crossNN is an explainable framework for cross-platform DNA methylation-based classification of tumors

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F65269705%3A_____%2F25%3A00082139" target="_blank" >RIV/65269705:_____/25:00082139 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14110/25:00141527
Result on the web
<a href="https://www.nature.com/articles/s43018-025-00976-5" target="_blank" >https://www.nature.com/articles/s43018-025-00976-5</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1038/s43018-025-00976-5" target="_blank" >10.1038/s43018-025-00976-5</a>

Result language
angličtina
Original language name
crossNN is an explainable framework for cross-platform DNA methylation-based classification of tumors
Original language description
DNA methylation-based classification of (brain) tumors has emerged as a powerful and indispensable diagnostic technique. Initial implementations used methylation microarrays for data generation, while most current classifiers rely on a fixed methylation feature space. This makes them incompatible with other platforms, especially different flavors of DNA sequencing. Here, we describe crossNN, a neural network-based machine learning framework that can accurately classify tumors using sparse methylomes obtained on different platforms and with different epigenome coverage and sequencing depth. It outperforms other deep and conventional machine learning models regarding accuracy and computational requirements while still being explainable. We use crossNN to train a pan-cancer classifier that can discriminate more than 170 tumor types across all organ sites. Validation in more than 5,000 tumors profiled on different platforms, including nanopore and targeted bisulfite sequencing, demonstrates its robustness and scalability with 99.1% and 97.8% precision for the brain tumor and pan-cancer models, respectively.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
30204 - Oncology

Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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