Can Targeted EM-seq work with very low cfDNA amounts?

Yes. The method supports cfDNA inputs of around 10 ng or more when extracted with good quality. Lower inputs may be attempted in pilot runs, but QC will determine whether the data are reliable.

What sample types are accepted?

Plasma is the most common choice, but urine or other biofluids can also be used if integrity is sufficient. All samples should be from human research, and we ask for clear documentation of collection, extraction, and storage conditions.

What regions of the genome does the capture panel target?

Our standard panels focus on promoters, enhancers, and disease-relevant DMRs curated from major databases (UCSC, ENCODE, Ensembl). Custom panels can be designed if you have specific regions of interest.

Why is enzymatic conversion better for cfDNA than bisulfite?

Enzymatic conversion is gentler on fragmented cfDNA, preserving molecule integrity and reducing bias. This leads to higher-quality libraries and more interpretable methylation calls compared with bisulfite-based workflows.

Are the data and results publication-ready?

Yes. You receive per-CpG and regional calls, differential analyses, and pathway context, accompanied by figure-ready outputs such as heatmaps, volcano plots, and coverage tracks. All parameters and methods are documented for reproducibility.

Can I use this workflow for longitudinal or intervention studies?

Absolutely. Targeted EM-seq is well suited to repeated sampling, making it useful for time-course studies or evaluating responses to interventions. Let us know your design in advance so we can plan capture and QC accordingly.

Targeted EM-seq for cfDNA Methylation in Liquid Biopsy

What Researchers Need from cfDNA Methylation

Working with plasma cfDNA is rarely straightforward. The fragments are short, the yield is limited, and every handling step risks losing what little material you have. Harsh conversion methods often make things worse—bias creeps in, signals flatten, and you're left questioning whether a pattern is biological or just technical noise.

Signal versus noise

True CpG changes are easy to drown in context effects, PCR skew, or artifacts that look deceptively like biology. A good workflow doesn't just generate reads; it has to separate real differences from background and make distortions visible before they reach the statistics.

Depth where it matters

Not every CpG is worth chasing. Promoters, enhancers, and curated DMRs are the regions most likely to move a hypothesis forward. Pouring depth across the entire genome spreads signal too thin; focusing on relevant regions makes the results interpretable.

Beyond site lists

Reviewers rarely ask for just a spreadsheet of methylated sites. They expect cohort-level contrasts, region summaries, and pathway context—figures that can stand on their own without paragraphs of explanation.

Room for multi-signal work

Today, methylation is often paired with fragment length or nucleosome-based metrics. A flexible pipeline should handle cfDNA as the primary signal while leaving hooks for those additional features when they strengthen the research question.

The practical backdrop

Tube type, extraction chemistry, storage conditions—all shape the outcome. A method for cfDNA methylation has to tolerate the realities of sample handling while making it clear when inputs are drifting off spec.

Our Answer: Targeted EM-seq for cfDNA

Targeted EM-seq was developed with liquid biopsy in mind. Instead of forcing fragile cfDNA through harsh bisulfite chemistry, it uses an enzymatic conversion that preserves fragment structure and improves mapping. Combined with targeted capture panels, the workflow delivers higher-quality data from smaller inputs—making cfDNA methylation a practical tool for discovery and cohort analysis.

What sets it apart:

Preserves scarce material – Enzymatic conversion reduces damage and keeps more molecules available for sequencing.
Depth where biology lives – Target capture enriches promoters, enhancers, and disease-relevant DMRs instead of spreading reads thin.
Built-in quality checks – Metrics tuned for enzymatic libraries flag duplication, coverage skew, or off-target effects early.
Actionable results – Beyond site lists, you receive per-CpG calls, region summaries, and pathway context—ready for figures or manuscripts.
Flexible design – Hooks for fragment size or nucleosome metrics can be included when they strengthen the study.

In short: Targeted EM-seq turns low-yield cfDNA into reliable, interpretable methylation data that can support biomarker discovery, mechanism studies, and longitudinal research.

Why Targeted EM-seq vs. Bisulfite for cfDNA

Feature	Bisulfite Sequencing	Targeted EM-seq
DNA integrity	Harsh chemical conversion fragments DNA further	Gentle enzymatic conversion preserves cfDNA profiles
Input tolerance	Often requires higher DNA amounts	Compatible with low-input cfDNA
Library quality	Increased bias, uneven coverage	Higher complexity, cleaner representation
On-target efficiency	Reads lost to damage and noise	More reads usable in targeted panels
Interpretability	Artifacts can resemble biology	Reduced background, clearer contrasts

In short: Targeted EM-seq is kinder to cfDNA, producing cleaner, more interpretable methylation data for liquid biopsy research.

Applications

Where Targeted EM-seq Fits in Your Work

Biomarker discovery in plasma cfDNA

Apply targeted panels to distinguish case/control groups in disease-focused studies. Well-suited for early-signal exploration and validation of candidate biomarkers.

Mechanism-driven panels

Design capture sets around promoters, enhancers, or pathways to investigate how methylation changes shape regulatory programs in your model system.

Longitudinal and intervention studies

Track cfDNA methylation profiles over time or before/after treatment. Combine targeted methylation with other cfDNA features when a multi-signal view strengthens your analysis.

These use cases show how Targeted EM-seq adapts to discovery, mechanism studies, and dynamic tracking within liquid biopsy research.

Workflow

How It Works

From sample intake to data delivery, the Targeted EM-seq workflow is built to protect cfDNA integrity and concentrate sequencing effort on regions that matter. Each step is transparent, with quality checks embedded along the way so you can trust the output before moving into analysis.

Horizontal workflow for Targeted EM-seq cfDNA methylation: Scope → cfDNA → Enzymatic → Capture → Sequence → QC → Align → Quantify → Contrast → Pathways.

Study design alignment: Define your research question, sample type, and target regions. We confirm capture space and analysis scope before starting.
cfDNA preparation & QC: Plasma-derived cfDNA or DNA from biofluids is reviewed for integrity, yield, and potential gDNA carryover.
Enzymatic conversion & library prep: Gentle enzymatic conversion preserves fragment structure, followed by library construction optimized for short cfDNA inserts.
Targeted capture: Panels enrich promoters, enhancers, and curated DMRs, focusing sequencing depth on regions of biological relevance.
Sequencing & quality monitoring: Sequencing runs are tuned for cfDNA libraries, with checks on duplication, on-target rate, and coverage distribution.
Data delivery: Clean reads and initial QC metrics are provided, ready for downstream bioinformatics and interpretation.

Bioinformatics

Data Processing & Bioinformatics

Raw reads are only the starting point. Our bioinformatics pipeline is tuned for enzymatic cfDNA libraries, ensuring that data is not only technically sound but also biologically meaningful.

Core processing steps

Conversion-aware QC – Assess library complexity, coverage distribution, and on-target performance with metrics specific to enzymatic conversion.
Alignment & deduplication – Map cfDNA reads with parameters that respect short fragments, avoiding over-cleaning of true molecules.
Methylation calling – Generate per-CpG methylation values across the capture space and roll them up into regional summaries.

Research-ready outputs

Cohort contrasts – Identify differential methylation at sites and regions with effect size and concordance checks.
Pathway and regulatory context – Map methylation shifts to genes, functional categories, and pathways for interpretation.
Figure pack – Volcano plots, heatmaps, coverage tracks, and clustering visuals provided in publication-friendly formats.
Documentation for reproducibility – Capture definitions, pipeline parameters, and method notes are versioned for repeat or follow-up studies.

This combination of rigorous processing and ready-to-use outputs ensures that your cfDNA methylation data is both trustworthy and actionable.

Demo

Partial results are shown below:

Sample Requirements

Sample Guidance

Requirement	Details
Sample type	Liquid biopsy samples such as plasma or urine; contact us for collection guidelines.
DNA input	≥10 ng of high-quality DNA.
Species	Human research samples only.

Advantages

Why Partner with CD Genomics

Liquid biopsy expertise

Our workflows are tuned for the realities of cfDNA—short, low-input, and variable in quality. Every stage, from enzymatic conversion to capture and sequencing, is designed with liquid biopsy samples in mind.

Targeted methylation know-how

We don't just generate reads—we help design capture panels that reflect your hypothesis. Whether focused on promoters, enhancers, or curated DMRs, we deliver depth where it matters most.

Analysis built for cohorts

From QC through CpG quantification and pathway mapping, outputs are structured to make group comparisons clear and reproducible. You receive data that supports exploration and publication without re-engineering.

Transparent and reproducible

Every step is documented: capture definitions, analysis parameters, and methods notes are versioned so your study can be repeated, scaled, or reviewed with confidence.

Working with CD Genomics means your cfDNA methylation study gets the care, context, and clarity it needs to move forward—research use only.

FAQ

Q1. Can Targeted EM-seq work with very low cfDNA amounts?
- - Yes. The method supports cfDNA inputs of around 10 ng or more when extracted with good quality. Lower inputs may be attempted in pilot runs, but QC will determine whether the data are reliable.
Q2. What sample types are accepted?
- - Plasma is the most common choice, but urine or other biofluids can also be used if integrity is sufficient. All samples should be from human research, and we ask for clear documentation of collection, extraction, and storage conditions.
Q3. What regions of the genome does the capture panel target?
- - Our standard panels focus on promoters, enhancers, and disease-relevant DMRs curated from major databases (UCSC, ENCODE, Ensembl). Custom panels can be designed if you have specific regions of interest.
Q4. Why is enzymatic conversion better for cfDNA than bisulfite?
- - Enzymatic conversion is gentler on fragmented cfDNA, preserving molecule integrity and reducing bias. This leads to higher-quality libraries and more interpretable methylation calls compared with bisulfite-based workflows.
Q5. Are the data and results publication-ready?
- - Yes. You receive per-CpG and regional calls, differential analyses, and pathway context, accompanied by figure-ready outputs such as heatmaps, volcano plots, and coverage tracks. All parameters and methods are documented for reproducibility.
Q6. Can I use this workflow for longitudinal or intervention studies?
- - Absolutely. Targeted EM-seq is well suited to repeated sampling, making it useful for time-course studies or evaluating responses to interventions. Let us know your design in advance so we can plan capture and QC accordingly.

Ready to Start Your Targeted EM-seq Study?

Your cfDNA methylation project deserves a workflow built for liquid biopsy—not a repurposed method that struggles with scarce input and fragmented DNA. With Targeted EM-seq, you can focus sequencing depth on the regions that matter, preserve integrity during conversion, and receive cohort-ready analyses you can trust.

Next steps are simple:

Share your research question, sample type, and any target regions of interest.
We'll propose a tailored capture strategy, conversion plan, and analysis outline.
You receive a clear, research-focused project roadmap.

[Request a Quote] or [Contact Us] today to discuss your study design and get started.

All services are provided for research use only.

If you are interested in exploring more liquid biopsy solutions, [click here] to learn about our full range of services.

Targeted EM-seq for Liquid Biopsy Research: Unlocking cfDNA Methylation Insights