This article is part of the supplement: Beyond the Genome 2012

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Massively parallel sequencing of formalin-fixed paraffin-embedded tissues

Rachel L Erlich*, Emanuele Palescandolo, Robert T Jones, Ashwini Sunkavalli, Alina Raza, Matthew Ducar, Charles Hatton, Christina Go, Christine Roden, Megan Hanna, Adri Mills, Ravali Adusumilli, Prateek Kumar, Priscilla K Brastianos, Matthew L Meyerson, William C Hahn, Laura E MacConaill and Paul Van Hummelen

  • * Corresponding author: Rachel L Erlich

Author Affiliations

Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA

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BMC Proceedings 2012, 6(Suppl 6):P40  doi:10.1186/1753-6561-6-S6-P40

The electronic version of this article is the complete one and can be found online at:

Published:1 October 2012

© 2012 Erlich et al; licensee 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.

Poster presentation

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.