Chinese University of Hong Kong (CUHK) research team led by Prof Dennis Lo have developed a new method that greatly improves the detection of DNA cytosine methylation using Pacific Biosciences single-molecule real-time sequencing data.

The approach, called the holistic kinetic (HK) model considers kinetic signals from the DNA polymerase used in PacBio sequencing, as well as the sequence context, to determine cytosine methylation sites. After training a methylation classification model using aconvolutional neural network, it was reported being able to detect cytosine methylation, or 5-methyl-C, with 90% specificity and 94% sensitivity, with a 99% correlation of overall methylation level with bisulfite sequencing.

The advantage of the method is that it allows simultaneous determination of DNA sequence and CpG methylation in one go, with high base-calling accuracy, and without the use of a step that is destructive to the input DNA which is always a problem with the traditional method of bisulfite sequencing. More importantly, PacBio long read sequencing platform can overcome the problem of short read sequencing platform on generating methylation data over larger distances in the genome to generate methylation haplotypes.

The potential applications of the patent-pending method include epigenetic studies in humans and other organisms as well as molecular diagnostics

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