Introduction

Targeted Bisulfite Sequencing (TBS) is a high-resolution, cost-effective approach for analyzing DNA methylation within predefined genomic regions. By focusing on CpG islands, gene promoters, enhancers, and other regions of interest, TBS delivers accurate methylation profiling while significantly reducing sequencing costs compared to whole-genome approaches. It is an ideal solution for biomarker validation, targeted epigenetic studies, and large-scale methylation screening.

How Targeted Bisulfite Sequencing Works

Targeted Bisulfite Sequencing combines bisulfite conversion with targeted enrichment to measure DNA methylation at single-base resolution.

Depending on the study design, target regions are enriched using:

• • Hybridization-based capture with custom or pre-designed probe panels

• • Multiplex PCR amplification using bisulfite-specific primers

Following enrichment, sequencing is performed on Illumina platforms, enabling highly accurate quantification of methylation levels across selected genomic loci.

Advantages of Targeted Bisulfite Sequencing

• • Single-base resolution DNA methylation analysis
• • High sensitivity and accuracy for targeted regions
• • Cost-effective alternative to whole-genome methylation sequencing
• • Simultaneous detection of methylation patterns and sequence variants
• • Flexible custom panel design for genes or pathways of interest
• • Ideal for large sample cohorts and validation studies

Applications

• • DNA methylation biomarker discovery and validation
• • Gene regulation and epigenetic research
• • Cancer and disease epigenetics
• • Clinical and translational research
• • Plant and animal breeding studies
• • Population-scale targeted methylation analysis

Targeted Bisulfite Sequencing Workflow

Our streamlined workflow ensures reliable and reproducible methylation profiling from sample preparation to data analysis.

• Genomic DNA extraction and quality assessment

• Bisulfite conversion of genomic DNA

• Target enrichment using multiplex PCR or hybridization capture

• Library preparation with barcode indexing

• High-throughput sequencing on Illumina platforms

• Bioinformatics analysis, methylation calling, and comprehensive reporting

Service Specifications

	Sample requirements and preparation Samples sources including human, animals, plants and microorganisms Genomic DNA: Recommended Quantity≥500 ng; Minimum Quantity: 50 ng concentration≥10 ng/µl, OD260/280=1.8~2.0 Cell : Recommended Quantity≥1×106 Tissue : Recommended Quantity≥ 20 mg Sample preparation protocol probably include genomic DNA extraction, purification, quantification, QC, etc.
	Sequencing Illumina HiSeq platforms, paired-end 150 bp More than 80% of bases with a ≥Q30 quality score Sequencing depth > 100X
	Data Analysis We provide multiple customized bioinformatics analyses: Raw data statistics Alignment against reference genome Methylation site prediction & CG, CHG, CHH categorization Estimation of DNA methylation level and distribution trend 5mC level in different gene structural elements Identification of differential methylated regions Function annotation of the proximate genes near differential methylated regions Multi-sample methylation differential analysis

Analysis Pipeline

Deliverables

• • The original sequencing data
• • Experimental results
• • Data analysis report
• • Details in Targeted Bisulfite Sequencing for your writing (customization)

1. When should I choose Targeted Bisulfite Sequencing?

Targeted Bisulfite Sequencing is the ideal choice when you need high-resolution DNA methylation analysis of specific genomic regions rather than the entire genome. It combines bisulfite conversion with targeted enrichment and next-generation sequencing to deliver single-base resolution methylation profiling. This approach is particularly useful for biomarker validation, candidate gene studies, and confirming results obtained from WGBS, RRBS, or MeDIP-Seq.

2. What are the advantages of Targeted Bisulfite Sequencing over other methylation sequencing methods?

Targeted Bisulfite Sequencing provides a cost-effective alternative to whole-genome methylation analysis by focusing only on regions of interest. Compared with WGBS, it significantly reduces sequencing costs while maintaining high accuracy. It also offers broader target flexibility than RRBS and enrichment-based methods, making it well suited for large cohort studies, targeted methylation profiling, and validation of disease-associated biomarkers.

3. How are probes or primers designed for Targeted Bisulfite Sequencing?

Successful targeted methylation analysis depends on carefully designed probes or bisulfite-specific primers. Target regions are selected based on the study objectives, followed by computational design and experimental validation to ensure high specificity, efficient amplification, and reliable methylation detection. Custom probe and primer panels can be developed for virtually any genomic region of interest.

4. What is the workflow of Targeted Bisulfite Sequencing?

The typical Targeted Bisulfite Sequencing workflow includes:

• Genomic DNA extraction and quality assessment

• Bisulfite conversion of DNA

• Target enrichment using multiplex PCR or hybridization capture

• Library preparation with barcode indexing

• High-throughput sequencing on Illumina platforms

• Bioinformatics analysis, methylation calling, and comprehensive reporting