PacBio reveals strategies to enhance methylation identification in High-Fidelity chemistry
PacBio Introduces New Technology for Enhanced DNA Methylation Detection
Pacific Biosciences (PacBio) has announced a significant advancement in its HiFi sequencing technology with the introduction of the Holistic Kinetic Model 2 (HK2). This new technology enhances PacBio HiFi sequencing's DNA methylation detection, offering more accurate and sensitive identification of methylated bases directly from native DNA reads without additional chemical treatment.
The HK2 model uses a refined computational framework that integrates polymerase kinetic rate changes holistically across the DNA sequence context. This approach improves the detection accuracy of modified bases in native DNA, contrasting with earlier methods that used simpler kinetic metrics or partial modeling of polymerase behavior.
Key enhancements from the HK2 technology include the utilization of multi-molecule kinetic information from the same DNA molecule to model polymerase pauses and interpulse durations more comprehensively. This results in improved discrimination of methylation signals from sequencing noise or other modifications through advanced probabilistic modeling.
With the HK2 technology, PacBio HiFi sequencing provides a comprehensive and simultaneous readout of the genome and epigenome from native DNA without the need for chemical conversion, additional sample preparation, or parallel workflows. The technology allows for increased resolution of methylation states at a single-base level across the genome alongside PacBio’s long and accurate sequence reads.
Moreover, the new capabilities from the HK2 model will be delivered to existing customers through software updates, with no changes to sequencing protocols and no additional cost. This means that customers can access the new capability powered entirely by software and existing sequencing signals, with no added cost or workflow changes.
The new capability expands the applications of PacBio's HiFi sequencing to include high-resolution, native detection of 5-methylcytosine (5mC), 6-methyladenine (6mA), and 5-hydroxymethylcytosine (5hmC). The ability to profile 5hmC, a dynamic and tissue-specific epigenetic mark, opens new frontiers in areas such as liquid biopsy, cancer detection, and cell-free DNA analysis.
PacBio's native detection of 5mC, 6mA, and 5hmC maintains DNA integrity and supports haplotype-resolved analysis in complex genomic regions. The new technology includes an enhanced AI deep learning framework known as Holistic Kinetic Model 2 (HK2), which is designed to significantly improve the accuracy of 5mC and N6-methyladenine (6mA) detection and introduces native 5hmC calling in single molecules.
PacBio plans to bring these capabilities to its Revio and Vega systems, expanding the potential for researchers to uncover new biology and ask more sophisticated questions. According to Mark Van Oene, Chief Operating Officer at PacBio, the new capability will enable researchers to profile epigenetic modifications with the same data used for high-fidelity genome sequencing, providing a more comprehensive view of genetic and epigenetic variation in one assay.
This advancement in PacBio's technology follows the introduction of on-instrument 5mC detection in April 2022 and extended support to 6mA in December 2024 for Fiber-seq chromatin architecture studies. The licensed technology is designed to enhance PacBio HiFi sequencing with improved detection of DNA base modifications, including 5-hydroxymethylcytosine (5hmC) and hemimethylated 5-methylcytosine (5mC).
The improvement will be achieved through licensing advanced DNA methylation detection methods developed by Professor Dennis Lo and colleagues at the Chinese University of Hong Kong (CUHK) and Centre for Novostics. CUHK, together with Take2 Technologies Limited, pioneered robust 5mC detection in 2021 using the PacBio platform.
HiFi 5-base sequencing has already been adopted by institutions such as Children's Mercy Kansas City and GeneDx. PacBio's native detection method differs from chemical-based methods like bisulfite or TAPS sequencing, which degrade DNA and diminish phasing and structural context.
In conclusion, the new HK2 technology advances the capability of PacBio HiFi sequencing by enabling accurate, direct detection of epigenetic modifications with the same data used for high-fidelity genome sequencing, providing a more comprehensive view of genetic and epigenetic variation in one assay.
- The HK2 technology, integrated within PacBio's HiFi sequencing, leverages science and technology to deliver a more accurate and sensitive identification of epigenetic modifications such as 5-methylcytosine (5mC), 6-methyladenine (6mA), and 5-hydroxymethylcytosine (5hmC), directly from native DNA reads, enhancing our understanding of genetics and epigenetics through digital health.
- The advancements in PacBio's HiFi sequencing technology, including the Holistic Kinetic Model 2 (HK2), not only provide long and accurate sequence reads but also enable the detection of epigenetic marks like 5mC, 6mA, and 5hmC, harnessing the power of science, technology, and digital health to revolutionize fields such as liquid biopsy, cancer detection, and cell-free DNA analysis.
