Targeted Region Sequencing
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CD Genomics has been providing the fast and affordable targeted region sequencing service for decades. We employ the state-of-the-art sequencing instruments to help you obtain full DNA information of the selected targets in a cost-effective manner, which can greatly increase both the breadth and the depth of your genomics research.
The Introduction of Targeted Region Sequencing
Targeted region sequencing is an effective approach for investigating your selected region(s) of interest by next generation sequencing. By utilizing targeted region sequencing panels, you can discover single-nucleotide polymorphisms (SNPs), insertions/deletions (InDels), copy number variations (CNVs), and structural variants (SVs). Compared with whole genome sequencing, targeted region sequencing enables accurate detection of rare variants with higher sensitivity and specificity. This approach is very cost-effective when handling a large number of samples, which significantly reduces the cost per sample.
The process of targeted region sequencing includes probes/primers designing/synthesis, target regions capture, library construction, paired-end sequencing, and bioinformatics analysis based on target sequences. Specific probe/primer sets are designed to enrich targeted regions using either hybridization or amplification methods. In the hybrid capture method, biotinylated oligonucleotide probes are designed to target regions of interest within a DNA fragment library. After a hybridization incubation, streptavidin-coated magnetic beads are used to capture the biotinylated probe/target hybrids, which results in a library that is highly enriched for the targeted DNA. The current amplification method relies on multiplex PCR or some form of primer extension across regions of interest.
The targeted region sequencing has a wide range of applications, including:
Detection of SNPs/InDels/CNVs/SVs
Discovery of germline or somatic mutations
Detection and quantification of rare variants and low-frequency alleles
Linkage analysis for inherited diseases
Discovery of biomarkers and therapeutic targets
Advantages of Targeted Region Sequencing
Identification of variants at low allele frequencies (down to 1%).
A smaller data set for bioinformatics analysis.
Much lower cost with a large number of samples.
High depth (500-1000X, or higher), allowing identification of rare variants.
Targeted Region Sequencing Workflow
CD Genomics employs Illumina HiSeq instruments to provide the fast and accurate targeted region sequencing and bioinformatics analysis. Our highly experienced experts execute quality management, following every procedure to ensure high quality results. The general workflow for targeted region sequencing is outlined below.
Service Specifications
Sample Requirements
DNA amount ≥ 10 ng, DNA concentration ≥ 1 ng/μl, OD260/280=1.8~2.0.
All DNA samples are validated for purity and quantity.
Note: Sample amounts are listed for reference only. For detailed information, please contact us with your customized requests.
Depth of coverage ≥ 100x; ≥ 500X is recommended for cancer samples.
More than 80% of bases with a ≥Q30 quality score.
Bioinformatics Analysis We provide customized bioinformatics analysis including:
Raw data quality control
Filtering and alignment
SNP/InDel/CNV/SV calling and annotation
Cancer somatic mutation analysis
Complex disease analysis
Mendelian disease analysis
De novo mutation analysis for family samples
DMR annotation and enrichment analysis (GO/KEGG)
More analyses upon your request
Note: Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.
Analysis Pipeline
Deliverables
The original sequencing data
Experimental results
Data analysis report
Details in Targeted Region Sequencing for your writing (customization)
CD Genomics provides full targeted region sequencing service package including sample standardization, probe/primer designing, targeted capture, library construction, deep sequencing, raw data quality control and bioinformatics analysis. We can tailor this pipeline to your research interest. If you have additional requirements or questions, please feel free to contact us.
Demo Results
Targeted Region Seq FAQs
1. What is the difference between whole exome sequencing and targeted region sequencing?
In spite of probably the same principle and workflow, whole exome sequencing focuses on exome while targeted region sequencing focuses on any genes that are defined by you.
2. What do I need to submit?
The customer who requires the targeted region service need submit the DNA or tissue samples, as well as the list of gene candidates or the chromosomal localization of your target region. We are responsible for the probes generation, target enrichment, library construction, sequencing, and bioinformatics analysis.
We accept the following sample types for targeted region sequencing: purified genomic DNA, PCR amplicons, frozen cell pellets, bacterial colonies, FFPE (formalin-fixed, paraffin-embedded) tissue sections, tissues, blood, and swabs.
3. How about the turnaround time?
The targeted region sequencing requires custom-made probes, and the custom-made probe need further optimization for an effective enrichment of target regions. It often takes 40 working days to complete the customization of probes and the deep sequencing. But there are commercial solutions for targeted region sequencing, such as the SeqCap EZ Prime Choice Probes, which can eliminate the process of the customization of probes.
4. How to validate variants?
Variants identified through the next-generation sequencing (NGS) require further confirmation using either NGS or Sanger sequencing. According to the survey did by Coppieters in September 2014, almost 70% of 178 respondents indicated that they are currently validating their NGS findings using NGS or Sanger sequencing. We will validate variants using NGS and Sanger sequencing.
Figure 1. A survey of the variant confirmation methods (Coppieters et al. 2016).
