xGen® Lockdown® Probes
XGEN-LOCKDOWN-MINIxGen® Custom Target Capture Probes(최소 주문수량 200개)Mini (1 rxn/probe)-로그인
XGEN-LOCKDOWN-STDxGen® Custom Target Capture Probes(최소 주문수량: 96개)Standard (8 rxns/probe)-로그인
XGEN-LOCKDOWN-XLxGen® Custom Target Capture Probes(최소 주문수량: 96개)XL (64 rxns/probe)-로그인
XGEN_PRE_GENEPROBE16[IDT]xGen® Predesigned Gene Capture Pool(최소 주문수량: 10 genes, gene 당 가격)16 rxn-로그인
XGEN_PRE_GENEPROBE96[IDT]xGen® Predesigned Gene Capture Pool(최소 주문수량: 10 genes, gene 당 가격)96 rxn-로그인

xGen® Lockdown® Probes

Target capture probe pools for NGS

Generate custom capture panels for targeted sequencing to enhance the performance of existing panels. Select from predesigned and custom probes.


  • Achieve higher performance with individually synthesized and quality-controlled capture probes
  • Develop custom panels with xGen Predesigned Gene Capture Pools or xGen Custom Target Capture Probes
  • Start your project sooner with a 7–10 day turnaround time


  • 5' biotin modified probes manufactured using our proprietary synthesis method with the highest coupling efficiency
  • Individually assessed by mass spectrometry for QC
  • Up to 2000 probes per pool; larger probe pools by request
  • xGen Predesigned Gene Capture Pools are available for any human RefSeq coding gene

Customized capture panels and probe spikes for existing panels

xGen® Lockdown® Probes are individually synthesized 5′-biotinylated oligos for target capture applications in next generation sequencing. xGen Lockdown Probes are produced using the same industry-leading, high-fidelity synthesis chemistry developed by IDT for our Ultramer® Oligonucleotides.

These probes can be used for creating custom capture panels that can be optimized, expanded, and combined with other panels. xGen Lockdown Probes can also be used to enhance the performance of existing capture panels, rescuing poorly represented regions such as areas of high GC content.


Create affordable custom capture panels against small target regions:
  • Develop specific sub-panels against target regions of interest
  • Achieve sufficient coverage depth to detect rare alleles
  • Sequence hundreds of samples cost effectively
  • Optimize, expand, or combine custom panels
Spike into array-derived baits to improve capture performance:
  • Rescue drop-out regions of array-derived exome captures or large captures
  • Improve uniformity of coverage across your target space
  • Discover more genetic mutations with high confidence
  • Selectively improve specific regions of interest without redesigning a new panel

Two types of probes for customized target capture panels

xGen Predesigned Gene Capture Pools

  • Target human coding regions only
  • Achieve more cost-effective enrichment than attainable with completely custom designs
  • Identify targets by gene symbols or gene IDs 
  • Select a minimum of 10 genes/target regions per entry

xGen Predesigned Gene Capture Pools are preconfigured probe designs available for all human gene coding sequences. These probes are the most cost-effective method for creating custom gene panels that at delivered quickest and at the most cost-effective price. Probe designs are generated using the same design engine used to create the xGen Pan-Cancer Panel, and use 1X tiling with repeat-masking. These probe sets have been demonstrated to provide ~5000-fold enrichment, high coverage over targeted regions, and minimal GC bias (see the Performance tab).

xGen Predesigned Gene Capture Pools are supplied either premixed in a single tube (16 or 96 reactions) or as individual gene pools delivered in 96-well plates (96 reactions only). With a minimum of 10 genes per pool, you are empowered to explore different panel compositions to identify the appropriate panel composition for specific projects. To include specific human non-coding sequences in your target capture panel, simply add xGen Custom Target Capture Probes.

xGen Custom Target Capture Probes

  • Design probes for any sequence in any species using your specified parameters for target definition, probe length, and tiling density
  • Use for human probe targets when Predesigned Gene Capture Pools do not match your criteria for design
  • Transition to high volume applications easily with 3 production scales
  • Use gene symbols, gene IDs, and BED files to identify human, mouse, and rat gene targets; the tools also accepts RefSeq accession numbers or FASTA-formatted sequences

xGen Custom Target Capture Probes are custom designed probe pools for specialized targeting (e.g., non-coding regions such as promoters and UTRs), and for targeting non-human species. The specialized design and synthesis of these custom probe pools may come at a higher cost compared to xGen Predesigned Gene Capture Pools.

Selecting your probes

Use the xGen Lockdown Design Tool (Order tab) to select target region probe pools for your customized target capture panels. The Design Tool will default to the more economical xGen Predesigned Gene Capture Pools. Using target input formats other than gene symbols or gene IDs, and/or changing the Custom Design Parameters, will allow you to select xGen Custom Target Capture Probes.

You can, of course, create your own customized targeting panel with a mixture of xGen Predesigned Gene Capture Pools and xGen Custom Target Capture Probes; e.g., create an order for 50 xGen Predesigned Gene Capture Pools, then add a second order for several xGen Custom Target Capture Probes to target UTRs of a subset of those genes.

High Target Coverage

xGen Lockdown Probes provide approximately 5000-fold enrichment, high coverage over targeted regions (Figure 1), and minimal GC bias.

Figure 1. xGen Lockdown Probes Yield High Coverage.
Ligation-based sequencing libraries were amplified by PCR using HiFi DNA polymerase (Kapa Biosystems). A set of 1000 xGen Lockdown Probes spanning the targeted region was used for in-solution hybrid selection with 2 µg of library input. Hybridization was performed for 24 hr and enriched targets were sequenced on a HiSeq 2000 System (Illumina) using 49 x 49 paired-end reads. The Lockdown Probes provided greater coverage than array/RNA baits.

Improve Coverage of Array-Synthesized Baits

xGen Lockdown Probes can be added to array-derived RNA baits to enhance the coverage of GC-rich targets, such as first exons (Figure 2).
Figure 2. Spiking In Individually Synthesized Oligonucleotide Baits Improves Sequencing Coverage of Array-Derived RNA Baits. Individually synthesized 5′-biotinylated Ultramer® Oligonucleotides (xGen® Lockdown® Probes) were spiked into commercial, array-synthesized RNA baits to improve coverage of areas with high GC content. Either (A) 1000 Ultramer oligo baits targeting a ~133 kb region, or (B) 3 Ultramer oligo baits targeting a single exon, were mixed with 1.1 MB RNA baits and hybridized for 24 hr, followed by target capture using streptavidin. Enriched targets were sequenced on a HiSeq 2000 system using 49 x 49 paired-end reads. Lockdown probes improved general coverage of GC-rich targets (A) and single GC-rich exons (B).


Additional reference protocols

  1. Nijman IJ, Mokry M, et al. (2010) Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples. Nat Methods, 7(11):913–915. A protocol for genomic enrichment of pooled barcoded samples using a single assay that increases experimental flexibility and efficiency. Identified known variants in N-ethyl-N-nitrosourea–mutagenized rats at >96% sensitivity.
  2. Harakalova M, Mokry M, et al. (2011) Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing. Nat Protoc, 6(12):1870–1886. An efficient protocol for parallel library preparation and targeted enrichment of pooled multiplexed barcoded samples that is compatible with both microarray- and solution-based capture methods. The protocol enables multiplexing of 3–5 samples for whole-exome experiments and up to 96 samples for targeted sequencing.

Number of reactions and resuspension volumes


  1. Centrifuge tubes before opening to ensure probes are at the bottom of the tube.
  2. Resuspend probes in IDTE, pH 8.0 (Catalog No. 11-01-02-05) according to the calculator below.
    • Choose 1X or 50X based on your tube size.
    • Before use, dilute 50X probe solutions to 1X probe solutions.

      For example, add 5 µL of 50X probe solution to 245 µL of IDTE, pH 8.0.

  3. Store at –20°C.

    If necessary, aliquot probes to limit freeze-thaw cycles.

Lockdown® Probes scale:    
Number of probes:      probes
Number of reactions available:    0 reactions
Resuspension volume for 1X:    0 µL
Resuspension volume for 50X:    0 µL

Posters, application highlights, and related articles


Application highlights

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