi.org/10.1038/s41698-025-00921-w
PDF: https://www.nature.com/articles/s41698-025-00921-w.pdf
OA Status: gold
Cited By: 2
References: 38
Related Works: 10
OpenAlex ID: https://openalex.org/W4410523444

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DOI: https://doi.org/10.1038/s41698-025-00921-w

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Title: An artificial intelligence-based model for prediction of clonal hematopoiesis variants in cell-free DNA samples

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Type: article

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Language: en

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Publication year: 2025

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Publication date: 2025-05-20

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Authors: Gustavo Arango-Argoty, Marzieh Haghighi, Gerald J. Sun, Elizabeth Choe, Aleksandra Markovets, J. Carl Barrett, Zhongwu Lai, Etai Jacob

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Landing page: https://doi.org/10.1038/s41698-025-00921-w

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Concepts: Somatic cell, Haematopoiesis, Biology, Cell-free fetal DNA, Computational biology, Biomarker, DNA, DNA sequencing, Genetics, Stem cell, Gene, Prenatal diagnosis, Fetus, Pregnancy

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Cited by: 2

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