Cell-free DNA methylome profiling by MBD-seq with ultra-low input
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, e...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2022-03-01
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| Series: | Epigenetics |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/15592294.2021.1896984 |
| _version_ | 1797678806927933440 |
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| author | Jinyong Huang Alex C. Soupir Liang Wang |
| author_facet | Jinyong Huang Alex C. Soupir Liang Wang |
| author_sort | Jinyong Huang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T23:05:17Z |
| format | Article |
| id | doaj.art-3752cb521d4a41b0949a160a1d78c9c2 |
| institution | Directory Open Access Journal |
| issn | 1559-2294 1559-2308 |
| language | English |
| last_indexed | 2024-03-11T23:05:17Z |
| publishDate | 2022-03-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Epigenetics |
| spelling | doaj.art-3752cb521d4a41b0949a160a1d78c9c22023-09-21T13:09:25ZengTaylor & Francis GroupEpigenetics1559-22941559-23082022-03-0117323925210.1080/15592294.2021.18969841896984Cell-free DNA methylome profiling by MBD-seq with ultra-low inputJinyong Huang0Alex C. Soupir1Liang Wang2H. Lee Moffitt Cancer CenterH. Lee Moffitt Cancer CenterH. Lee Moffitt Cancer CenterMethylation 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.http://dx.doi.org/10.1080/15592294.2021.1896984liquid biopsiescfdnambd-seqmethylomelow input dnanext-generation sequencing |
| spellingShingle | Jinyong Huang Alex C. Soupir Liang Wang Cell-free DNA methylome profiling by MBD-seq with ultra-low input Epigenetics liquid biopsies cfdna mbd-seq methylome low input dna next-generation sequencing |
| title | Cell-free DNA methylome profiling by MBD-seq with ultra-low input |
| title_full | Cell-free DNA methylome profiling by MBD-seq with ultra-low input |
| title_fullStr | Cell-free DNA methylome profiling by MBD-seq with ultra-low input |
| title_full_unstemmed | Cell-free DNA methylome profiling by MBD-seq with ultra-low input |
| title_short | Cell-free DNA methylome profiling by MBD-seq with ultra-low input |
| title_sort | cell free dna methylome profiling by mbd seq with ultra low input |
| topic | liquid biopsies cfdna mbd-seq methylome low input dna next-generation sequencing |
| url | http://dx.doi.org/10.1080/15592294.2021.1896984 |
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