DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing.
Nat Commun
; 14(1): 4054, 2023 07 08.
Article
in En
| MEDLINE
| ID: mdl-37422489
ABSTRACT
Long single-molecular sequencing technologies, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine in CpGs (5mCpGs), especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. Here, we present ccsmeth, a deep-learning method to detect DNA 5mCpGs using CCS reads. We sequence polymerase-chain-reaction treated and M.SssI-methyltransferase treated DNA of one human sample using PacBio CCS for training ccsmeth. Using long (≥10 Kb) CCS reads, ccsmeth achieves 0.90 accuracy and 0.97 Area Under the Curve on 5mCpG detection at single-molecule resolution. At the genome-wide site level, ccsmeth achieves >0.90 correlations with bisulfite sequencing and nanopore sequencing using only 10× reads. Furthermore, we develop a Nextflow pipeline, ccsmethphase, to detect haplotype-aware methylation using CCS reads, and then sequence a Chinese family trio to validate it. ccsmeth and ccsmethphase can be robust and accurate tools for detecting DNA 5-methylcytosines.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
DNA
/
5-Methylcytosine
Type of study:
Diagnostic_studies
/
Guideline
/
Prognostic_studies
Limits:
Humans
Language:
En
Journal:
Nat Commun
Year:
2023
Document type:
Article