Ultra-mild bisulfite outperforms EM-seq for 5-methylcytosine detection with low input DNA

He, C.; Dai, Q.; Baldwin, T.; Lyu, R.; Daniels, B.; Ye, C.; Cao, C.; Zhu, C.; Fan, D.; Lin, L.; Liu, Y.; Wang, Y.

doi:10.1101/2025.10.09.681456

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bioRxiv · 10.1101/2025.10.09.681456

Ultra-mild bisulfite outperforms EM-seq for 5-methylcytosine detection with low input DNA

He, C.·Dai, Q.·Baldwin, T.·Lyu, R.·Daniels, B.·Ye, C.·Cao, C.·Zhu, C.·Fan, D.·Lin, L.·Liu, Y.·Wang, Y.

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Abstract

We present Ultra-Mild Bisulfite Sequencing (UMBS-seq), a method for 5-methylcytosine (5mC) detection that minimizes DNA degradation and background noise. UMBS-seq outperforms conventional bisulfite and enzymatic methyl-sequencing (EM-seq) methods in library yield, complexity, and conversion efficiency when applied to low-input DNA samples. In particular, its effectiveness with low-input cell-free DNA (cfDNA) and hybridization-based target capture highlight its potential for clinical applications, including 5mC biomarker detection and early disease diagnosis.

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He, C., Dai, Q., Baldwin, T., Lyu, R., Daniels, B., Ye, C., Cao, C., Zhu, C., Fan, D., Lin, L., Liu, Y., Wang, Y.. 2025-10-10. Ultra-mild bisulfite outperforms EM-seq for 5-methylcytosine detection with low input DNA. https://doi.org/10.1101/2025.10.09.681456

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