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xGen™ Custom Amplicon Panels

Targeted sequencing of your most important genes

Tailored to meet your research needs, custom amplicon panels offer a completely curated targeted sequencing workflow to interrogate genomic targets relevant to you.

xGen NGS—made to discover.


  • Multiplex hundreds to thousands of targets in a single tube PCR
  • Compatible with low-input samples using 2-hour workflow
  • xGen Normalase™ compatible: Supports high throughput library quantification in a single enzymatic reaction
  • Designed for researching germline and somatic variants, or targeted pathogen sequencing
  • Provides high on-target and coverage uniformity
  • Support available to help design your panel

xGen Custom Amplicon Panels

This technology enables design of custom panels for targeted sequencing, offering a completely curated, targeted NGS workflow to rapidly interrogate genomic targets relevant to your research.

xGen Custom Amplicon HS Panel

This technology enables low-frequency variant identification ≤1% through the incorporation of molecular identifiers (MIDs or UMIs), to promote improved sensitivity and specificity by removing false positive errors introduced during PCR and sequencing.

Create designs for custom amplicon panels 

To submit a design request, use the form and template.

Design Request

Order my design 

Upload predesigned sequences using the form.

Order Request

Any xGen Custom Amplicon Panel (HS included) will require a custom part number to be generated at point of order.

For customers who wish to purchase the legacy rhAmpSeq™, please contact us today.

Product details

xGen Custom Amplicon Panels are custom-designed primer pools to create multiple overlapping amplicons for specific genetic targets in research studies (Figure 1). Panels can multiplex hundreds to thousands of targets in a single tube using a simple 2-hour workflow (Figure 2). Compatible with cell-free DNA and FFPE (formalin-fixed paraffin embedded) research samples starting with as little as 10 ng input or pathogen RNA/DNA in the picogram range. For a listing of the specifications for custom panels, see Table 1. If multiple libraries are being examined at the same time, the final NGS library can be normalized using the IDT proprietary xGen Normalase reagent.

The cost-effective and flexible custom design means the panel can be used for research applications such as:

  • Genotyping by sequencing
  • Variant detection with a limit of detection down to 1%
  • Detecting germline inherited SNPs and indels
  • Somatic cell variant detection
  • Targeted virus or pathogen sequencing
  • Genetic fingerprinting
  • Liquid biopsy

Figure 1. xGen Custom Amplicon Panels are used to create targeted NGS libraries for research studies. Whether you need to examine hundreds or thousands of targets, the xGen Custom Amplicon Panels can be tailored to your specific research needs. Once created, the panel is used in a simple, one-tube workflow that is compatible with high-throughput applications.

Table 1. Product specifications of the xGen Custom Amplicon Panels

Feature Specification
Input DNA range 10–25 ng of amplifiable DNA
Amplicon size Versatile size for compatibility with many research sample types: whole blood, cell culture, FFPE, cfDNA (default maximum is 150 bp)
Custom design coverage >90% of requested bases
Workflow time Single-tube with 2-hour DNA-to-library workflow
Components provided Custom primer pool
Limit of detection As low as 1% allele frequency for variants
Panel size range 15–1500 amplicons per panel; other options available upon request
Library multiplexing capability Depends on type of indexing primers used
On-target %>90% on-target reads
Coverage uniformity >80% coverage uniformity at a >0.2 of mean depth
Compatible platforms Illumina®


Simple, 2-hour workflow

From DNA to NGS library in as little as 2 hours, the workflow for the xGen Custom Amplicon Panels can be done in a single tube with minimal hands-on steps. As shown in Figure 2, the DNA sample is first amplified with the multiplex custom panel to create copies of each of your intended targets. Then the amplicons are converted into indexed libraries in a second PCR reaction with the appropriate indexing primers for your NGS instrument. When multiple libraries are pooled, IDT-proprietary xGen Normalase reagent is used to normalize the libraries for NGS analysis.

Figure 2. xGen Custom Amplicon Panels have a single tube workflow that is done in as little as 2 hours. Creating an NGS library starts with multiplex PCR. Your custom panel is combined with the DNA sample to amplify the targets of interest. The samples are then amplified with indexing primers to create a functional dual indexed library. As an optional step, the xGen Normalase reagent can be used after pooling multiple libraries to ensure each is equally represented in the final sample for the flowcell.


Frequently asked questions