xGen® Exome Research Panel v1.0

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 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.

Advantages

  • Obtain consistent results with individually synthesized target capture probes manufactured to GMP standards.
  • Minimize the need for further analysis with deep and uniform coverage.
  • Effortlessly integrate with common sequencing platforms including Ion Torrent™ and Illumina sequencers.
  • Generate your results quickly with 4 hour hybridization.


xGen® Exome Research Panel v1.0

The xGen Exome Research Panel v1.0 consists of 429,826 individually synthesized and quality controlled xGen Lockdown® Probes—spanning a 39 Mb target region and covering 51 Mb of end-to-end tiled space.

ProductPricing
16 rxn xGen® Exome Research Panel v1.0€ 3.600,00 EUR
96 rxn xGen® Exome Research Panel v1.0€ 18.000,00 EUR

Introduction

Exome sequencing is invaluable in both clinical and research settings for sequencing only the coding regions of the human genome. Exons represent only 3% of the human genome, making it critical to have an effective method of separating these regions from non-coding DNA to focus sequencing efforts on the regions of interest. The captured material must also be suitable for sequencing to a satisfactory depth of coverage.

The xGen® Exome Research Panel consists of 429,826 xGen Lockdown® Probes that span a 39 Mb target region (19,396 genes), covering 51 Mb of end-to-end tiled space. These 5′ biotin–modified oligonucleotide probes are individually synthesized, individually analyzed by electrospray ionization mass spectrometry (ESI-MS) and OD measurement, and then normalized before pooling to ensure that each probe is represented in the panel at the correct concentration. Probes that fail quality control are documented and 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.

Design Information

Exome panel comparison study

Independent analysis from a large genome center demonstrates superior performance of the xGen® Exome Research Panel compared to other vendors’ panels


Consistent performance with excellent reproducibility

Figure 1. Consistent Results from xGen® Exome Research Panel. Three users independently performed three capture experiments on different days. Each user prepared DNA libraries according to their preferred method, using well characterized Coriell Cell Repository cell lines. For each capture, 500 ng barcoded library, xGen Universal Blocking Oligos, and 5 µg Cot-1 DNA® were used. Hybridization, washes, PCR amplification, and QC were performed according to the xGen Rapid Capture Protocol v2.1. The data show that the percentage of unique, uniquely mapping, and paired reads mapped to targeted exons (aligned) or also within 150 bp of (flanking) targeted exons (padded) was consistent between users (n = 3 per group; Kruskal-Wallis: aligned p = 0.73, padded p = 0.19). The median percentage of mapped reads on target (aligned) was 83.4%, 86.0%, and 84.1% for Users 1, 2 and 3, respectively. The median percentage of reads mapped to targeted exons and also flanking targeted exons (padded) was 92.4%, 94.1%, and 94.1% for Users 1, 2 and 3, respectively. Bars represent median percent of mapped reads on target. Error bars are S.E.M.

Deeper coverage for exome sequencing

Figure 2. Deep Coverage of Human Gene Coding Sequences with the xGen® Exome Research Panel. DNA from 9 fragmented library samples was enriched for exon sequences using the xGen Exome Research Panel. Captured, adapter-ligated samples were sequenced in pools of 3 on a NextSeq® system (Illumina). To represent typical research practice, a random set of 50 million reads for each sample was mapped to the human genome (hg19). The percentage of bases in probe-targeted exons covered by unique and uniquely mapping (aligned) reads at the listed depths are shown. The median percentage of target bases covered at 2X, 10X, 20X, and 30X was 98.9%, 98.7%, 98.2%, and 96.3%, respectively. Bars represent median percent coverage. Error bars are S.E.M.

Uniform coverage with varying GC content

Figure 3. Uniform Coverage of GC-Rich Regions. Nine fragmented library samples were enriched for exon sequences using the xGen Exome Research Panel. Captured, adapter-ligated samples were sequenced in multiples of 3 on a NextSeq® system (Illumina). A random set of 50 million reads for each sample was mapped to the human genome (hg19). Average, log2 transformed, normalized probe coverage depth for all 9 samples shows even coverage with varying GC content. Hotter colors represent a higher probe density.