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xGen® Pan-Cancer Panel

The xGen® Pan-Cancer Panel v1.5 consists of 7816 individually synthesized and quality controlled xGen Lockdown® Probes that allow enrichment of 127 significantly mutated genes implicated across 12 tumor tissue types to enable deeper coverage during sequencing.

Benefits

  • High uniformity across all targets
  • Short list of driver mutations relevant to multiple cancer types
  • Easily expanded by adding custom xGen® Lockdown® Probes
  • Can be spiked into Nimblegen or Illumina Exome capture kits to enhance sensitivity of cancer exome sequencing
  • Easy online ordering and next day shipping

Features

  • 7816 xGen® Lockdown® Probes targeting 127 genes
  • Individually synthesized and quality controlled probes
  • Targets defined by whole genome and exome sequencing of >3000 tumors from 12 cancer types
  • Validated with the xGen® Rapid Capture Protocol developed at IDT


xGen® Pan-Cancer Panel

The xGen® Pan-Cancer Panel v1.5 consists of 7816 individually synthesized and quality controlled xGen Lockdown® Probes that provide deep enrichment of 127 significantly mutated genes implicated across 12 tumor types.

ProductPricing
16 rxn xGen® Pan-Cancer Panel v1.5$2,400.00 USD
96 rxn xGen® Pan-Cancer Panel v1.5$14,400.00 USD

Introduction

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 [1]. 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 short list 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 [2].

IDT has developed the xGen® Pan-Cancer Panel, a hybrid capture panel that is based on the findings of the TCGA network, using xGen® Lockdown® Probes. Lockdown Probes are 120mer oligonucleotides bearing a 5′ biotin modification and manufactured using IDT Ultramer® synthesis technology.

References

  1. SEER Stat Fact Sheets: All Cancer Sites. National Cancer Institute. Surveillance, Epidemiology, and End Results Program. http://seer.cancer.gov/statfacts/html/all.html. (Accessed Feb 2014.)
  2. Kandoth C, McLellan MD, et al. (2013) Mutational landscape and significance across 12 major cancer types. Nature, 502:333–339.

Panel


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.]

Design Information

Complete Coverage Across All Targets

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).

High Coverage Uniformity

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.

Consistent Performance With High Reproducibility

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.

References

  1. Cancer Genome Atlas Research Network (2013) Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med, 368(22):2059–2074.