Cell-free DNA methylome profiling by MBD-seq with ultra-low input

Here, we report an enrichment-based ultra-low input cfDNA methylation profiling method using methyl-CpG binding proteins capture, termed cfMBD-seq. We optimized the conditions of cfMBD capture by adjusting the amount of MethylCap protein along with using methylated filler DNA. Our data showed that cfMBD-seq performs equally to the standard MBD-seq (>1000 ng input) even when using 1 ng DNA as the input. cfMBD-seq demonstrated equivalent sequencing data quality as well as similar methylation profile when compared to cfMeDIP-seq. We showed that cfMBD-seq outperforms cfMeDIP-seq in the enrichment of CpG islands. This new bisulfite-free ultra-low input methylation profiling technology has a great potential in non-invasive and cost-effective cancer detection and classification. Overall design: Different conditions of cfMBD-seq