For automated purification of gDNA from FFPE tissues using the EZ1 Advanced XL or EZ2 Connect instrument.

50 preps: For use with QIAGEN DNA FFPE UNG kits.

Features

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

Product Details

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.

Performance

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 .

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 . This helps prevent false-positive reports of single-nucleotide variants (SNVs) in NGS.

Principle

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. In addition, it also makes the recovered DNA especially suitable for NGS analysis .

Procedure

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 .

Applications

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.

Supporting data and figures

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).

Specifications

Features                                        Specifications

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 proteinGenomic DNA

Technology                                Silica technology

Sample amount                       Tissue sections, each with a thickness of 5–10 µm, 

                                                       for a total volume of 4 mm3