Oncology Research

ACE Extended Cancer Panel for DNA 2017-08-29T18:27:57+00:00

Overview

Maximize the potential of your novel cancer drug candidates with advanced genomics and analytics. We offer comprehensive NGS assays that enable you to mine retrospective data to better understand mechanisms or resistance, to perform exploratory research to identify the next generation of targets, and much more:

  • Gain deeper insights into your product’s mechanism of action

  • Leverage advanced analytics to investigate mechanisms of resistance

  • Demonstrate product differentiation

  • Determine rational drug combinations

The ACE Extended Cancer Panel covers a core set of over 1,400 cancer-related genes including clinically actionable* genes and genes that have been identified in the literature. It provides robust coverage of gene pathways and functions known to be involved in cancer biology and can be used to identify SNVs, indels, copy number alterations and gene fusions. The accuracy of the ACE Extended Cancer Panel has been enhanced by augmenting and repairing coverage gaps, especially in regions with high-GC content. This approach results in the characterization of genes with more complete coverage.

*Genes referred to here as being clinically actionable reflects the fact that the efficacy of cancer drugs, FDA approved or in clinical trials, are thought to be modulated by variants in these genes. This does not imply that this panel is for clinical use – it is a Research Use Only service.

Technical Details
Genes covered >1,400
Depth of sequencing >500x
Assay sensitivity >99%
Assay specificity (PPA) >99%
Sample source FFPE, fresh frozen, fine needle aspirates, PBMCs
Analysis configuration Tumor only or paired tumor and normal

Related Assets:

The ACE Extended Cancer Panel for RNA provides unparalleled detection of unique variant types that are not identifiable by DNA sequencing analysis alone. The assay identifies gene expression levels, gene fusions, SNVs and indels in over 1,400 cancer-associated genes.  This panel enables extensive gene fusion discovery of both clinically actionable* fusions involving critical genes such as ALK, ROS1, RET, and novel fusions involving other targeted genes that might be missed with DNA analysis alone.

Personalis’ targeted approach to RNA sequencing provides researchers with higher quality RNA results compared to those achieved by conventional transcriptome sequencing practices. We accomplish this by focusing only on genes related to cancer biology (by excluding intronic RNA from unspliced transcripts) and by using a capture method that can isolate degraded RNA better than other methods. This results in higher quality RNA reads with minimized background.

Technical Details
Genes covered >1,400
Sequencing configuration Paired-end
2x 125 bp
Sample source FFPE, fresh frozen, fine needle aspirates, PBMCs
Analysis configuration Tumor only

Related Assets:

 

Using our patented ACE Technology, the ACE Cancer Exome outperforms conventional exome assays by augmenting coverage across intronic and difficult-to-sequence (high-GC content) regions, ensuring the capture of variants that would be otherwise missed.

Key features:

  • Even coverage across all exons (>20,000 genes) and enhanced coverage of >8,000 biomedically-important genes, including >1,400 cancer-related genes.
  • Augmentation and repair of coverage gaps, especially in high-GC regions.
  • Somatic variant detection of SNPs, indels, and CNVs.
  • Sample sparing protocols for all cancer sample types, including challenging sample types such as FFPE, fresh frozen, FNAs, and PBMCs.
Technical Details
Genes covered >20,000
Genes augmented >8,000 biomedically important genes, including >1,400 cancer-related genes
Sequencing depth ≥100x (tumor)/≥65x (normal)
Sample source FFPE, fresh frozen, fine needle aspirates, PBMCs
Analysis configuration Tumor only or paired tumor and normal

Related Assets:

The same accuracy and coverage enhancements demonstrated by the ACE Cancer Exome (see above) are also incorporated into RNA analysis using our ACE Cancer Transcriptome enrichment protocol.

Many clinical studies depend on tissue archives that have been fixed using FFPE procedures. This preservation process makes it difficult to obtain a pure sample and often leads to RNA degradation. To overcome this challenge, Personalis has developed an exome-capture transcriptome protocol based on our ACE Technology that allows us to produce high-quality transcriptome sequencing results from challenging FFPE samples.

Key features:

  • Multiple probes target each transcript, capturing transcripts even when the poly-A tail is lost due to RNA degradation, making it ideal for cancer FFPE samples.
  • Sequencing protocol demonstrates that >95% of the bases are mapped within the coding and UTR regions of the RNA.
  • Fusion detection and gene expression analysis.
  • Sample sparing protocols for all cancer sample types, including challenging sample types such as FFPE, fresh frozen, FNAs, and PBMCs.
Technical Details
Genes covered >20,000+
Genes augmented >8000 biomedically important genes, including >1,400 cancer-related genes
Sequencing configuration Paired-end 2×125 bp
Sample source FFPE, fresh frozen, fine needle aspirates, PBMC
Analysis configuration  Tumor only

Related Assets:

DNA Analysis RNA Analysis
  • Raw data files: FASTQ, BAM files
  • Somatic variant (SNVs, indels) analysis and report: VCF file
  • Somatic CNV Reports and Plots
  • LOH Reports and Plots (exome only)
  • Somatic variant annotation: VAR file
  • Filtering and annotation of variants by cancer relevance and frequency
  • Quality Control report and Statistical Summary Report
  • Raw data files: FASTQ, BAM files
  • Variant (SNVs, indels) analysis: VCF file
  • Gene-associated variant analysis with additional filtering by cancer relevance
  • Fusion gene analysis and report
  • Gene-based expression results
  • Quality Control report and Statistical Summary report