In cancer genomics, methylation patterns and somatic variants tell different parts of the same story. Methylation data reveals epigenetic silencing and tissue-of-origin signals critical for multi-cancer early detection (MCED) and minimal residual disease (MRD) monitoring. Variant data catches the mutations driving tumor growth. Ideally, you’d get both from every sample.
In practice, most labs run them as separate NGS library prep workflows because traditional bisulfite-based methylation sequencing makes multimodal analysis genuinely hard. Here’s why, and what a newer approach changes.
Why Bisulfite Sequencing Struggles with Multimodal Analysis
Bisulfite treatment works by converting unmethylated cytosines to thymines a chemical reaction that lets you infer methylation status from sequencing reads. But that conversion comes with significant tradeoffs.
The three-base problem. When ~95% of cytosines are converted to thymines, the genome effectively collapses from four bases (ATCG) to three (ATG). Reduced sequence complexity makes read alignment harder, increases multi-mapping, and degrades variant calling accuracy. For a 30X genome, this translates to hours of unnecessary compute time and higher false positive rates.
DNA damage. Bisulfite chemistry is harsh. It can destroy up to 80% of available ctDNA in a liquid biopsy sample a serious problem when working with low-input cfDNA or degraded FFPE tissue where every molecule matters.
Workflow duplication. Because bisulfite-prepared libraries are poorly suited for variant calling, labs typically run methylation and somatic variant sequencing as parallel workflows separate NGS library preps, separate sequencing runs, duplicate reagent costs, and more chances for error.
What is TAPS-Based Sequencing and How Does It Work Differently?
TET-Assisted Pyridine Borane Sequencing (TAPS) takes a fundamentally different approach. Rather than converting unmethylated cytosines, TAPS converts methylated cytosines (5mC/5hmC) to thymine a “positive readout” of methylation status.
This distinction matters because unmethylated cytosines are left intact. The four-base complexity of the genome is preserved, which means standard alignment tools work normally, variant calling accuracy is maintained, and the same library can yield both methylation and genomic variant data.
Researchers sometimes describe this as sequencing a "five-base genome": the standard four bases (ATCG) plus epigenomic 5mC information, all captured in a single NGS library prep.
Key Capabilities of TAPS for Multimodal NGS
- Simultaneous methylation and variant detection from a single NGS library, enabling integrated analysis without splitting samples.
- Low-input compatibility: gentle chemistry works with inputs as low as 1 ng, making it suitable for cfDNA and FFPE samples.
- High conversion accuracy: >98% 5mC conversion rate and ≤0.3% false positive rate for confident detection of rare methylation signals.
- Faster bioinformatics: preserved base complexity reduces computational analysis time by 30% or more compared to bisulfite workflows on equivalent coverage.
- Accurate SNV, indel, and CNV detection alongside CpG methylation profiling no need for separate variant sequencing runs.
Who Benefits Most From Multimodal Sequencing?
TAPS-based multimodal sequencing is particularly well-suited to:
- MCED assay developers who need both methylation and variant signals to build accurate, tissue-of-origin-aware classifiers.
- MRD monitoring teams working with ultra-low ctDNA fractions in liquid biopsy, where sample loss from bisulfite damage is unacceptable.
- Oncology researchers studying the interplay between epigenetic modification and somatic mutation in tumor evolution, especially if they’re working with low quality or low input samples, such as FFPE.
- High-throughput labs looking to reduce parallel workflow complexity, lower reagent costs, and increase sample throughput.
Bottom Line
Bisulfite sequencing was a breakthrough but its chemistry was never designed for the demands of modern multimodal cancer genomics. TAPS-based approaches resolve the core technical limitations: base complexity is preserved, DNA damage is minimized, and a single library yields both epigenomic and genomic data.
For labs working at the intersection of methylation profiling and somatic variant detection, that’s a meaningful shift in data quality, workflow efficiency, and the value extracted from every sample.
References
- Vavoulis DV, et al. Multimodal cell-free DNA whole-genome TAPS is sensitive and reveals specific cancer signals. Nat Commun. 2025;16:430.