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xGen® Exome Research Panel

Deep, uniform coverage of the human exome with best-in-class capture panel

The xGen Exome Research Panel v1.0 consists of 429,826 individually synthesized, and quality controlled xGen Lockdown® Probes. The Exome Research Panel spans a 39 Mb target region (19,396 genes) of the human genome and covers 51 Mb of end-to-end tiled probe space. All probes in the panel are manufactured using GMP standards. Mass spectrometry and OD measurements are taken for each probe to ensure appropriate representation of the correctly manufactured probes in the pool.

  • Obtain consistent results with individually synthesized target capture probes manufactured to GMP standards
  • Achieve deep and uniform coverage even across difficult GC-rich regions
  • Integrate with common sequencing platforms

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xGen Exome Research Panel v1.0

Exome sequencing is invaluable for sequencing only the coding regions of the human genome. With exons representing only 3% of the genome, it is critical to have an effective method of separating these regions from non-coding DNA to focus on potentially important mutations implicated in disease. The captured material must also be suitable for sequencing to a satisfactory depth of coverage for reliable detection of variant alleles.

The xGen Exome Research Panel consists of 5′ biotin–modified oligonucleotide probes that are individually synthesized and individually analyzed by electrospray ionization mass spectrometry (ESI-MS) and OD measurement. The probes are then normalized before pooling to ensure that each probe is represented in the panel at the correct concentration. Probes that fail quality control are resynthesized. This rigorous manufacturing process gives the xGen Exome Research Panel a unique advantage over array-derived pools, in which missing or truncated probes cannot be identified before sequencing. Using IDT proprietary synthesis methods, even probes with high GC and AT content are appropriately represented in the panel.

To provide increased depth of coverage and enable high multiplexing of samples, the xGen Exome Research Panel targets only the coding sequences (CDS) of human coding genes in the RefSeq database.

Superior on-target coverage and uniformity

Figure 1. Highest on-target performance is achieved by xGen Exome Research Panel. Sequencing libraries were prepared using standard shearing and ligation-based library preparation, and then pooled into a 12-plex. The 12-plex pool was split into four 6 µg aliquots to assess each vendor’s exome panel. Target capture was performed according to each vendor’s recommended protocol. Enriched libraries were sequenced on a HiSeq® 2500 instrument (Illumina) in high output mode using 2 x 100 paired-end reads. On-target bases were determined with Picard (selected bases), using 35M reads per library.

Excellent coverage of RefSeq database with minimal sequencing

Figure 2. Most uniform coverage of exome achieved with xGen Exome Research Panel. (A) Coverage of exons 1 and 2 of RB1 shows that the xGen Exome Research Panel is the only panel to efficiently capture first exons. The xGen exome panel displays no decrease in first exon coverage with increasing sequencing depth. (B) The xGen Exome Research Panel provides the most complete end-to-end gene coverage using 100M reads.

Figure 3. Coverage profile of xGen Exome Research Panel most closely resembles whole genome data. A comparison of coverage depths of different exome panels to coverage depth from whole genome sequencing (WGS) of a matched library shows that the xGen Exome Research Panel provides the closest match to WGS. Analysis of GC content shows that the higher coverage of the xGen panel is driven by the more effective capture of GC content.