Targeted Region Sequencing
What Is Targeted Region Sequencing?
Targeted sequencing and custom NGS panel sequencing, uses the power of Next-Generation Sequencing (NGS) to zero in on the exact genes, exons, or hotspots you need. At AUGenomics, we leverage hybrid capture sequencing (biotinylated probes that enrich selected DNA fragments) or amplicon sequencing (multiplex PCR primers designed for specific loci). This is accomplished by selecting only your regions of interest, washing away background DNA, and sequencing with ultra-deep coverage—often 500×–1,000× per base.
This cost-effective targeted NGS approach slashes unnecessary data volume, sequencing cost, and analysis time per sample compared to WES or WGS, while delivering the sensitivity required for low-frequency variant detection, mosaic mutation calling, and high-confidence biomarker discovery. Ideal for clinical diagnostics, cancer gene panels, and custom research panels, targeted sequencing supports multiplexing dozens to hundreds of samples in a single run and offers fully-customizable gene panel design.
At AUGenomics, we offer fully-customizable targeted sequencing panels designed to match your research goals, whether you’re validating known mutations, screening biomarker panels, or profiling key pathways.
Amplicon & Hybrid Capture:
What’s the difference?
Amplicon Sequencing
Amplicon sequencing is a targeted next-generation sequencing (NGS) method that focuses on specific regions of DNA amplified by PCR. It’s a fast, cost-effective, and high-sensitivity approach for detecting mutations, profiling microbial communities, or validating known genetic variants.
At AUGenomics, we offer flexible amplicon sequencing services for a wide range of applications, from clinical hotspot panels to environmental microbiome studies.
Hybrid Capture
Hybrid capture targeted sequencing leverages biotinylated DNA or RNA probes to selectively “pull down” hundreds of kilobases to megabases of genomic regions in a single reaction. Unlike amplicon-based methods, hybrid capture excels at large or complex panels, covering entire gene families, GC-rich exons, noncoding regulatory elements, and hotspot regions- all in one go. In practice, high-molecular-weight DNA is fragmented, ligated to sequencing adapters, then mixed with a custom probe set. Probe–target hybrids bind to streptavidin beads, non-target DNA is washed away, and the enriched library is PCR-amplified and sequenced to deliver uniform, ultra-deep coverage across every tile.
What Is Amplicon Sequencing Used For?
Amplicon sequencing is commonly used for:
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Mutation detection in targeted regions (e.g., cancer hotspots)
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Microbiome profiling (16S/18S/ITS)
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Viral or bacterial genotyping
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CRISPR editing validation
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Gene fusion detection and custom assay development
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Sample multiplexing for high-throughput screening
With scalable workflows and expert consultation, AUGenomics is your trusted partner for PCR-based targeted sequencing.
What Is Hybrid Capture Used For?
Hybrid capture panels power projects where breadth and depth matter, including:
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Comprehensive Disease-Specific Gene Panels: Detect SNVs, indels, CNVs, and fusion breakpoints (e.g., cancer hotspots, cardiomyopathies, immune disorders)
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Pharmacogenomics & Clinical Diagnostics: Profile dozens of drug-response and adverse-event loci (CYP, HLA, TPMT) with high confidence.
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Large-Scale Research Panels: Survey coding and noncoding elements in population studies, GWAS follow-ups, or custom pathway analyses.
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Rare Variant Discovery and ultra-deep coverage: Uncover low-frequency mosaic mutations or subclonal events in cfDNA and tumor biopsies.
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Non-Human & Model Organisms: Build custom reference panels for agricultural traits, conservation genomics, or novel model systems.
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Custom research panels designed for specific biological pathways or networks
Sample Submission Guidelines
For Amplicon Sequencing:
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Accepted Sample Types: Genomic DNA, cDNA, or amplicons (pre-PCR or post-PCR), from blood, saliva, microbial cultures, or environmental samples
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Input Requirement:
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≥10–50 ng of input DNA for most workflows
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Pre-validated primer pools also accepted
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Sequencing Recommendations:
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250–500 bp amplicons ideal for paired-end 2x150 or 2x250 reads
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Multiplexing available for up to 384+ samples
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Suitable for small- to mid-size panels (e.g., 5–500 targets)
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Please refer to our Shipping Guidelines for project-specific guidance.
For Hybrid Capture:
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Accepted Sample Types: Isolated cells, blood, saliva, buccal swabs, tissue, FFPE blocks, or extracted genomic DNA
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Input Requirement: ≥100 ng of DNA (≥1 ng for low-input workflows)
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Sequencing Recommendations:
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Coverage typically ranges from 500x to 1000x depending on region size and application
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Amplicon-based or hybrid capture panels available
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Up to hundreds of samples multiplexed per run
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Please refer to our Shipping Guidelines for project-specific guidance.
Turnaround Time
Our standard turnaround time is 10-14 business days from sample receipt, depending on panel size and sequencing depth. Expedited options are available for urgent timelines.
Frequently Asked Questions (FAQs)
Q: When should I choose targeted sequencing over WES or WGS?
A: If your research is focused on specific genes or regions, especially those already implicated in your study, targeted sequencing provides deeper coverage, faster analysis, and lower costs than whole exome or genome sequencing.
Q: Should we opt for amplicon-based or hybrid capture technology?
A: Amplicon‐based technology uses multiplex PCR to deliver ultra‐deep, uniform coverage for small panels (<100 kb), low‐input DNA, and rapid turnarounds. Hybrid capture technology enriches large or complex panels (hundreds of kb to Mb) with flexible design and uniform coverage across GC‐rich or repetitive regions for high-throughput projects.
Q: Can AUGenomics help design a custom gene panel?
A: Yes. We offer full support for panel design, from initial gene list consultation to probe synthesis and validation.
Q: What enrichment methods do you offer?
A: We support both amplicon-based and hybrid capture workflows depending on the size and complexity of your target regions.
Q: What on-target rate and uniformity can I expect?
A: Hybrid capture panels typically achieve ≥ 80% on-target reads with > 90% of bases covered at ≥ 0.2× the mean depth. Amplicon panels often exceed 95% on-target with highly uniform coverage.
Q: What’s the difference between WGS and WES (Whole Exome Sequencing)?
A: WGS captures the entire genomic sequence,including non-coding regions, intergenic areas, and regulatory elements; while WES focuses only on exons, which make up ~1–2% of the genome. WGS is more comprehensive but requires more data and cost.
Q: Can you perform shallow WGS for copy number variation (CNV) detection?
A: Yes, our shallow whole genome sequencing options are optimized for CNV and structural variant analysis.
Q: Do you support both human and non-human genome sequencing?
A: Absolutely. We offer WGS for human, animal, microbial, and plant genomes, including de novo assembly and reference-based workflows.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
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Targeted Sequencing: Sequencing focused on specific regions of the genome
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Hybrid Capture: Enrichment method using biotin-labeled probes to isolate genomic regions
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Amplicon: PCR-amplified DNA fragment used for targeted sequencing
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Hotspot Panel: A gene panel focusing on common mutation sites in disease genes
