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Volume 6 Supplement 6

Beyond the Genome 2012

Massively parallel sequencing of formalin-fixed paraffin-embedded tissues

Formalin fixation followed by paraffin embedment (FFPE) is the most common method of preserving resected tissues. FFPEs can be easily stored, retrieved and processed for further analysis when compared to the logistical complications of processing fresh frozen (FF) material. Conversely, they may not be ideal for sequencing because of the nucleic acid fragmentation and artifacts introduced by fixation. Here we report our efforts in performing next-generation sequencing on more than 70 specimens comprising >40 FFPE samples, from low to high quality, and compared the performance of FFPE, FF and commercially available cell lines.

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Erlich, R.L., Palescandolo, E., Jones, R.T. et al. Massively parallel sequencing of formalin-fixed paraffin-embedded tissues. BMC Proc 6 (Suppl 6), P40 (2012).

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  • Public Health
  • Nucleic Acid
  • Paraffin
  • Common Method
  • Parallel Sequencing