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PAXgene Tissue DNA Kit

For isolation and purification of DNA from tissues fixed and stabilized using the PAXgene Tissue FIX Container

  • Effective purification of high-quality, unmodified DNA from tissue with preserved morphology
  • Protocols for paraffin-embedded or paraffin-free tissues
  • Automated purification on the QIAcube

 

Feature Specification
Format Spin column
Technology Silica membrane
Main sample type Human tissue
Sample amount Up to 10 mg from PF* tissue
2–5 sections 10 µm thick from PFPE** tissue with a maximum size
of 15 x 15 mm
Elution volume 14–40 µl
Time per run 30 min + 120 min incubation/8 samples
Processing Manual: centrifugation
Automated: QIAcube

* PAXgene Tissue fixed
** PAXgene Tissue fixed, paraffin-embedded

 

Intended Use

The PAXgene Tissue DNA Kit is intended for the purification of DNA from PAXgene Tissue fixed (PF) and PAXgene Tissue fixed, paraffin-embedded (PFPE) tissue samples. The kit is intended to be used as part of the PAXgene Tissue System, which additionally includes the PAXgene Tissue FIX Container and the PAXgene Tissue STABILIZER Concentrate for the collection, fixation, stabilization, and storage of tissue samples.

For research use only. Not for use in diagnostic procedures. No claim or representation is intended to provide information for the diagnosis, prevention, or treatment of a disease. The performance characteristics of this product have not been fully established.

The PAXgene Tissue DNA Procedure
Tissue sample lysis is performed in lysis buffer, Buffer TD1, with proteinase K digestion. Binding conditions are adjusted with Buffer TD2 and ethanol to provide optimal DNA-binding conditions, and [...]
High-quality DNA from PFPE tissue with preserved morphology
(A) Hematoxylin and eosin (H&E) staining of PAXgene Tissue fixed, paraffin-embedded (PFPE) human colorectal cancer tissue and (B) DNA on agarose gel electrophoresis using 0.8 % TBE buffered gels with [...]
DNA without chemical modifications can be used for demanding downstream applications
Multiplex and long-range PCR of DNA from PAXgene Tissue fixed, paraffin-embedded (PFPE) human colorectal cancer tissue (modified according to Viertler et al., J Mol Diagn. 2012). (A) Multiplex PCR of [...]
Significant hands-on time savings compared to the manual purification.
Comparison of sample preparation times between manual and QIAcube procedures for preparation of 12 PAXgene Tissue fixed, paraffin-embedded (PFPE) samples. Hands-on time without incubation times.
DNA yield of high-quality, high molecular weight DNA from 12 different PAXgene Tissue fixed (PF) tissue types, processed on the QIAcube.
Twelve different PAXgene Tissue fixed (PF) rat tissue types, including fibrous or fatty, DNA rich and DNA poor tissue, processed with the PAXgene Tissue DNA Kit on the QIAcube in one single run. DNA [...]
Absorbance ratio of high-quality, high molecular weight DNA from 12 different PAXgene Tissue fixed (PF) tissue types, processed on the QIAcube.
Twelve different PAXgene Tissue fixed (PF) rat tissue types, including fibrous or fatty, DNA rich and DNA poor tissue, processed with the PAXgene Tissue DNA Kit on the QIAcube in one single run. [...]
Agarose gel electrophoresis of high-quality, high molecular weight DNA from 12 different PAXgene Tissue fixed (PF) tissue types, processed on the QIAcube.
Twelve different PAXgene Tissue fixed (PF) rat tissue types, including fibrous or fatty, DNA rich and DNA poor tissue, processed with the PAXgene Tissue DNA Kit on the QIAcube in one single run. 300 [...]
Comparison of manual and automated procedure: DNA yield from sections of PAXgene Tissue fixed, paraffin-embedded (PFPE) tissue.
DNA yield from 3 sections (thickness 10 µm) each of eight different PAXgene Tissue fixed, paraffin-embedded (PFPE) rat tissue types processed in triplicates with the PAXgene Tissue DNA kit on the [...]
Comparison of manual and automated procedure: Absorbance ratio from sections of PAXgene Tissue fixed, paraffin-embedded (PFPE) tissue.
Ratio of absorbance at 260 and 280 nm from 3 sections (thickness 10 µm) each of eight different PAXgene Tissue fixed, paraffin-embedded (PFPE) rat tissue types processed in triplicates with the [...]
Comparison of manual and automated procedure: Agarose gel electrophoresis from sections of PAXgene Tissue fixed, paraffin-embedded (PFPE) tissue.
Agarose gel electrophoresis from 3 sections (thickness 10 µm) each of eight different PAXgene Tissue fixed, paraffin-embedded (PFPE) rat tissue types processed in triplicates with the PAXgene Tissue [...]
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Performance

Total DNA purified using the PAXgene Tissue DNA Kit is highly pure. DNA has A260/A280 ratios of 1.7–1.9, and absorbance scans show a symmetrical peak at 260 nm, confirming high purity of genomic DNA. Contamination is minimal and purified DNA is ready to use in downstream applications with no detectable inhibition of PCR (see High-quality DNA from PFPE tissue with preserved morphology and DNA without chemical modifications can be used for demanding downstream applications).
 

Principle

The PAXgene Tissue DNA Kit enables purification of DNA from tissues fixed and stabilized using the PAXgene Fixation and Stabilization products, which preserve tissue morphology and biomolecule integrity by avoiding destructive cross-linking and degradation found in formalin-fixed tissues. The purified DNA has no inhibitory chemical modifications and thus, can be used in sensitive downstream applications.

 

Procedure

PAxgene Tissue fixed (PF) or PAXgene Tissue fixed, paraffin-embedded (PFPE) tissue samples are lysed in Buffer TD1 with proteinase K. Conditions are adjusted for optimal binding of DNA to the silica membrane and the lysate is loaded on the PAXgene DNA spin column. DNA binds to the membrane while contaminants pass through. Enzyme inhibitors are effectively removed with subsequent washes and pure DNA is eluted in a low-salt elution buffer (see The PAXgene Tissue DNA Procedure).

The PAXgene Tissue DNA Kit provides 3 protocols for purification of DNA from different starting materials:

  • Sections of PFPE tissue
  • PF tissue samples (without paraffin embedding)
  • Blocks of PFPE tissue samples

 

Automation

DNA purification using the PAXgene Tissue DNA Kit can be automated on the QIAcube, enabling:

 

Two protocols are available for automated purification from different starting materials:

 

Applications

The purified DNA is ready to use in a wide range of downstream applications (see Resources), including:

  • PCR, multiplex, long-range, and quantitative, real-time PCR
  • Southern blotting
  • SNP genotyping
  • Sequencing

 

Handbooks (1)

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PAXgene Tissue DNA Kit Handbook 307 KB pdf

Supplementary Protocols (5)

File sizeFormatDownload
Simultaneous purification of genomic DNA and total RNA, including miRNA, from sections of PAXgene Tissue fixed, paraffin-embedded (PFPE) tissue 85 KB pdf
Simultaneous purification of genomic DNA and total RNA from sections of PAXgene Tissue fixed, paraffin-embedded (PFPE) tissue 84 KB pdf
Deparaffinization of PAXgene Tissue fixed, paraffin-embedded tissue sections with Deparaffinization Solution 86 KB pdf
Purification of genomic DNA from sections of PAXgene® Tissue fixed, cryo-embedded (PFCE) tissue placed directly into a microcentrifuge tube 603 KB pdf
Purification of genomic DNA from microdissected PAXgene® Tissue-fixed, paraffin-embedded (PFPE) and PAXgene Tissue-fixed, cryo-embedded (PFCE) tissues 716 KB pdf

Brochures (2)

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DNA Isolation with the PAXgene Tissue DNA Kit 2018 KB pdf
PAXgene Tissue System Brochure 4792 KB pdf

Technical information (2)

File sizeFormatDownload
Quantitative analysis of KRAS and BRAF mutational status in DNA from PAXgene Tissue fixed, paraffin-embedded (PFPE) tissue using Pyrosequencing technology 1404 KB pdf
Detection of PI3K mutational status in DNA from human breast cancer PFPE tissue using the PI3K Mutation Test Kit (QIAGEN) 1028 KB pdf

Safety Data Sheets (1)

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MSDS PAXgene Tissue DNA Kit Link

Posters (6)

File sizeFormatDownload
New Fixation Technology For Simultaneous Preservation of Morphology and Nucleic Acids in Tissue; Groelz et al., AMP 2008 529 KB pdf
Morphological, Epigenomic and Mutational Analyses of PAXgene Tissue Fixed, Paraffin-Embedded (PFPE) Colorectal Cancer (CRC) Specimens - Comparison to Formalin Fixed, Paraffin-Embedded (FFPE) and Snap-Frozen Samples; Groelz et al., AMP 2010 1189 KB pdf
PAXgene Tissue: A New Fixation Technology for Simultaneous Preservation of Morphology and Nucleic Acids; Groelz et al., BRN Symposium 2011 555 KB pdf
Preservation of Morphology and Biomolecules Within Tissue Stored for Three Years at -80°C in PAXgene Tissue Stabilizer Reagent; Groelz et al., ISBER 2012 912 KB pdf
PAXgene Tissue Fixation Technology for Simultaneous Preservation of Morphology and Biomolecules; Groelz et al., ECP 2012 1231 KB pdf
DNA quality measurement and somatic mutation profiling in PAXgene tissue samples with qBiomarker Somatic Mutation PCR Arrays; Long et al., ADAPT 2012 1223 KB pdf

References (7)

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Feature-based analysis of mouse prostatic intraepithelial neoplasia in histological tissue sections. Ruusuvuori P. et al., J Pathol Inform. 2016 Jan 29;7:5 Link
Pathogen Inactivating Properties and Increased Sensitivity in Molecular Diagnostics by PAXgene, a Novel Non-Crosslinking Tissue Fixative. Loibner M. et al., PLoS One. 2016 Mar 14;11(3):e0151383. Link
Protocol for HER2 FISH determination on PAXgene-fixed and paraffin-embedded tissue in breast cancer. Oberauner-Wappis L et al., Int J Exp Pathol. 2016 Apr;97(2):202-6 Link
The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data. Korenkova V et al., Sci Rep. 2016 Jul 7;6:29023. doi: 10.1038/srep29023 Link
A Critical Evaluation of the PAXgene Tissue Fixation System:  Morphology, Immunohistochemistry, Molecular Biology, and Proteomics. Mathieson W. et al., Am J Clin Pathol. 2016 Jul;146(1):25-40. Link
Assessment of PAXgene Fixation on Preservation of Morphology and Nucleic Acids in Microdissected Retina Tissue. Liu Y and Edward DP, Curr Eye Res. 2016 Jul 13:1-7. Link
Next-gen tissue: preservation of molecular and morphological fidelity in prostate tissue; Gillard M. et al., Am J Transl Res 2015;7(7):1227-1235 Link

FAQ (8)

    Purification and quality of biomolecules from PAXgene Tissue treated samples

    1. Is it possilbe to use formalin-fixed, paraffin-embedded (FFPE) kits and protocols to isolate biomolecules from PAXgene Tissue-fixed, paraffin-embedded (PFPE) tissues?

    No. Procedures developed for the extraction of biomolecules from FFPE tissues include prolonged proteinase K digestion and heating steps to remove chemical modifications introduced by formalin. Since the PAXgene Tissue System does not chemically modify biomolecules, these steps are not necessary and, in fact, lead to degradation of biomolecules. Instead, use dedicated PAXgene Tissue Kits and supplementary protocols for extraction of biomolecules from PAXgene Tissue-treated samples.

    2. What is the purity of nucleic acids extracted with the PAXgene Tissue Kits?

    The PAXgene Tissue DNA and RNA, including miRNA, Kits are based on proven QIAGEN technologies. Nucleic acids isolated with these kits are generally of high purity.

    On average, measurements of the A260/A280 ratio for DNA purified with the PAXgene Tissue DNA Kit are >1.7, and ratios for RNA including miRNA purified with the PAXgene Tissue RNA/miRNA Kit are >1.8.

    3. How well is DNA integrity preserved in PAXgene Tissue-fixed, paraffin-embedded (PFPE) tissues?

    In contrast to DNA isolated from formalin-fixed, paraffin-embedded (FFPE) tissue, DNA from PFPE tissue exhibits high molecular weight. In most cases, a distinct 10 kb band is observed in electrophoretically separated DNA eluates. For an example, see Figure 2 in the Technical Note “Quantitative analysis of KRAS and BRAF mutational status in DNA from PAXgene Tissue fixed, paraffin-embedded (PFPE) tissue using Pyrosequencing technology“ under the Resources tab.

    4. What are the yield and integrity of nucleic acids isolated from blocks of PAXgene Tissue fixed, cryo-embedded (PFCE) tissues?

    DNA and RNA isolated from PFCE tissue specimens are of high quantity and quality, comparable to PFPE tissue.

    5. Are special kits and protocols required for the isolation of biomolecules from PAXgene Tissue fixed, cryo-embedded (PFCE) tissues?

    No. Regular PAXgene Tissue kits can be used for the isolation of RNA, miRNA and DNA from PFCE tissue. Supplementary protocols developed specifically for the extraction of biomolecules from PFCE samples are available under the Resources tab.

    6. Which kits and protocols can be used for the isolation of nucleic acids from microdissected PAXgene Tissue fixed, paraffin-embedded (PFPE) and PAXgene Tissue fixed, cryo-embedded (PFCE) specimens?

    Regular PAXgene Tissue kits can be used for the isolation of RNA, miRNA and DNA from microdissected PFPE and PFCE tissue. Supplementary protocols developed specifically for the extraction of biomolecules from microdissected PFPE and PFCE samples are available under the Resources tab.

    Molecular analysis of biomolecules purified from PAXgene Tissue-treated samples

    1. What is the PCR performance of DNA purified from PAXgene Tissue fixed, paraffin-embedded (PFPE) and PAXgene Tissue fixed, cryo-embedded (PFCE) tissues compared to DNA from snap frozen or formalin-fixed, paraffin-embedded (FFPE) tissues?

    In contrast to FFPE, DNA purified from PFPE and PFCE is of high molecular weight and free of chemical modifications. In demanding downstream applications, such as multiplex or long-range PCR, it performs similarly or identically to DNA isolated from frozen tissue. For examples, see, Figure 5 in Viertler et al., J Mol Diagn. 2012 Sep; 14(5).

    2. Is DNA purified from PAXgene Tissue fixed, paraffin-embedded (PFPE) tissues suitable for targeted NGS analysis?

    Yes. DNA purified from PFPE is of high molecular weight and free of chemical modifications. Several independent researchers successfully used DNA from PFPE for NGS with different sample types, workflows and platforms (data in preparation). The data confirm recent suggestions that some DNA sequence artifacts associated with FFPE can be avoided with PFPE (Högnäs et al. 2017).

ProductCatalog Nr.Price (USD)

PAXgene Tissue DNA Kit (50)

For 50 DNA preps: PAXgene DNA Mini Spin Columns, Processing Tubes, Microcentrifuge Tubes, Carrier RNA, and Buffers. To be used in conjunction with PAXgene Tissue FIX Containers + PAXgene Tissue STABILIZER reagent.
767134279.00