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SureSeq™ FFPE DNA Repair Mix*

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Effectively repairs DNA damage, common in FFPE samples, improving library yields, on-target rates and mean target coverage, while removing fixation and storage artefacts, and reducing the amount of starting material required.

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For more information about any OGT product or service, please contact us.

Email: contact@ogt.com
Phone: +44 (0)1865 856800 (US: 914 467 5285)

Details

The SureSeq FFPE DNA Repair Mix:

  • Optimised to repair a broad range of damage in FFPE-derived DNA — remove artefacts caused by fixation and long-term storage
  • Improves NGS library yields, %OTR and mean target coverage — get excellent sequencing data for confident variant calling from FFPE DNA
  • Allows decreased amount of input DNA — preserve your precious samples and get meaningful results from as little as 100 ng of FFPE DNA

Repair a broad range of damage in FFPE-derived DNA 

Detection of single nucleotide variants (SNVs) and insertion/deletions (indels) using next generation sequencing (NGS) technology is gaining increasing importance in research into cancer development and progression. Tissue biopsies are typically archived as formalin-fixed, paraffin-embedded (FFPE) blocks, which preserve tissue morphology and allow long-term storage at room temperature. However, the methods used for fixation significantly damage and compromise the quality of nucleic acids from these samples. Consequently, it may be difficult to distinguish between true and damage-induced low-frequency mutations in such samples. The SureSeq FFPE DNA Repair Mix is a mixture of enzymes that has been optimised to remove a broad range of damage that can cause artefacts in sequencing data (Table 1).

Table 1

Table 1: The SureSeq FFPE DNA Repair Mix is capable of removing a variety of DNA damage caused by fixation and long-term storage.

Improved NGS library yields, on-target rates (%OTR) and mean target coverage

Obtaining high-quality NGS libraries from FFPE-derived DNA can be a challenging task due to DNA degradation. SureSeq FFPE DNA Repair Mix has been shown to significantly improve NGS library yields (Figure 1), preserving original complexity and delivering high-quality sequencing data for confident calling of variants with low minor allele fractions (MAFs).

Figure 1Figure 1: Example traces from the Agilent® TapeStation illustrating the improvement in pre-capture NGS library yields. Input: 100 ng FFPE DNA.

One way of increasing NGS test sensitivity is to sequence to very high depths by reducing the number of samples in a run. This approach, however, increases the cost of sequencing reagents per sample processed. By repairing your DNA you can maximise depth of coverage as well as %OTR and therefore increase the sensitivity of your assay without compromising on cost or throughput (Figure 2).

Figure 2

Figure 2: The SureSeq FFPE DNA Repair Mix significantly improves mean target coverage resulting in more confident calls. Data obtained using 500 ng of FFPE DNA from ovarian and colon cancer samples; 16 samples per MiSeq® lane.

More accurate data with lower input DNA

Pathology labs often have to work with very limited amounts of material. Additionally, FFPE samples are usually irreplaceable. This leads to the need to reduce DNA input in downstream applications including NGS. Often amplicon-based approaches are chosen as they require very little input material. Unfortunately, due to PCR bias and lower complexity from smaller input amounts, these methods are not well suited to detect low-frequency mutations in heterogenous tumour samples. Hybridisation-based approaches eliminate the problem of PCR bias providing much more reliable data but they typically require higher DNA inputs of 500 ng – 1 μg. Using the SureSeq FFPE DNA Repair Mix a reduction in the amount of starting material down to 100 ng depending on required depth of coverage is possible (Figure 3).

Figure 3

Figure 3: The SureSeq FFPE DNA Repair Mix allows reduced amount of DNA input by improving mean target coverage. Data obtained using 500, 100 and 50 ng of FFPE DNA.

Ordering Information

Product Contents Cat. No. Price
Sure Seq FFPE DNA Repair Mix (16 reactions)* Enzyme mix and buffer sufficient for 16 FFPE DNA samples 500079 Get a quote
SureSeq NGS Library Preparation Kit (16)  Bundle of 1 x library preparation kit (16) containing adaptors, PCR primers and enzymes sufficient for 16 samples and 1 x SureSeq NGS Index Kit – Collection A 500070 Get a quote
SureSeq NGS Library Preparation Kit (48)  Bundle of 3 x library preparation kit (16), containing adaptors, PCR primers and enzymes sufficient for 48 samples and 1 x SureSeq NGS Index Kit – Collection B 500073 Get a quote
SureSeq NGS Index Kit - Collection A (16) 16 different indexes, each sufficient for 4 samples [included with SureSeq NGS Library Preparation Kit (16)] 500071 Get a quote
SureSeq NGS Index Kit - Collection B (48) 48 different indexes, each sufficient for 4 samples [included with SureSeq NGS Library Preparation Kit (48)] 500072 Get a quote
SureSeq NGS Cancer panels Enrichment baits; SureSeq Interpret Software various Get a quote
Dynabeads™ M270 Streptavidin, 2ml Sample capture beads, sufficient for 20 samples 500080** Get a quote
AMPure® XP beads, 10ml Sample purification beads, sufficient for 16 samples 500081** Get a quote


* The SureSeq™ FFPE DNA Repair Mix can only be purchased in conjunction with SureSeq NGS panels, not as a standalone product.

** Only for use with SureSeq NGS panels

SureSeq: For research use only; not for use in diagnostic procedures.

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