SureSeq™ FFPE DNA Repair Mix*
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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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: 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 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: 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: 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 Cancer panels | Enrichment baits; SureSeq Interpret Software | various | Get a quote |
| SureSeq NGS Library Preparation Complete Solution (16) | Bundle of 1x SureSeq library preparation kit (16), containing adaptors, PCR primers and enzymes, 1x SureSeq NGS Index Kit – Collection A, 1x SureSeq Hyb & Wash Kit (16), 1x Dynabeads M270 Streptavidin (2ml) and 1x AMPure XP beads (10ml). Sufficient for 16 samples | 500084 | Get a quote |
| SureSeq NGS Library Preparation Complete Solution (48) | Bundle of 3x SureSeq NGS Library Preparation Kit (16), containing adaptors, PCR primers and enzymes, 1x SureSeq NGS Index Kit – Collection B, 3x SureSeq NGS Hyb & Wash Kit (16), 3x Dynabeads M270 Streptavidin (2ml) and 3x AMPure XP beads (10ml). Sufficient for 48 samples | 500085 | Get a quote |
| SureSeq NGS Library Preparation and Hyb & Wash Kit (16) | Bundle of 1x SureSeq NGS Library Preparation Kit (16), containing adaptors, PCR primers and enzymes, 1x SureSeq NGS Index Kit – Collection A and 1x SureSeq Hyb & Wash Kit (16). Sufficient for 16 samples | 500082 | Get a quote |
| SureSeq NGS Library Preparation and Hyb & Wash Kit (48) | Bundle of 3x SureSeq NGS Library Preparation Kit (16), containing adaptors, PCR primers and enzymes, 1x SureSeq NGS Index Kit – Collection B and 3x SureSeq Hyb & Wash kit (16). Sufficient for 48 samples | 500083 | 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 Hyb & Wash Kit (16) | Hybridisation buffer, Wash buffer, Cot and blocking oligos. Sufficient for 16 samples | 500075 | Get a quote |
| SureSeq NGS Hyb & Wash Kit (48) | Bundle of 3x SureSeq NGS Hyb & Wash Kit (16), containing Hybridisation buffer, Wash buffer, Cot and blocking oligos. Sufficient for 48 samples | 500086 | 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 |
| 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 OGT's NGS panels
Disclaimer
SureSeq: For research use only; not for use in diagnostic procedures.
Images
Resources
Poster
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Optimised, 1-day hybridisation-based NGS protocol yields 1% variant detection in MPN samples, as quickly and cost-effectively as multiplex PCR
Presented at AMP 2016, this poster outlines how the SureSeq™ Core MPN Panel can accurately detect alleles down to 1% variant allele fraction (VAF) in JAK2 (V617F) at a read depth of >1000x, facilitating reliable detection.
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The accurate detection by next-generation sequencing (NGS) of difficult to sequence genes (CALR, CEBPA, FLT3) associated with myeloid disorders using a hybridisation-based enrichment approach
Presented at CGC 2017, this poster highlights the excellent uniformity of coverage obtained from the hybridisation-based enrichment using the SureSeq myPanel NGS Custom AML Panel.
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The analysis of myeloproliferative neoplasm samples using a rapid (30 minute) hybridisation-based enrichment protocol for next-generation sequencing (NGS)
Presented at the CGC 2017 annual summer meeting in Denver, USA, this poster illustrates the excellent quality data generated by the OGT 1-day hybridisation-based SureSeq LPK protocol in combination with the SureSeq Core MPN Panel.
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The application of a hybridisation-based next-generation sequencing (NGS) enrichment panel for the analysis of key genes involved in ovarian and breast tumours using DNA from FFPE samples
This poster illustrates the SureSeq™ hybridisation-based approach as a robust method for the identification of germline and somatic mutations in TP53, BRCA1, and BRCA2.
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The application of a hybridisation-based NGS enrichment panel for the analysis of somatic variants in tumour samples and reference standards
Presented at AGT 2017, this poster outlines the application of a hybridisation-based NGS enrichment panel for the analysis of solid tumour somatic variants, demonstrating 100% concordance in variant detection in both genomic and formalin-compromised DNA.
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The application of a one-day hybridisation-based enrichment protocol for NGS incorporating a rapid (30 minute) hybridisation step
Presented at AGT 2017, this poster outlines how OGT has optimised a one-day hybridisation-based enrichment protocol for NGS incorporating a rapid 30 hybridisation step.
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The use of a hybridisation-based NGS enrichment panel for the confident identification of a broad range of low frequency variants from as little as 50ng of challenging clinical research FFPE samples
Presented at AMP 2016, this poster outlines how the SureSeq FFPE DNA Repair Mix significantly improves NGS library yields, with an increase of mean target coverage (increased by >2.2 fold), resulting in more meaningful data.
Application note
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Evaluation of enzymatic DNA digestion as an alternative to mechanical DNA fragmentation (sonication) for targeted NGS using the SureSeq™ Myeloid Panel
DNA fragmentation is a crucial first step in the preparation of libraries for NGS. In this application note, Oxford Gene Technology has evaluated an alternative method of fragmentation using the NEBNext® dsDNA Fragmentase®.
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Greater confidence in calling low-frequency variants – from as little as 10ng of severely formalin-compromised DNA
In this study, carried out in collaboration with Horizon Discovery, formalin-compromised DNA (fcDNA) samples of differing severity were repaired with the SureSeq™ FFPE repair mix and sequenced using a SureSeq custom hybridisation-based panel.
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Improving experimental reproducibility through automated hybridisation-based NGS library preparation
In this app note, an Agilent Bravo A Automated Liquid Handling Platform was configured to run the SureSeq NGS library preparation protocol. The results demonstrate marked improvement not only in hands-on-time, but also a number of quality metrics.
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Selecting the best NGS enrichment assay for your needs
With NGS now in routine use for a broad range of research and clinical applications, this application note details the value of making the correct choice for the initial sequence enrichment step.
Catalogue
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OGT Product Catalog - USA and Canada
Including Cytocell® FISH probes for Constitutional Cytogenetics and Hematology/Pathology Cytogenetics, CytoSure™ NGS and Array Products for Cytogenetics and Rare Disease Research and SureSeq™ NGS Products for Hematology and Solid Tumor Cancer Research.
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OGT Product Catalogue
Including Cytocell® FISH Probes for Cancer and Inherited Genetic Disease, CytoSure™ NGS and Array Products for Cytogenetics and Rare Disease, and SureSeq™ NGS Products for Haematology and Solid Tumour Cancers.
White paper
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The role of NGS in stratified cancer medicine
In this white paper, two Clinical Scientists, Dr Matthew Smith and Dr George Burghel, share their views on the use of NGS in cancer genomics and its integration into the laboratory.
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Understanding myeloid disorders with next-generation sequencing
This white paper describes how OGT’s SureSeq™ Myeloid Panel helps researchers identify and decipher the complex genetic origins of myeloproliferative disorders.
Handbook
Brochure
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An integrated approach to profiling haematological disorders
For accurate detection of all types of genetic aberrations, various technologies are used. View OGT's integrated portfolio of products that allow the accurate analysis of haematological disorders.
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An integrated approach to tumour profiling
Various technologies are available to study the mutations that cause cancer, but none is capable of accurate detection of all types of genetic aberrations. View OGT's integrated portfolio of products that allow the accurate analysis of solid tumours.