What type of samples do you accept?

We accept high-quality genomic DNA, cfDNA, FFPE-derived DNA, or tissue-extracted DNA. Please refer to our sample requirements for minimum input and purity guidelines.

How is this different from whole-genome bisulfite sequencing (WGBS)?

This targeted panel focuses on >25,000 CpG islands (~20 Mb) instead of sequencing the entire genome, providing deeper coverage in regulatory regions with lower sequencing cost and data volume.

Can I use this service with mouse samples?

Yes. We support both human and mouse genomes. Our panel designs are species-specific and optimized for high CpG density regions in each genome.

What is the expected coverage and data output?

Each sample typically achieves 20–30× average coverage over target regions. Sequencing generates around 10 Gb per sample, depending on project setup.

Do you perform differential methylation and functional annotation?

Yes. We provide DMR detection, gene-based annotation, and GO/KEGG enrichment analysis with visualizations included in the final report.

What will I receive at the end of the project?

You'll receive clean sequencing data, alignment files, methylation tables, DMRs, enrichment results, and a detailed project summary—all organized for easy interpretation.

Is the analysis pipeline customizable?

Yes. While we offer a robust standard pipeline, we can adjust certain steps (e.g., thresholds, annotation strategies) based on your study design.

Can you help interpret the results?

Absolutely. Our bioinformatics specialists are available to assist with data interpretation, figure generation, and downstream integration upon request.

CpG Island Panel Sequencing for Human and Mouse - High-Resolution Methylation Profiling

High-Resolution Methylation Profiling of Regulatory Regions

CD Genomics offers targeted methylation profiling using a bisulfite-based capture panel covering over 2 million CpG sites across 25,000+ CpG islands in the human and mouse genomes—enabling precise, strand-specific methylation profiling in key regulatory regions.

Highlights:

Focused coverage of promoters, CGI shores, enhancers, and gene bodies
Single-base resolution using bisulfite-based, liquid-phase capture
Compatible with tissue DNA, cfDNA, and FFPE samples
Ideal for cancer epigenetics, developmental studies, and DMR analysis
A cost-effective alternative to WGBS with high data quality and reproducibility

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Illustration of DNA methylation showing a CpG island on a DNA strand, with CH₃ (methyl) groups attached to cytosine bases in the CpG sites.

Service Workflow

CpG Island Panel Sequencing Workflow – From Sample to Data

Our CpG Island Panel Sequencing service is designed to make your research process seamless—from low-input DNA to high-resolution methylation data.

1. Sample Preparation & Bisulfite Conversion

We accept cfDNA, FFPE, blood, and tissue samples. Genomic DNA is bisulfite-converted to distinguish methylated from unmethylated cytosines, with internal controls ensuring conversion accuracy.

2. Targeted Capture & Library Prep

Using our specialized panel, we enrich for over 2 million CpG sites across key regulatory regions including promoters, enhancers, and CpG islands. Strand-aware probe design ensures deep, consistent coverage.

3. High-Throughput Sequencing

Libraries are sequenced with paired-end 150 bp reads on Illumina platforms. The process is optimized for high specificity and uniform depth across ~20 Mb of methylation-rich regions.

4. Integrated Bioinformatics

Reads are processed, mapped to the reference genome, and analyzed to calculate site-specific methylation levels. Differential methylation and functional analysis are included in the full pipeline—details in the next section.

Consultation & Project Setup → Sample Submission → Bisulfite Conversion & Library Preparation → Sequencing & Quality Control → Data Analysis & Delivery

Bioinformatics

CpG Methylation Data Analysis: From Reads to Results

Comprehensive Methylation Data Interpretation from Base to Biology

Our CpG island panel sequencing service includes a full-featured bioinformatics workflow tailored for bisulfite sequencing data. From raw reads to differential methylation interpretation, we provide high-confidence outputs ready for downstream biological analysis and publication.

1. Data Quality Control

Low-quality read filtering
Adapter trimming
Quality assessment (Q20/Q30, GC content, duplication rate)

2. Genome Alignment

Mapping to reference genome (GRCh38 or mm10) using bisulfite-aware algorithms
Analysis of mapping efficiency, enzyme digestion bias, and sequencing depth

3. Methylation Information Extraction

CpG methylation level quantification (CG/CHG/CHH contexts)
Methylation state evaluation and non-conversion rate estimation
Motif identification and IGV-compatible visualization

4. Methylation Landscape Profiling

Methylation distribution across genome, chromosomes, and functional regions
Analysis of genomic elements: promoters, exons, introns, CGI shores
Multi-sample comparison and clustering

5. Differential Methylation Analysis

DMR (Differentially Methylated Region) detection
Functional annotation of DMR-linked genes
GO and KEGG enrichment analysis to interpret regulatory relevance

Deliverables

Deliverables – What You Will Receive

All the Data You Need – Clearly Organized and Research-Ready

Project Summary & Sample Metadata
Sequencing Quality Reports
CpG Methylation Profiling Results
Genomic Visualization Outputs
Inter-Sample Comparative Profiles
Differential Methylation Analysis (DMR)
Functional Enrichment Results
File Organization & Usability

Average Methylation Levels Across Samples

Chromosome-Wide Methylation Distribution

Methylation Distribution Across Genomic Features

Sample Correlation Analysis (Based on CpG Methylation Levels)

Average Methylation Levels in DMRs

IGV Visualization of DMR Regions

Genome-Wide Distribution of DMRs (Circos Plot)

Dot Plot of Enriched KEGG Pathways

Applications

Applications of CpG Island Panel Sequencing

Investigating Cancer-Associated Methylation

Aberrant DNA methylation in CpG islands—especially within gene promoters—is widely studied in tumor biology. Our panel enables researchers to:

Identify hypermethylated promoters in cancer-related genes
Explore methylation alterations across different tumor types or models
Study epigenetic patterns associated with gene silencing

Studying Developmental & Tissue-Specific Methylation

Epigenetic regulation is dynamic across developmental stages and tissue types. This platform helps:

Map methylation changes during differentiation or organogenesis
Compare methylation landscapes in various biological systems
Examine sex-specific or lineage-specific methylation variation

Profiling Regulatory Regions

Gene expression is influenced by methylation at regulatory sites such as promoters, enhancers, and CGI shores. This panel allows researchers to:

Detect differentially methylated regions (DMRs) associated with transcriptional activity
Measure methylation around transcription start sites, gene bodies, and upstream elements
Investigate regulatory region dynamics in normal and altered states

Analyzing Cell-Free DNA in Model Systems

Cell-free DNA (cfDNA) reflects epigenetic signatures from various tissues. With high coverage of CpG-rich regions, this panel supports:

Investigation of tissue-released DNA methylation in fluid-based samples
Comparative studies on methylation from different biological sources
Tracking methylation changes across experimental conditions

Building Methylation-Based Research Models

Methylation data provide informative features for integrative analysis and computational modeling. With our panel, researchers can:

Develop classification models to distinguish biological states or sample groups
Integrate CpG methylation profiles with transcriptomic or genomic data
Identify informative regions for epigenetic biomarker discovery in experimental studies

CpG Island Panel vs. WGBS and Arrays: What's the Difference

Choosing the right methylation profiling method depends on your research goals, sample type, and resolution needs. Here's how our targeted CpG island panel stacks up against WGBS and array-based platforms.

Feature / Method	CpG Island Panel Sequencing	Whole-Genome Bisulfite Sequencing (WGBS)	Methylation Arrays (450K / 850K)
Coverage Scope	~20 Mb focused on >25,000 CpG islands	Entire genome (~3 Gb)	~450K–850K fixed CpG loci
Target Regions	Promoters, enhancers, CGI shores & gene bodies	All CpG sites, including intergenic regions	Mainly promoters & high-density CpG loci
Resolution	Single-base, strand-specific	Single-base, genome-wide	Probe-based, limited resolution
Flexibility	Species-customizable panels (human/mouse)	Fully customizable, but resource-intensive	Fixed content, no customization
Data Volume & Cost Efficiency	Low-to-moderate sequencing burden	Very high sequencing and storage requirements	Cost-efficient but limited depth
Compatibility with Low Input / cfDNA	Excellent (cfDNA, FFPE, tissue)	Limited—requires high-quality, high-input DNA	Moderate, limited by probe accessibility
Bioinformatics Complexity	Streamlined for regulatory regions	Complex, large-scale methylome analysis	Predefined pipeline, less flexible
Typical Research Use Cases	Focused epigenetic studies, cfDNA research, DMR mapping in regulatory elements	Comprehensive methylome mapping, developmental biology, evolutionary epigenetics	Broad screening studies, population cohorts, large-scale methylation profiling

Sample Requirements

Sample Requirements for CpG Methylation Sequencing

Ensure High-Quality Results with Proper Sample Preparation

To help you get the most out of our CpG island panel sequencing service, please follow the sample submission guidelines below.

Sample Type	Requirements
DNA Source	Genomic DNA extracted from blood, tissue, cell pellets, cfDNA, or FFPE
Minimum Input	≥ 100 ng (for high-quality gDNA); cfDNA ≥ 10 ng recommended
Purity (OD260/280)	1.8–2.0 (measured by NanoDrop or equivalent)
Integrity	High molecular weight; DIN > 6 preferred (for gDNA); cfDNA should be intact
Elution Buffer	TE buffer or nuclease-free water (no EDTA)
Storage	DNA stored at –20 °C; ship on dry ice
Contaminants to Avoid	No protein, RNA, phenol, ethanol, or salt contamination

Advantages

Why Choose Our CpG Island Panel

Focused, Efficient, and Research-Ready

Our Human/Mouse CpG Island Panel is engineered to target the most biologically meaningful methylation regions—offering researchers a focused, high-resolution view of epigenetic regulation without the cost or complexity of whole-genome bisulfite sequencing (WGBS).

Extensive CpG Coverage

Covers >2 million CpG sites across more than 25,000 CpG islands (~20 Mb), including high-value regions like promoters, CGI shores, enhancers, and repeat elements based on UCSC, Ensembl, and ENCODE databaseshuman methylome 2M_repo….

Compatible with Challenging Samples

Supports cfDNA, FFPE, blood, and tissue samples with low input requirements—making it ideal for liquid biopsy, archived samples, or rare material studies.

Bisulfite-Based Precision

Our platform combines bisulfite conversion with liquid-phase capture for strand-specific, base-resolution methylation detection. CHH sites are used as internal controls to ensure >99% bisulfite conversion efficiencyhuman methylome 2M_repo….

Cost-Effective Alternative to WGBS

Gain deep coverage of regulatory regions without sequencing the entire genome—reducing data volume, improving analysis resolution, and cutting costs significantly.

Reproducible & Scalable

Validated across large sample sets with high mapping rates (up to 90%) and consistent performance in both male and female human samples

Backed by a team with deep epigenetics experience, CD Genomics supports your project every step of the way—with optimized workflows, responsive communication, and reliable data you can trust.

FAQs