Enrich for genes implicated in several cancers
The xGen Pan-Cancer Panel v1.5 consists of 7816 xGen Lockdown Probes, spanning 800 kb of the human genome, for
Every year, ~500 people in every 100,000 are diagnosed with cancer. Of these, 34% will not survive past five years. Cancer resulted in more than 500,000 deaths in 2013 alone . Next generation sequencing has enabled the discovery and characterization of gene-specific mutations that have the potential to be tumorigenic; however, the technology also implicates a large number of genes that are not relevant to an individual’s cancerous state. A shortlist of mutated genes that are relevant to a multitude of cancer types, and that can be expanded to include additional cancer type–specific genes, would be invaluable in clinical and research applications. The Cancer Genome Atlas (TCGA) network performed a systematic analysis of more than 3000 tumors from 12 cancer types to investigate underlying mechanisms of cancer initiation and progression and have identified 127 significantly mutated genes (SMGs) across these tumor types .
The xGen Pan-Cancer Panel is a hybrid capture panel based on the findings of the TCGA network. The panel comprises xGen Lockdown Probes, individually synthesized and quality controlled 120mer oligonucleotides bearing a 5′ biotin modification and manufactured using proprietary Ultramer® synthesis technology.
Figure 1. Significantly mutated genes across 12 cancer types. 127 genes found to be significantly mutated in 12 cancer types are shown organized by gene pathway. The percentage of samples that contain the mutated form of the gene is shown for each of the cancer types. The highest percentage for each cancer type is shown in bold text. [Source: Kandoth, et al. (2013) Nature 502:333–339.]
Figure 1. Complete coverage across all targets using the xGen Pan-Cancer Panel. Uniformity of coverage for 2 replicate captures using the xGen Pan-Cancer Panel were compared. The panel achieved 97% of all targets covered at ≥30X with only 1M reads on the Illumina MiSeq® Sequencing System (300-base paired-end reads).
Figure 2. Excellent uniformity of coverage obtained with xGen Pan-Cancer Panel. The uniformity of coverage of targeted regions is represented as the proportion of targets with >0.2 x mean coverage (blue), >0.5 x mean coverage (green) and >1.0 x mean coverage (grey). The data demonstrate that with a mean coverage depth of 100X, 99.9% of the targets captured using the xGen Pan-Cancer Panel will have >20X depth of coverage. Sequencing was performed on the MiSeq System (Illumina) using 2 x 150 paired-end reads.
Figure 3. Consistent performance and high reproducibility with xGen Pan-Cancer Panel. A comparison of target-by-target coverage between 2 sample replicates captured using the xGen Pan-Cancer Panel shows excellent reproducibility, with an R2 value of 0.9013, demonstrating the consistent, high performance of the panel. The data shown are from 1M reads obtained by sequencing on the MiSeq System (Illumina) using 2 x 150 paired-end reads.