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

xGen Lockdown Probes

Individually quality controlled capture probes for targeted sequencing

xGen Lockdown Probes are individually synthesized and quality controlled 5-biotinylated probes for hybridization capture target enrichment in next generation sequencing.

  • Achieve higher performance with individually synthesized and quality-controlled capture probes
  • Develop cost-effective custom panels that are delivered quickly
  • Optimize, expand, or combine custom panels

xGen Lockdown Probes


Minimum Order

Mini (1 rxn/probe)

200 probes

Standard (8 rxns/probe)

96 probes

XL (64 rxns/probe)

96 probes

xGen Lockdown Probes are individually synthesized 5-biotinylated oligos for hybridization capture enrichment in next generation sequencing. xGen Lockdown Probes are produced using the same industry-leading, high-fidelity synthesis chemistry developed for 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.

With xGen Lockdown Probes, you can:

  • 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 xGen 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 Predesigned Gene Capture Pools

Preconfigured probe pools designed to target human gene coding sequences for cost-effective custom panels.

xGen Predesigned Gene Capture Pools contain individually synthesized Lockdown Probes pre-formulated into individual gene pools for easy selection and setup of custom target panels.

  • Generate deep and uniform coverage data through superior hybridization capture performance
  • Choose only the genes you want, delivered quickly with a choice of formats
  • Obtain full exon coverage for a given gene with each gene pool design

 xGen Predesigned Gene Capture Pools

Reaction Size (Rxn)

Minimum Order

16 rxn

10 Genes

96 rxn

10 Genes

xGen Predesigned Gene Capture Pools are preconfigured probe designs available for all human gene coding sequences. These probe pools are the best choice for creating cost-effective, custom gene panels that are delivered quickly. Probe designs are generated using the same design engine used to create the xGen Exome Research Panel, and use 1X tiling with repeat-masking. These probe sets have been demonstrated to provide high target region coverage and uniformity and minimal GC bias (see the Performance tab).

xGen Predesigned Gene Capture Pools are designed using the GRCh37/hg19 reference genome and are available for any human RefSeq coding gene. Enter your target gene symbols into the xGen Lockdown Design Tool and receive your panel in 7–10 days. The 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 can explore different panel compositions to identify the appropriate panel composition for specific projects. To include specific non-coding sequences in your target capture panel, simply add custom xGen Lockdown Probes.

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 –20C.

    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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