by Ludwig Cancer Research

Development of wglrTAPS. (A) Schematic representation of the wglrTAPS. (B) Sequence length distribution of wglrTAPS HiFi read. (C) Conversion rate of wglrTAPS at methylated CpG sites and false-positive rate of wglrTAPS at non-methylated CpG sites from C^mCGG-methylated 4-kb spike-in. (D) Fraction of mapped reads with ≥Q20 in wglrTAPS. Credit: Nucleic Acids Research (2022). DOI: 10.1093/nar/gkac612

In a new paper published in Nucleic Acids Research, a team led by Ludwig Oxford's Chunxiao Song reported a method for whole-genome long-read sequencing using TAPS (for Tet-assisted pyridine borane sequencing), the method his and Benjamin Schuster-Böckler's groups published in 2019 for the detection of cytosine methylation and hydroxymethylation.

Unlike other DNA methylation sequencing methods, TAPS does not rely on the harsh chemical bisulphite, which degrades a lot of the DNA sample. This has allowed Song's group to adapt the method for applications such as liquid biopsies. Long-read sequencing, meanwhile, permits the mapping of repetitive and complex genomic regions, which can reveal new information about the genome. Song and his team show that whole-genome long-read TAPS uncovered many sites of methylation that were not present in data from short-read TAPS. The method also enabled the detection of allele-specific methylation in imprinting genes.

More information: Jinfeng Chen et al, Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology, Nucleic Acids Research (2022). DOI: 10.1093/nar/gkac612

Journal information: Nucleic Acids Research 

Provided by Ludwig Cancer Research