Open Access Highly Accessed Research article

Targeted high throughput sequencing in clinical cancer Settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity

Martin Kerick1, Melanie Isau12, Bernd Timmermann1, Holger Sültmann3, Ralf Herwig1, Sylvia Krobitsch1, Georg Schaefer45, Irmgard Verdorfer56, Georg Bartsch4, Helmut Klocker4, Hans Lehrach1 and Michal R Schweiger1*

Author affiliations

1 Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany

2 Free University Berlin, Department of Biology, Chemistry and Pharmacy, Takustrasse 3, 14195 Berlin, Germany

3 Unit Cancer Genome Research, DKFZ German Cancer Research Center and National Center for Tumor Diseases, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany

4 Innsbruck Medical University, Department of Urology, Anichstr. 35, A 6020 Innsbruck, Austria

5 Innsbruck Medical University, Department of Pathology, Muellerstr. 40, A-6020 Innsbruck, Austria

6 Innsbruck Medical University, Department for Medical Genetics, Molecular and Clinical Pharmacology, Division of Human Genetics, Schöpfstraße 4, 6020 Innsbruck, Austria

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Citation and License

BMC Medical Genomics 2011, 4:68  doi:10.1186/1755-8794-4-68

Published: 29 September 2011



Massively parallel sequencing technologies have brought an enormous increase in sequencing throughput. However, these technologies need to be further improved with regard to reproducibility and applicability to clinical samples and settings.


Using identification of genetic variations in prostate cancer as an example we address three crucial challenges in the field of targeted re-sequencing: Small nucleotide variation (SNV) detection in samples of formalin-fixed paraffin embedded (FFPE) tissue material, minimal amount of input sample and sampling in view of tissue heterogeneity.


We show that FFPE tissue material can supplement for fresh frozen tissues for the detection of SNVs and that solution-based enrichment experiments can be accomplished with small amounts of DNA with only minimal effects on enrichment uniformity and data variance.

Finally, we address the question whether the heterogeneity of a tumor is reflected by different genetic alterations, e.g. different foci of a tumor display different genomic patterns. We show that the tumor heterogeneity plays an important role for the detection of copy number variations.


The application of high throughput sequencing technologies in cancer genomics opens up a new dimension for the identification of disease mechanisms. In particular the ability to use small amounts of FFPE samples available from surgical tumor resections and histopathological examinations facilitates the collection of precious tissue materials. However, care needs to be taken in regard to the locations of the biopsies, which can have an influence on the prediction of copy number variations. Bearing these technological challenges in mind will significantly improve many large-scale sequencing studies and will - in the long term - result in a more reliable prediction of individual cancer therapies.