title: Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Max Planck Institute for Molecular Genetics, Ihnestr, Berlin, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Kerick
authors.forename: Melanie
authors.initials: M
authors.lastname: Isau
authors.forename: Bernd
authors.initials: B
authors.lastname: Timmermann
authors.forename: Holger
authors.initials: H
authors.lastname: Sültmann
authors.forename: Ralf
authors.initials: R
authors.lastname: Herwig
authors.forename: Sylvia
authors.initials: S
authors.lastname: Krobitsch
authors.forename: Georg
authors.initials: G
authors.lastname: Schaefer
authors.forename: Irmgard
authors.initials: I
authors.lastname: Verdorfer
authors.forename: Georg
authors.initials: G
authors.lastname: Bartsch
authors.forename: Helmut
authors.initials: H
authors.lastname: Klocker
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.forename: Michal R
authors.initials: MR
authors.lastname: Schweiger
mesh_terms: D056915:DNA Copy Number Variations; D004273:DNA, Neoplasm / Q000737:chemistry / Q000378:metabolism; D005557:Formaldehyde / Q000737:chemistry*; D018740:Genetic Heterogeneity; D006801:Humans; D008297:Male; D016612:Paraffin Embedding; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004273:DNA, Neoplasm; D005557:Formaldehyde