text.skipToContent text.skipToNavigation


For automated purification of gDNA from FFPE tissues using the EZ1 Advanced XL or EZ2 Connect instrument
  • High recovery of amplifiable DNA
  • Paraffin removal without xylene or similar solvents
  • Option to remove uracil (deaminated cytosine) artifacts
  • Ready-to-use DNA for PCR, digital PCR (dPCR) and next-generation sequencing (NGS)
  • Automated heating and reagent-pipetting pretreatment steps, available on the EZ2 Connect

Purify large amounts of amplifiable DNA from hard-to-lyse formalin-fixed, paraffin-embedded (FFPE) tissue. The EZ1&2 DNA FFPE protocol uses double lysis to recover DNA effectively, while the optional uracil-N-glycosylase (UNG) step removes deaminated cytosine artifacts to limit the risk of nucleotide read errors.

The EZ1&2 DNA FFPE protocols are automatable on either the EZ1 Advanced XL or the EZ2 Connect.

The EZ2 Connect features cardless protocols, expanded applications and remote connectivity options. Click here to learn more about the EZ2 Connect, or contact your sales representative to discover how easily you can get an EZ2 Connect for your lab.

Buy Products

Cat No./ID: 19160
Uracil-N-Glycosylase (2 x 1 ml)

50 preps: For use with QIAGEN DNA FFPE UNG kits

Cat No./ID: 954404
EZ1&2 DNA FFPE Kit (48)

For 48 preps: EZ1&2 DNA FFPE cartridge, disposable filter-tips and tip-holders, tubes, Paraffin Removal Solution, Proteinase K, RNase A, RNase-free water and buffers

Cat No./ID: 954414
EZ1&2 DNA FFPE UNG Kit (48)

For 48 preps: Uracil-N-glycosylase, EZ1&2 DNA FFPE cartridge, disposable filter-tips and tip-holders, tubes, Paraffin Removal Solution, Proteinase K, RNase A, RNase-free water and buffers

EZ1&2 DNA FFPE Kits are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.

Product Details

Artificial C→T/G→A transitions.

Sample fixation can lead to artifacts in the DNA sequence. The most common artifact in FFPE tissues is the deamination of cytosine to uracil, which results in a single nucleotide variation (SNV).

Reduction in artifactual C→T | G→A transitions.
DNA was extracted from a colon cancer sample, with and without UNG treatment. When compared to the reference sequence, UNG treatment reduced the relative error rate resulting from C→T | G→A exchanges in reads.
Optimized for PCR performance.
FFPE samples of different origin. qPCR analysis showed that DNA isolated with the EZ1&2 DNA FFPE Kit showed lower Cq values for all but one of the tested samples.
Reliable dPCR and NGS results.
Similar mutation levels were detected by dPCR (QIAcuity system) and NGS (QIAseq Targeted DNA Human Colorectal Cancer Panel) from DNA isolated from human KRAS colon carcinoma FFPE samples using the EZ1&2 DNA FFPE Kit or the QIAamp DNA FFPE Advanced Kit.
EZ1&2 DNA FFPE Kit workflow.
Lyse sample with Proteinase K. Remove crosslinks by heat incubation. Remove artifacts with UNG (optional). Digest RNA, relyse sample. Transfer to the EZ1 for wash, bind and and elute steps. NOTE: Lysis to elution are automated on EZ2 Connect.

Under UV-vis, fluorometric, and qPCR analysis, most of the samples processed with the EZ1&2 DNA FFPE Kit showed a higher abundance of dsDNA (see figure “Optimized for PCR performance”).

For NGS analysis, the EZ1&2 DNA FFPE UNG Kit significantly reduces artificial C→T/G→A transitions, which commonly occur in FFPE material due to cytosine deamination (see “Artificial C→T/G→A transitions”). This helps prevent false-positive reports of single-nucleotide variants (SNVs) in NGS (see figure “Reduction in artifactual C→T | G→A transitions”).


The EZ1&2 DNA FFPE Kit maximizes DNA yields from limited sample inputs in two ways: By implementing a two-step lysis procedure, it helps ensure high DNA extraction even from difficult-to-lyse samples. In addition, its wash-free no-solvent deparaffinization technique minimizes the risk of losing of any sample material, which is difficult to avoid with multiple-wash solvent-based deparaffinization methods.

Crosslink removal further increases the amount of recovered amplifiable DNA (see figure “Optimized for PCR performance”). In addition, it also makes the recovered DNA especially suitable for NGS analysis (see figure “Reliable dPCR and NGS results”).


The EZ1&2 DNA FFPE Kit fully automates the bind, wash and elute steps on the EZ1 Advanced XL or the EZ2 Connect. The preparation steps (i.e., Proteinase K digestions, crosslink removal and RNase A digestion) are done manually on the EZ2 Advanced XL; on the EZ2 Connect, many of these preparation steps can be automated (see figure “EZ1&2 DNA FFPE workflow”).


DNA isolated with the EZ1&2 DNA FFPE Kit can be used immediately for PCR, dPCR or NGS. Alternatively, it can be stored at −30 to −15°C.


Applications PCR, digital PCR, next-generation sequencing
Elution volume 60 and 100 µl
Format Magnetic bead
Main sample type Formalin-fixed paraffin-embedded tissue samples
Processing Automated with the EZ1 Advance XL or EZ2 Connect
Purification of total RNA, miRNA, poly A+ mRNA, DNA or protein Genomic DNA
Sample amount Tissue sections, each with a thickness of 5–10 µm, for a total volume of 4 mm3
Technology Silica technology

Product Resources

fragment fix placeholder