Variant discovery with xGen Exome Hyb Panel v2
Whole exome sequencing (WES) is a targeted next generation sequencing (NGS) approach that uses modified oligonucleotide probes to “capture” and enrich the DNA sample for protein coding regions (exons). Focusing only on protein-coding genomic regions can lower the cost and time of sequencing, as exons make up approximately 1% of the genome but contain 85% of the variants that are associated with disease .
The xGen Exome Hyb Panel v2 consists of 415,115 probes that spans a 34 Mb target region (19,433 genes) of the human genome and 39 Mb of probe space—the genomic regions covered by probes. Our probes are designed using a new “capture-aware” algorithm and assessed with proprietary off-target analysis. All probes in the panel are manufactured under ISO13485:2016 standards, and then, mass spectrometry and dual quantification measurements of each probe are performed before they are pooled into the xGen Exome Hyb Panel v2. These measures ensure the quality of the probe and its appropriate representation in the final panel.
On-target coverage and uniformity of the xGen Exome Hyb Panel v2
To test the xGen Exome Hyb Panel v2, a singleplex and 12-plex capture of genomic DNA was done and the resulting fragments were sequenced to assess what percentage of reads were on-target (Figure 1). The same libraries were analyzed for uniformity (Figure 2). Approximately 95% of the reads were on-target for both singleplex and 12-plex, and greater than 97% of the target space had 20X coverage. Three other vendors were compared to the IDT xGen Exome Hyb Panel v2 for on-target coverage, and even though the panels were used according to their recommendations, the on-target percentage was lower than the 12-plex capture using the xGen Exome Hyb Panel v2.