Archiving of clinical materials as Formalin-Fixed, Paraffin-Embedded (FFPE) samples is a common practice. However, the methods used for fixation and storage significantly damage and compromise the quality of DNA from these samples. As a result, it can be challenging to obtain useful information, including high-quality sequence data, especially when sample amounts are limited.
The NEBNext FFPE DNA Repair Mix is a cocktail of enzymes formulated to repair DNA, and specifically optimized and validated for repair of FFPE DNA samples.
The NEBNext FFPE DNA Repair Mix contains enzymes and buffers that are optimized to repair FFPE DNA in next generation sequencing workflow. The mix can be used upstream of any next generation sequencing library construction method, for any sequencing platform.
For larger volume requirements, customized and bulk packaging is available by purchasing through the OEM/Bulks department at NEB. Please contact [email protected] for further information.
Table 1: Types of FFPE DNA damage and their ability to be repaired by the NEBNext FFPE DNA Repair Mix
FFPE DAMAGE TYPE
REPAIRED BY THE FFPE DNA ENZYME REPAIR MIX?
Deamination of cytosine to uracil
Yes
Nicks and gaps
Yes
Oxidized bases
Yes
Blocked 3´ ends
Yes
DNA fragmentation
No
DNA-protein crosslinks
No
Figure 1: FFPE DNA repair increases NGS library yields
An example of Agilent Bioanalyzer® traces of libraries prepared from stomach tumor FFPE DNA that was treated with the FFPE DNA Repair Mix, or was untreated, before library construction. Yield improvements of 10% to 458% have been observed.
Figure 2. FFPE DNA repair increases NGS library yields
FFPE DNA samples (25 ng or 50 ng) from a variety of tissue types were treated with the NEBNext FFPE DNA Repair Mix, or were untreated, before library construction. Library yields were measured using the Agilent Bioanalyzer, and ratios of library yields with and without treatment with the NEBNext FFPE DNA Repair Mix were calculated. Yield improvements with these samples ranged from 101% to 458%.
Figure 3. FFPE DNA Repair improves sequence quality from FFPE samples and does not introduce new mutations
Genomic DNA was extracted using standard DNA purification. Each DNA sample was treated with the NEBNext FFPE DNA Repair Mix, or was untreated, before library construction and Illumina® sequencing.
Panel A: The effect of DNA repair on the percentage of mappable reads. Reads were mapped to the human genome (hg19) using BWA (1).
Panel B: The effect of DNA repair on the percentage of reads that were properly paired from a paired-end sequencing protocol.
Lot Control
The lots provided are managed separately and qualified by additional functional validation. Individual reagents undergo standard enzyme activity and quality control assays, and also meet stringent criteria in the additional quality controls listed on each individual component page
Reagents Supplied
The following reagents are supplied with this product:
Library Construction Reagents [NEBNext Ultra DNA Library Prep Kit (NEB #E7370) for Illumina, NEBNext DNA Library Prep Master Mix Set for Illumina (NEB #E6040), or other
Quality Control tests are performed on each new lot of NEB product to meet the specifications designated for it. Specifications and individual lot data from the tests that are performed for this particular product can be found and downloaded on the Product Specification Sheet, Certificate of Analysis, data card or product manual. Further information regarding NEB product quality can be found here.
The Specification sheet is a document that includes the storage temperature, shelf life and the specifications designated for the product. The following file naming structure is used to name these document files: [Product Number]_[Size]_[Version]
The Certificate of Analysis (COA) is a signed document that includes the storage temperature, expiration date and quality controls for an individual lot. The following file naming structure is used to name these document files: [Product Number]_[Size]_[Version]_[Lot Number]
This product is covered by one or more patents, trademarks and/or copyrights owned or controlled by New England Biolabs, Inc (NEB).
New England Biolabs (NEB) is committed to practicing ethical science – we believe it is our job as researchers to ask the important questions that when answered will help preserve our quality of life and the world that we live in. However, this research should always be done in safe and ethical manner. Learn more.
While NEB develops and validates its products for various applications, the use of this product may require the buyer to obtain additional third party intellectual property rights for certain applications.
For more information about commercial rights, please contact NEB's Global Business Development team at [email protected].
This product is intended for research purposes only. This product is not intended to be used for therapeutic or diagnostic purposes in humans or animals.
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