MPI für molekulare Genetik / Department of Vertebrate Genomics |
|Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis.|
|Authors:||Schweiger, Michal R.; Kerick, Martin; Timmermann, Bernd; Albrecht, Marcus W.; Borodina, Tatjana; Parkhomchuk, Dmitri; Zatloukal, Kurt; Lehrach, Hans|
|Research Context:||This work was supported by the Austrian Genome Programme GEN-AU and the Max Planck Society. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.|
|Date of Publication (YYYY-MM-DD):||2009-05-14|
|Title of Journal:||PLoS ONE|
|Journal Abbrev.:||PLOS ONE|
|Issue / Number:||5|
|Full name of Issue-Editor(s):||Jordan, I. King|
|Copyright:||2009 Schweiger et al. 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 author and source are credited.|
|Review Status:||not specified|
|Abstract / Description:||Cancer re-sequencing programs rely on DNA isolated from fresh snap frozen tissues, the preparation of which is combined with additional preservation efforts. Tissue samples at pathology departments are routinely stored as formalin-fixed and paraffin-embedded (FFPE) samples and their use would open up access to a variety of clinical trials. However, FFPE preparation is incompatible with many down-stream molecular biology techniques such as PCR based amplification methods and gene expression studies.
Here we investigated the sample quality requirements of FFPE tissues for massively parallel short-read sequencing approaches. We evaluated key variables of pre-fixation, fixation related and post-fixation processes that occur in routine medical service (e.g. degree of autolysis, duration of fixation and of storage). We also investigated the influence of tissue storage time on sequencing quality by using material that was up to 18 years old. Finally, we analyzed normal and tumor breast tissues using the Sequencing by Synthesis technique (Illumina Genome Analyzer, Solexa) to simultaneously localize genome-wide copy number alterations and to detect genomic variations such as substitutions and point-deletions and/or insertions in FFPE tissue samples.
The application of second generation sequencing techniques on small amounts of FFPE material opens up the possibility to analyze tissue samples which have been collected during routine clinical work as well as in the context of clinical trials. This is in particular important since FFPE samples are amply available from surgical tumor resections and histopathological diagnosis, and comprise tissue from precursor lesions, primary tumors, lymphogenic and/or hematogenic metastases. Large-scale studies using this tissue material will result in a better prediction of the prognosis of cancer patients and the early identification of patients which will respond to therapy.
|Comment of the Author/Creator:||E-mail: firstname.lastname@example.org|
|External Publication Status:||published|
|Version Comment:||Automatic journal name synchronization|
|Communicated by:||Hans Lehrach|
|Affiliations:||MPI für molekulare Genetik|
|External Affiliations:||1.Institute for Medical Genetics, Charité Universitätsmedizin, Berlin, Germany;
2.Institute of Pathology, Medical University, Graz, Austria.
|You have privileges to view the following file(s):|
|journal.pone.0005548.pdf [576,00 Kb] [Comment:Open access] |
The scope and number of records on eDoc is subject
to the collection policies defined by each institute
- see "info" button in the collection browse view.