GeneLLM: A Large cfRNA Language Model for Cancer Screening from Raw Reads

Deng, S.; Sha, L.; Jin, Y.; Zhou, T.; Wang, C.; Liu, Q.; Guo, H.; Xiong, C.; Xue, Y.; Li, X.; Li, Y.; Gao, Y.; Hong, M.; Xu, J.; Chen, S.; Wang, P.

doi:10.1101/2024.06.29.601341

bioRxiv · 10.1101/2024.06.29.601341

GeneLLM: A Large cfRNA Language Model for Cancer Screening from Raw Reads

Deng, S.·Sha, L.·Jin, Y.·Zhou, T.·Wang, C.·Liu, Q.·Guo, H.·Xiong, C.·Xue, Y.·Li, X.·Li, Y.·Gao, Y.·Hong, M.·Xu, J.·Chen, S.·Wang, P.

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Abstract

We present GeneLLM, a novel large language model that offers a transformative approach to non-invasive cancer detection and biomarker discovery by directly interpreting plasma cell-free RNA (cfRNA) sequences. Unlike traditional annotation-dependent methods, GeneLLM operates without prior knowledge, achieving significantly improved multi-cancer detection accuracy. Critically, GeneLLM identifies novel cfRNAs ( pseudo-biomarkers) originating from previously unannotated genomic regions-overlooked by existing methods-offering new therapeutic targets and insights into intercellular communication. This innovative, cost-effective approach bypasses traditional bioinformatics tools, generating novel pseudo-biomarkers that outperform existing methods even with low-depth sequencing data. Consequently, GeneLLM opens new avenues for biomarker discovery and expands our understanding of the extracellular transcriptomes role in cancer development.

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Deng, S., Sha, L., Jin, Y., Zhou, T., Wang, C., Liu, Q., Guo, H., Xiong, C., Xue, Y., Li, X., Li, Y., Gao, Y., Hong, M., Xu, J., Chen, S., Wang, P.. 2024-07-02. GeneLLM: A Large cfRNA Language Model for Cancer Screening from Raw Reads. https://doi.org/10.1101/2024.06.29.601341

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