Still using xylene to manually extract DNA from your FFPE samples?

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For decades, formalin-fixed paraffin-embedded (FFPE) tissue samples have been collected and archived for long-term storage. They’re extremely valuable for carrying out research like mutation screening or pathogen detection.

In general, deparaffinization of the FFPE tissue sections is achieved by manual xylene pretreatment, which dissolves the paraffin from the tissue, and a series of ethanol washes followed by proteinase K digestion. This manual processing is not only very laborious and time consuming but also carries the risk of xylene exposure.

Xylene is a cyclic hydrocarbon, widely used for processing and staining tissues and cover slipping in the histology laboratory. Exposure to xylene can not only occur via inhalation but also through ingestion, skin or eye contact (1). Depending on the amount of xylene and duration, exposure can cause both acute (<14 days) or chronic (>365 days) health effects (2).

We have developed an alternative deparaffinization method that can be used for automated DNA extraction on the QIAsymphony SP instrument, enabling parallel deparaffinization and lysis of the FFPE tissue material without using hazardous substances like xylene. The deparaffinization method in combination with the QIAsymphony SP aims to:

·  Significantly reduce hands-on time – total processing time of approximately 6 h for 96 samples
·  Eliminate risk of losing precious samples by minimizing manual transfer and centrifugation steps
·  Obtain comparable DNA concentration and purity vs. a manual xylene deparaffinization method

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References:

  1. 1. Kamal, N. et al. (2015) A review of environmental and occupational exposure to xylene and its health concerns. EXCLI J. 14, 1167. Link
  2. 2. Kandyala, R. et al. (2010) Xylene: An overview of its health hazards and preventive measures. Oral Maxillofac. Pathol. 14, 1. Link
Kjell Kirschbaum

Kjell Kirschbaum, M.Sc., Global Market Manager in the Discovery Sciences, trained as a bioveterinary scientist at the University of Utrecht in the Netherlands. He has hands-on experience in nucleic acid and protein purification, cell culture, PCR and qPCR technology. Kjell joined QIAGEN in 2011 as a telemarketing specialist, regularly interacting with customers about their day-to-day experimental needs and offering relevant solutions. Currently, he is involved in managing global projects for sample preparation and assay technologies.

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