Histological Assessment of PAXgene Tissue Fixation and Stabilization Reagents

Kap, Marcel; Smedts, Frank; Oosterhuis, Wolter; Winther, Rosa; Christensen, Nanna; Reischauer, Bilge; Viertler, Christian; Groelz, Daniel; Becker, Karl‐Friedrich; Zatloukal, Kurt; Langer, Rupert; Slotta‐Huspenina, Julia; Bodó, Koppany; Jong, Bas de; Oelmüller, Uwe; Riegman, Peter

doi:10.1371/journal.pone.0027704

Cited by 73 publications

(82 citation statements)

References 18 publications

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“…46 In fact, we analyzed two cases of meningioma using genomic DNA extracted from formalin-fixed paraffin-embedded tissue and obtained similar but imprecise results of copynumber alterations (data not shown), mostly because of DNA fragmentation by formalin fixation. [47][48][49] For an appropriate clinical sequencing system, concomitance of conserved histology and high-quality nucleotide extraction must be achieved, therefore an alternative sample preparation method, other than snap-frozen or formalin fixation, such as the PAXgene Tissue System, would be considered.…”

Section: Modern Pathology (2016) 29 708-716mentioning

confidence: 74%

Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system

et al. 2016

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Recent genetic analyses using next-generation sequencers have revealed numerous genetic alterations in various tumors including meningioma, which is the most common primary brain tumor. However, their use as routine laboratory examinations in clinical applications for tumor genotyping is not cost effective. To establish a clinical sequencing system for meningioma and investigate the clinical significance of genotype, we retrospectively performed targeted amplicon sequencing on 103 meningiomas and evaluated the association with clinicopathological features. We designed amplicon-sequencing panels targeting eight genes including NF2 (neurofibromin 2), TRAF7, KLF4, AKT1, and SMO. Libraries prepared with genomic DNA extracted from PAXgenefixed paraffin-embedded tissues of 103 meningioma specimens were sequenced using the Illumina MiSeq. NF2 loss in some cases was also confirmed by interphase-fluorescent in situ hybridization. We identified NF2 loss and/or at least one mutation in NF2, TRAF7, KLF4, AKT1, and SMO in 81 out of 103 cases (79%) by targeted amplicon sequencing. On the basis of genetic status, we categorized meningiomas into three genotype groups: NF2 type, TRAKLS type harboring mutation in TRAF7, AKT1, KLF4, and/or SMO, and 'not otherwise classified' type. Genotype significantly correlated with tumor volume, tumor location, and magnetic resonance imaging findings such as adjacent bone change and heterogeneous gadolinium enhancement, as well as histopathological subtypes. In addition, multivariate analysis revealed that genotype was independently associated with risk of recurrence. In conclusion, we established a rapid clinical sequencing system that enables final confirmation of meningioma genotype within 7 days turnaround time. Our method will bring multiple benefits to neuropathologists and neurosurgeons for accurate diagnosis and appropriate postoperative management.

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Section: Modern Pathology (2016) 29 708-716mentioning

confidence: 74%

Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system

et al. 2016

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“…An alternative to FFPE and fresh frozen preservation is the noncrosslinking PAXgene Tissue System (PreAnalytiX, Hombrechtikon, Switzerland), which has proven to be efficient for preservation of the morphology and allows high-quality extraction of proteins, RNA, and DNA from the fixed tissues [10][11][12][13] The focus on high-quality molecules has increased as the search for new biomarkers has intensified, especially in cancer research. It is now well accepted that the required molecular alterations for neoplastic initiation and progression can, in addition to genetic changes, be acquired through epigenetic mechanisms [14].…”

Section: Introductionmentioning

confidence: 99%

Improved reproducibility in genome-wide DNA methylation analysis for PAXgene-fixed samples compared with restored formalin-fixed and paraffin-embedded DNA

Andersen

Hager

Hansen

et al. 2015

Analytical Biochemistry

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Formalin fixation has been the standard method for conservation of clinical specimens for decades. However, a major drawback is the high degradation of nucleic acids, which complicates its use in genome-wide analyses. Unbiased identification of biomarkers, however, requires genome-wide studies, precluding the use of the valuable archives of specimens with long-term follow-up data. Therefore, restoration protocols for DNA from formalin-fixed and paraffin-embedded (FFPE) samples have been developed, although they are cost-intensive and time-consuming. An alternative to FFPE and snap-freezing is the PAXgene Tissue System, developed for simultaneous preservation of morphology, proteins, and nucleic acids. In the current study, we compared the performance of DNA from either PAXgene or formalin-fixed tissues to snap-frozen material for genome-wide DNA methylation analysis using the Illumina 450K BeadChip. Quantitative DNA methylation analysis demonstrated that the methylation profile in PAXgene-fixed tissues showed, in comparison with restored FFPE samples, a higher concordance with the profile detected in frozen samples. We demonstrate, for the first time, that DNA from PAXgene conserved tissue performs better compared with restored FFPE DNA in genome-wide DNA methylation analysis. In addition, DNA from PAXgene tissue can be directly used on the array without prior restoration, rendering the analytical process significantly more time- and cost-effective.

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“…In proteomic and genomic assays, proteins and nucleic acids derived from PAXgene-fixed, paraffin-embedded (PFPE) tissues react as those derived from fast frozen tissues. [7][8][9][10] Recently, Cadoret et al 11 showed that DNA isolated from PAXgene-fixed tissue of Atlantic salmon gills could be used to detect Neoparamoeba perurans DNA by polymerase chain reaction (PCR). Also, conventional histological staining and immunohistochemistry (IHC) could be performed on PAXgene-fixed tissue to visualize the amoeboid parasite in salmon gills.…”

Section: Introductionmentioning

confidence: 99%

Inactivation ofInfluenza A virus,Adenovirus,andCytomegaloviruswith PAXgene Tissue Fixative and Formalin

Kap

Arron²,

Loibner³

et al. 2013

Biopreservation and Biobanking

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Formalin fixation is known to inactivate most viruses in a vaccine production context, but nothing is published about virus activity in tissues treated with alternative, non-crosslinking fixatives. We used a model assay based on cell culture to test formalin and PAXgene Tissue fixative for their virus-inactivating abilities. MDCK, A549, and MRC-5 cells were infected with Influenza A virus, Adenovirus, and Cytomegalovirus, respectively. When 75% of the cells showed a cytopathic effect (CPE), the cells were harvested and incubated for 15 min, or 1, 3, 6, or 24 hours, with PBS (positive control), 4% formalin, or PAXgene Tissue Fix. The cells were disrupted and the released virus was used to infect fresh MDCK, A549, and MRC-5 cells cultured on cover slips in 24-well plates. The viral cultures were monitored for CPE and by immunocytochemistry (ICC) to record viral replication and infectivity. Inactivation of Adenovirus by formalin occurred after 3 h, while Influenza A virus as well as Cytomegalovirus were inactivated by formalin after 15 min. All three virus strains were inactivated by PAXgene Tissue fixative after 15 min. We conclude that PAXgene Tissue fixative is at least as effective as formalin in inactivating infectivity of Influenza A virus, Adenovirus, and Cytomegalovirus.

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Histological Assessment of PAXgene Tissue Fixation and Stabilization Reagents

Cited by 73 publications

References 18 publications

Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system

Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system

Improved reproducibility in genome-wide DNA methylation analysis for PAXgene-fixed samples compared with restored formalin-fixed and paraffin-embedded DNA

Inactivation ofInfluenza A virus,Adenovirus,andCytomegaloviruswith PAXgene Tissue Fixative and Formalin

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