PacBio's Holistic Kinetic Model 2 Revolutionizes Epigenetic Analysis
PacBio reveals strategy for enhancing methylation identification in HiFi technology
Pacific Biosciences (PacBio) has made significant strides in epigenetic analysis with the introduction of the Holistic Kinetic Model 2 (HK2). This advanced computational model, licensed from Professor Dennis Lo and colleagues at the Chinese University of Hong Kong and the Centre for Novostics, promises to improve the sensitivity and specificity of methylation detection in PacBio's HiFi sequencing data.
Background
PacBio's HiFi sequencing technology is renowned for its ability to deliver highly accurate long reads through circular consensus sequencing (CCS). In addition to basecalling accuracy, this platform also enables the detection of DNA modifications by analyzing the polymerase kinetics during sequencing. Variations in the interpulse duration (IPD) and pulse width (PW) can signal the presence of modified bases such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC).
Holistic Kinetic Model 2 (HK2)
HK2 is an advanced computational and statistical model designed to improve the accuracy of methylation detection in PacBio HiFi data. It builds on earlier models by more effectively integrating kinetic signal features and contextual sequence information, thus enabling a more comprehensive and nuanced interpretation of polymerase behavior on modified DNA.
Key Improvements with HK2
- Enhanced Differentiation between 5mC and 5hmC: Earlier methods sometimes struggled to distinguish between 5mC and its oxidized derivative 5hmC because both modifications can subtly alter polymerase kinetics. HK2 incorporates refined kinetic signatures that enable more accurate classification of these epigenetic marks.
- Improved Sensitivity and Specificity: By holistically modeling the kinetic data over a broader sequence context and integrating multiple kinetic parameters simultaneously, HK2 reduces false positives and negatives in methylation calls.
- Better Adaptation to HiFi Reads: The higher accuracy of HiFi sequencing, combined with HK2's sophisticated modeling, allows for confident methylation calling even at lower coverage or within complex genomic regions.
- Quantitative Methylation Profiling: HK2 supports quantitative estimates of methylation levels, facilitating studies of epigenetic heterogeneity across cell populations or tissue types.
Impact on Epigenetic Studies
- The ability to reliably identify both 5mC and 5hmC from the same PacBio HiFi dataset enhances multi-layered epigenetic profiling without the need for separate chemical treatments or sequencing runs.
- Researchers can leverage HK2 for deeper insights into DNA demethylation pathways, gene regulation, and disease-associated epigenetic changes.
- The improved accuracy supports applications in clinical and basic research, including cancer epigenetics, neurobiology, and developmental biology.
5hmC, implicated in brain development, cancer, and neurodegenerative diseases, is a key focus of this advancement. PacBio's native detection of 5mC, 6mA, and 5hmC maintains DNA integrity and supports haplotype-resolved analysis in complex genomic regions.
Institutions such as Children's Mercy Kansas City and GeneDx have already adopted HiFi 5-base sequencing. The new capability is powered entirely by software and existing sequencing signals, allowing customers to access it with no added cost or workflow changes.
Mark Van Oene, Chief Operating Officer at PacBio, states that the high-resolution, native detection empowers researchers to ask more sophisticated questions and uncover new biology. 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.
PacBio plans to bring these capabilities to its Revio and Vega systems. HiFi sequencing, available on both the Revio and Vega platforms, 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 native detection method does not degrade DNA like chemical-based methods such as bisulfite or TAPS sequencing.
The licensed technology aims to improve detection of DNA base modifications, including 5-hydroxymethylcytosine (5hmC) and hemimethylated 5-methylcytosine (5mC), in native DNA. PacBio, a sequencing platform provider, plans to enhance its methylation detection capabilities in HiFi chemistry.
Digital health technology, powered by the Holistic Kinetic Model 2 (HK2), is set to revolutionize medical-conditions research by enabling more accurate identification of key epigenetic marks like 5-hydroxymethylcytosine (5hmC), which is implicated in brain development, cancer, and neurodegenerative diseases. This advancement in health-and-wellness research, brought about by improvements in sensitivity and specificity, also supports haplotype-resolved analysis in complex genomic regions. Researchers and institutions can take advantage of these improvements without incurring any additional cost or workflow changes in their digital health studies.
