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FFPE Sections

Base-Seq | Sanger Sequencing & qPCR

Identify and Control Variability within your Assay

View Base-Seq HDx™ Reference Standards for Sanger & qPCR Sequencing

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FFPE-derived Reference Standards are ideal tools used to test the full integrity of a molecular assay workflow from extraction through to quantification to molecular testing and data analysis.

Laboratories often assume that a failed assay is as a result of a failed analytical step, however root cause analysis often shows that problems with DNA extraction or issues with DNA quantification are really at fault (e.g. over-estimating sample DNA concentration leading to the assay being under loaded). Analyzing the cause of a failed assay is a particular challenge for laboratories not used to handling FFPE samples, or for laboratories using quantification methodologies that tend to overestimate the amount of DNA in a sample when measuring concentrations below 20 ng per microliter (e.g. NanoDrop).

Mutant cell lines embedded in FFPE are all heterozygotes, and in the majority of cases this means there is a single mutant allele and a single normal allele. Where the copy number is 2N, a 100% mutant gDNA sample indicates that 100% of the cells the DNA was extracted from contained the mutation, however as only one of the two copies of the gene from that cell will actually contain the mutation, the sample actually will have an allelic frequency of 50% for that mutation. Mutant and “normal” cell lines can be precisely blended to generate samples with specific allelic frequencies typically ranging between 1% and 50%.


  • Pre-configured reference standards are available to order at allelic frequencies of 5-10% and 50% for most genotypes
  • Custom standards can be generated using either Horizon cell lines or cell lines appropriately sourced from international cell banks
  • Horizon Diagnostics can offer a custom extraction service to generate FFPE derived DNA from FFPE blocks

Key Features

  • A range of allelic frequencies is available. Alternative allelic frequencies can be generated as required
  • Standards mimic cancer patient genetics
  • Precisely validated for copy number and allelic frequency using digital PCR
  • FFPE format allows for authentic, in process control from extraction to reporting
  • HDx™ Reference Standards are a highly consistent and renewable resource


  • Evaluation of workflow integrity from extraction to reporting
  • Full in-process control
  • Method testing e.g. DNA extraction, DNA quantification
  • Assay/ platform optimization
  • Staff training

Also available as Genomic DNA.

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