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

ABSTRACT

Methylation signatures in cell-free DNA (cfDNA) have shown great sensitivity and specificity in the characterization of tumour status and classification of tumour types, as well as the response to therapy and recurrence. Currently, most cfDNA methylation studies are based on bisulphite conversion, especially targeted bisulphite sequencing, while enrichment-based methods such as cfMeDIP-seq are beginning to show potential. 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 for cfMBD capture by adjusting the amount of MethylCap protein along with using methylated filler DNA. Our data show high correlation between low input cfMBD-seq and standard MBD-seq (>1000 ng input). When compared to cfMEDIP-seq, cfMBD-seq demonstrates higher sequencing data quality with more sequenced reads passed filter and less duplicate rate. cfMBD-seq also outperforms cfMeDIP-seq in the enrichment of CpG islands. This new bisulphite-free ultra-low input methylation profiling technology has great potential in non-invasive and cost-effective cancer detection and classification.

KEYWORDS:

• Liquid biopsies
• cfDNA
• MBD-seq
• methylome
• low input DNA
• next-generation sequencing

Availability of materials and data

The sequencing data is available from GEO under the accession number GSE161331.

The data analysis pipeline is available at https://github.com/LiangWangLab/cfMBD-seq.

Disclosure statement

No potential conflicts of interest were disclosed.

Author contributions

Conceptualization, LW; Experiment, JYH; Data analysis, JYH, AS; Writing—original draft preparation, JYH; Writing—proofreading and editing, JYH, AS, and LW; Supervision, LW; funding acquisition, LW.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

This research was supported in part by the National Institute of Health [R01CA212097] and by the H. Lee Moffitt Cancer Center & Research Institute.