Product Class: Kit

NEBNext® FFPE DNA Library Prep Kit

Product Introduction

FFPE DNA poses many challenges for library preparation, including low input amounts and highly variable damage from fixation, storage, and extraction methods. Regions of interest are often enriched using hybrid capture-based approaches, and these workflows require a high input of diverse, uniform DNA library.

The NEBNext FFPE DNA Library Prep Kit is designed for pre-sheared FFPE DNA and improves yields and quality of libraries from a range of sample inputs (5-250 ng) and quality. The kit repairs damage to DNA caused by the FFPE process and includes reagents and a protocol optimized for library prep of FFPE DNA. The workflow is streamlined and user-friendly, with minimal hands-on time.

View or download extensive performance data in our Data Supplement.

  • Includes FFPE DNA repair reagents plus optimized library prep reagents and protocol
  • Increased library yields
  • Improved sequencing metrics
  • Greater sensitivity of somatic variant calling
  • 5-250 ng input range
  • Automation-friendly workflow

For further performance and workflow improvement, the NEBNext UltraShear FFPE DNA Library Prep Kit (NEB #E6655) also incorporates specialized enzymatic DNA fragmentation.

Bioz Badge Exists : True
Catalog # Size Concentration
E6650S 24 reactions
E6650L 96 reactions

Product Information

Description

View or download extensive performance data in our Data Supplement.

FFPE DNA is often compromised in quality and quantity and is a challenging sample type for library prep and sequencing. The NEBNext FFPE DNA Library Prep Kit addresses these challenges in multiple ways:

  • Repairs FFPE-induced damage using the NEBNext FFPE DNA Repair Mix v2
  • Uses NEBNext Ultra II library prep reagents in a protocol optimized for FFPE DNA
  • Robustly amplifies libraries using NEBNext MSTC™ FFPE Master Mix
  • High library yields, sufficient for input into target enrichment workflows
  • User-friendly workflow with minimal hands-on time and multiple safe stopping points

The NEBNext FFPE DNA Library Prep Kit reduces damage from deamination and oxidation due to the fixation, storage, and extraction process for FFPE DNA samples, thereby reducing false positive variant calls.

For further performance improvement, the NEBNext UltraShear FFPE DNA Library Prep Kit (NEB #E6655) also incorporates specialized enzymatic DNA fragmentation.


FIGURE 1: NEBNext FFPE DNA Library Prep Kit workflow

Image of Workflow
The NEBNext FFPE DNA Library Prep kit has a streamlined workflow with minimal hands-on time. The protocol has been optimized for the user to safely store the reaction after any step in the workflow overnight at -20°C without affecting library yield or quality.



FIGURE 2: The NEBNext FFPE DNA Library Prep Kit enables robust library preparation from a range of sample inputs and quality

Image of library yield
Libraries were prepared from 5, 50 or 250 ng of Covaris®-sheared normal tissue FFPE DNA ranging in quality from DNA Integrity Number (DIN) 1.8 to 6.8 with the indicated PCR cycles. Libraries were made in triplicate for 5 and 50 ng input and 1 replicate for 250 ng. Each bar represents the average of triplicates with error bars indicating standard deviation for the 5 and 50 ng inputs. Robust library yields were obtained across sample qualities and input amounts. Most target enrichment workflows require 200 ng of library for hybrid capture input, and sufficient library yield can be obtained using a minimum of 50 ng FFPE DNA with the NEBNext FFPE DNA Library Prep Kit.



FIGURE 3: NEBNext FFPE DNA Library Prep Kit reduces damage-derived sequencing artifacts

Image of artifact reduction graph    
Libraries were prepared from 50 ng of Covaris-sheared normal tissue FFPE DNA of either low (DIN 1.8) or high (DIN 6.8) quality using the NEBNext FFPE DNA Library Prep Kit and other library prep kits as shown. Libraries were sequenced on the Illumina® NextSeq® 500 (2 x 76 bases). Libraries were downsampled to 600,000 paired-end reads, mapped using bowtie2 (version 2.3.2.2) to the GrCh38 reference, and duplicates marked using Picard MarkDuplicate (version 1.56.0). The average frequency of C→T mutations at each C position in Read 2 was calculated for two technical replicates using Tasmanian (version 1.0.7). C→T mutations arising from cytosine deamination damage in low quality FFPE DNA are effectively repaired by the NEBNext FFPE DNA Repair v2 mix included in the NEBNext FFPE DNA Library Prep Kit. Other kits show a high level of C→T artifacts in low quality FFPE DNA (DIN 1.8) due to a lack of DNA damage repair.



FIGURE 4: The NEBNext FFPE DNA Library Prep Kit detects expected variants in formalin-compromised reference standard DNA

IMage of charts on expected variants
Libraries were prepared in triplicate from 50, 100, or 250 ng of Covaris-sheared formalin-compromised reference standard DNA (severe) (Horizon Discovery HD803) using either the NEBNext FFPE DNA Library Prep Kit or NEBNext Ultra™ II DNA Library Prep Kit. The full library yield was used in a target enrichment workflow with a custom cancer panel (Twist Bioscience®) as a 6-plex capture reaction. Libraries were sequenced on the Illumina NovaSeq® 6000 (2 x 100 bases). All fastq files were downsampled to 22 million paired-end reads, mapped using BWA mem (version 0.7.17) to the T2T reference, and duplicates marked using Picard MarkDuplicates (version 1.56.0). Variant allele frequencies (VAF) were calculated from Mpileup using Samtools (version 1.16.1) and plotted against the expected VAF in the Horizon reference DNA. A variant with a frequency of 0.88% was missed at 50 ng input for 1/3 replicates, but all variants were detected in all replicates at 100 and 250 ng input. The NEBNext FFPE DNA Library Prep kit improves the correlation of expected to observed VAF in low input libraries (50 ng) compared to standard library prep (NEBNext Ultra II DNA), indicating the benefit of the yield and coverage obtained with the NEBNext FFPE DNA Library Prep Kit including repair with NEBNext FFPE DNA Repair v2.




This product is related to the following categories:
FFPE DNA,
Library Preparation for Element Biosciences,
Next Generation Sequencing Library Preparation,

Kit Components

Kit Components

The following reagents are supplied with this product:

NEB # Component Name Component # Stored at (°C) Amount Concentration
  • NEB # Stored at (°C)
    E6650S Multi-temperature
    Component Name Component # Stored at (°C) Amount Concentration
    NEBNext® FFPE DNA Library Prep Kit E6650-2 -20 1 x 24 reactions Not Applicable
    NEBNext® FFPE DNA Repair Mix v2 E7361AVIAL -20 1 x 0.048 ml Not Applicable
    NEBNext® Thermolabile Proteinase K E7362AVIAL -20 1 x 0.048 ml Not Applicable
    NEBNext® FFPE DNA Repair Buffer v2 E7363AVIAL -20 1 x 0.168 ml Not Applicable
    NEBNext® Ultra II End Prep Enzyme Mix E7646AVIAL -20 1 x 0.072 ml Not Applicable
    NEBNext® Ultra™ II Ligation Master Mix E7648AVIAL -20 1 x 0.72 ml Not Applicable
    NEBNext® Ligation Enhancer E7374AVIAL -20 1 x 0.024 ml Not Applicable
    NEBNext® MSTC FFPE Master Mix E6651AVIAL -20 1 x 0.6 ml 2 X
    NEBNext® Sample Purification Beads E6652S 25 1 x 24 reactions Not Applicable
    NEBNext® Sample Purification Beads E6652AVIAL 25 1 x 4.3 ml Not Applicable
  • NEB # Stored at (°C)
    E6650L Multi-temperature
    Component Name Component # Stored at (°C) Amount Concentration
    NEBNext® FFPE DNA Library Prep Kit E6650-3 -20 1 x 96 reactions Not Applicable
    NEBNext® FFPE DNA Repair Mix v2 E7361AAVIAL -20 1 x 0.192 ml Not Applicable
    NEBNext® Thermolabile Proteinase K E7362AAVIAL -20 1 x 0.192 ml Not Applicable
    NEBNext® FFPE DNA Repair Buffer v2 E7363AAVIAL -20 1 x 0.672 ml Not Applicable
    NEBNext® Ultra II End Prep Enzyme Mix E7646AAVIAL -20 1 x 0.288 ml Not Applicable
    NEBNext® Ultra™ II Ligation Master Mix E7648AAVIAL -20 3 x 0.96 ml Not Applicable
    NEBNext® Ligation Enhancer E7374AAVIAL -20 1 x 0.096 ml Not Applicable
    NEBNext® MSTC FFPE Master Mix E6651AAVIAL -20 2 x 1.2 ml 2 X
    NEBNext® Sample Purification Beads E6652L 25 1 x 96 reactions Not Applicable
    NEBNext® Sample Purification Beads E6652AAVIAL 25 1 x 17 ml Not Applicable

Properties & Usage

Materials Required but not Supplied

  • 80% Ethanol
  • Nuclease-free Water
  • 0.1X TE (1 mM Tris-HCl, pH 8.0, 0.1 mM EDTA)
  • DNase-, RNase-free PCR strip tubes
  • NEBNext Multiplex Oligos for Illumina® (www.neb.com/oligos)
  • Magnetic rack/stand (NEB #S1515S, Alpaqua® cat. #A001322, or equivalent)
  • Thermal cycler
  • Agilent® Bioanalyzer® or TapeStation® and associated reagents and consumables
  • Adaptor Dilution Buffer NEB #B1430S or NEBNext Unique Dual Index UMI Adaptor Dilution Buffer supplied with NEBNext Unique Dual Index UMI Adaptor DNA Sets (NEB #E7395/E7874/E7876/E7878)

Tools & Resources

Selection Charts

FAQs & Troubleshooting

FAQs

  1. What sample types can I use with the NEBNext FFPE DNA Library Prep Kit?
  2. How much starting material is required for the NEBNext FFPE DNA Library Prep Kit?
  3. Is size selection recommended?
  4. What input amount (nanograms) is recommended for standard versus target enrichment library prep with FFPE DNA samples?
  5. Can I use this NEBNext kit with adaptors and primers from vendors other than NEB?
  6. What do I do if I see a precipitate in the NEBNext FFPE DNA Repair Buffer v2
  7. Will treating my DNA with the FFPE DNA Repair Mix v2 as part of the NEBNext FFPE DNA Library Prep Kit hurt my downstream reaction?
  8. Which NEBNext Multiplex Oligos can be used with the NEBNext FFPE DNA Library Prep Kit?
  9. Does the FFPE DNA Repair v2 Mix repair DNA-protein crosslinks?
  10. Does the FFPE DNA Repair v2 Mix fix blocked 3′ ends?
  11. Can the FFPE DNA Repair v2 Mix repair damage in both single- and double-stranded DNA? Or, does it require double stranded DNA as a template?
  12. If I had a DNA template with mutation sites (i.e. 8-oxoguanine or deaminated cytosines) that are directly adjacent to each other on opposite strands would treatment with the FFPE DNA Repair v2 Mix cause a double strand nick/break?
  13. What gap lengths can be repaired with the FFPE DNA Repair v2 Mix?

Quality, Safety & Legal

Quality Assurance Statement

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.

Specifications

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]

Certificate Of Analysis

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]

Safety DataSheets

The following is a list of Safety Data Sheet (SDS) that apply to this product to help you use it safely.

Legal and Disclaimers

Products and content are covered by one or more patents, trademarks and/or copyrights owned or controlled by New England Biolabs, Inc (NEB). The use of trademark symbols does not necessarily indicate that the name is trademarked in the country where it is being read; it indicates where the content was originally developed. The use of this product may require the buyer to obtain additional third-party intellectual property rights for certain applications. For more information, please email busdev@neb.com.

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.

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.

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