Non-invasive, research-focused approach to discover disease subtypes and biomarkers using cfDNA methylation and hydroxymethylation profiling.
Key Highlights:
Dual-route analysis: comprehensive 5mC and 5hmC profiling from cfDNA.
Non-invasive sampling: plasma/serum cfDNA enables molecular subtyping without tissue biopsies.
Biomarker discovery: identify and validate subtype-specific epigenetic signatures.
Research-ready deliverables: reproducible data, clear interpretation, and publication-quality outputs.
End-to-end support: from cfDNA processing to bioinformatics-driven subtyping.
Introduction
How cfDNA Epigenetics Advances Molecular Subtyping Studies
Understanding disease heterogeneity requires more than mutation analysis. cfDNA epigenetic subtyping opens a new layer of insight by leveraging DNA methylation (5mC) and hydroxymethylation (5hmC) marks circulating in plasma or serum.
Revealing hidden diversity: Epigenetic signatures in cfDNA distinguish molecular subgroups that may not be apparent through genomic sequencing alone.
Overcoming tissue barriers: Subtyping directly from cfDNA enables non-invasive research where tissue access is limited or impractical.
Reliable biomarker source: 5mC and 5hmC modifications are stable, reproducible, and suitable for identifying subtype-specific markers.
Dynamic monitoring: cfDNA reflects real-time biological changes, allowing researchers to track subtype evolution across cohorts or experimental conditions.
Cross-platform compatibility: Subtyping results can be integrated with RNA-seq, proteomics, or other omics layers for comprehensive systems biology research.
With cfDNA epigenetic profiling, researchers gain a practical and scalable solution to stratify disease models, discover biomarkers, and deepen understanding of molecular mechanisms—without relying on invasive procedures.
Our Solutions
Our Dual-Route Solution for Molecular Subtyping
To help researchers uncover the full spectrum of disease heterogeneity, our solution integrates two complementary epigenetic routes from cfDNA:
1. cfDNA 5mC Methylation Pathway
Our cfDNA methylation route is based on a stepwise biomarker discovery and validation framework, offering flexible strategies depending on research design and available resources:
Subtype associations are confirmed through reproducible analysis pipelines and robust bioinformatics.
This approach enables researchers to move seamlessly from biomarker discovery to validation, ensuring confidence in cfDNA-based molecular subtyping results.
2. cfDNA 5hmC Hydroxymethylation Pathway
Dynamic signals: 5hmC reflects gene activity and regulatory changes, offering insights beyond traditional methylation.
Complementary value: When combined with 5mC, hydroxymethylation improves the granularity of subtype classification and enhances biomarker discovery.
Research applications: Particularly useful for understanding cancer progression, lineage-specific activity, and disease evolution.
By offering both 5mC and 5hmC profiling routes, we give researchers the flexibility to choose the strategy that best fits their study design—or combine them for a more comprehensive molecular subtyping approach.
Service Workflow
Workflow at a Glance
Our cfDNA epigenetic subtyping workflow is designed to provide researchers with a clear, reproducible path from plasma collection to subtype interpretation:
Project Consultation & Design
Define study objectives and select the most appropriate route (5mC, 5hmC, or combined).
Tailor the workflow to match sample availability, cohort size, and research goals.
Sample Preparation & cfDNA Processing
Plasma or serum cfDNA isolation with standardized quality practices.
Optimized library construction compatible with low-input material.
Sequencing & Data Generation
High-throughput sequencing of cfDNA libraries to capture methylation and/or hydroxymethylation signals.
Rigorous QC to ensure data integrity before analysis.
Subtype Discovery & Profiling
Identification of epigenetic features (DMRs, 5hmC peaks) associated with molecular subtypes.
Statistical clustering and subtype assignment.
Biological Interpretation
Integrative reporting with functional annotation, pathway mapping, and biomarker insights.
Clear visual outputs designed for direct use in research publications or collaborative studies.
This streamlined process ensures that every step—from cfDNA collection to final data interpretation—contributes directly to the accurate discovery and validation of disease subtypes.
Bioinformatics
Bioinformatics Analysis
A core strength of our cfDNA epigenetic subtyping solution lies in the bioinformatics pipeline, designed to transform sequencing reads into reproducible subtype insights:
Data Quality Control
Read filtering, adapter trimming, duplication checks, and coverage assessment.
Removal of low-confidence data to ensure robust downstream interpretation.
Feature Identification
5mC methylation: detection of differentially methylated regions (DMRs).
5hmC hydroxymethylation: enrichment peak calling and signal quantification.
Subtype Discovery
Unsupervised clustering to reveal natural subgroup structures.
Dimensionality reduction (PCA, t-SNE, UMAP) for visualizing subtype separation.
Construction of predictive models to classify new samples into defined subtypes.
Validation & Robustness
Cross-validation of subtype markers to confirm reproducibility.
Comparative analysis across cohorts to ensure consistency.
Functional Interpretation
Pathway and network enrichment to link subtypes with biological processes.
Integration with metadata or multi-omics datasets for deeper contextual insights.
Data Visualization
Publication-ready heatmaps, clustering trees, subtype classification plots, and correlation matrices.
By combining rigorous computational pipelines with clear interpretive reporting, we ensure that cfDNA methylation and hydroxymethylation data can be confidently applied to molecular subtyping research.
Deliverables
Deliverables – What You Receive
Our cfDNA epigenetic subtyping service provides a comprehensive package of results, ensuring that your research receives not only raw data but also well-structured, interpretable outputs:
Subtype Classification Report
Clear identification of molecular subgroups derived from cfDNA methylation and hydroxymethylation patterns.
Candidate Biomarker Lists
Subtype-specific 5mC/5hmC markers, annotated with genomic context and statistical significance.
Comparative Analysis Outputs
Heatmaps, clustering dendrograms, subtype separation plots, and summary statistics.
Functional Annotation Results
Pathway and network insights linking identified subtypes to biological processes or regulatory mechanisms.
Publication-ready visualizations and summary documents.
Every deliverable is structured to support research publication, hypothesis development, and downstream experimental validation, giving you confidence that your cfDNA subtyping data will be immediately actionable.
Applications
Research Applications
The cfDNA epigenetic subtyping solution supports a wide range of research areas where molecular heterogeneity plays a critical role:
Cancer Subtype Identification
Distinguish molecular subgroups in heterogeneous tumors using cfDNA methylation and hydroxymethylation patterns.
Facilitate studies on disease classification without relying solely on tissue biopsies.
Biomarker Discovery & Validation
Identify subtype-specific epigenetic signatures as potential biomarkers.
Validate candidate markers across cohorts to ensure reproducibility in experimental studies.
Longitudinal and Comparative Research
Monitor dynamic subtype changes over time or under treatment conditions.
Compare subtype distributions across different experimental groups, populations, or disease stages.
Multi-omics Integration
Combine cfDNA subtyping with transcriptomics, proteomics, or metabolomics to generate comprehensive molecular profiles.
Enable system-level insights into disease mechanisms and regulation.
Non-invasive Model Development
Build subtype prediction models that leverage cfDNA data for preclinical and translational studies.
Reduce reliance on invasive tissue sampling in experimental settings.
By applying cfDNA subtyping in these research contexts, investigators gain access to a powerful tool for uncovering disease heterogeneity, discovering robust biomarkers, and designing more precise experimental models.
Recommendation: Seal samples securely; transport on dry ice.
Advantages
Why Choose Us
When selecting a partner for cfDNA epigenetic subtyping, researchers look for more than just sequencing. Our solution is designed to give you confidence at every step of your project:
Focused on Molecular Subtyping
Unlike generic cfDNA sequencing services, our workflows are tailored to reveal molecular subgroups through 5mC and 5hmC profiling.
End-to-End Scientific Support
From project design to data interpretation, we ensure that each stage contributes directly to subtype discovery and biomarker identification.
Flexible and Customizable
Whether your study requires broad methylome coverage or focused 5hmC enrichment, our pipelines adapt to your experimental design and available material.
Publication-Ready Deliverables
Outputs include annotated biomarker lists, functional insights, and visualization files formatted for seamless use in academic publications and presentations.
Trusted by Research Communities
Our standardized workflows, transparent reporting, and reproducible analyses are aligned with international research practices, supporting both collaborative projects and independent investigations.
By choosing our cfDNA subtyping solution, you gain a research partner committed to turning fragmented cfDNA signals into clear, reproducible molecular insights.
Case Study
Case Study
Start Your cfDNA Molecular Subtyping Project Today
Turn circulating DNA into actionable insights with our cfDNA epigenetic subtyping solution. Whether you are exploring 5mC methylation, 5hmC hydroxymethylation, or a combined strategy, our workflows deliver research-ready results tailored to your study design.
