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
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.
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 – 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
Applications of CpG Island Panel Sequencing
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
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
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
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
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 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 |
Why Choose Our CpG Island Panel
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).
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….
Supports cfDNA, FFPE, blood, and tissue samples with low input requirements—making it ideal for liquid biopsy, archived samples, or rare material studies.
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….
Gain deep coverage of regulatory regions without sequencing the entire genome—reducing data volume, improving analysis resolution, and cutting costs significantly.
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.