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

Kerick, M., Isau, M., Timmermann, B., Sultmann, H., Herwig, R., Krobitsch, S., et al. (2011). Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Med Genomics, 4, 68. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192667/pdf/1755-8794-4-68.pdf?tool=pmcentrez.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7865-E Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7866-C
Genre: Journal Article

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 Creators:
Kerick, M.1, Author              
Isau, M.1, Author              
Timmermann, B.2, Author              
Sultmann, H., Author
Herwig, R., Author
Krobitsch, S.3, Author              
Schaefer, G., Author
Verdorfer, I., Author
Bartsch, G., Author
Klocker, H., Author
Lehrach, H.4, Author              
Schweiger, M. R.1, Author              
Affiliations:
1Cancer Genomics (Michal-Ruth Schweiger), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479649              
2Sequencing, Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433559              
3Neurodegenerative Disorders (Sylvia Krobitsch), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479661              
4Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              

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Free keywords: DNA Copy Number Variations; DNA, Neoplasm/chemistry/metabolism; Formaldehyde/ chemistry; Genetic Heterogeneity; Humans; Male; Paraffin Embedding; Prostatic Neoplasms/ genetics/metabolism/pathology; Sequence Analysis, DNA/ methods
 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.

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 Dates: 2011
 Publication Status: Published in print
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Title: BMC Med Genomics
Source Genre: Journal
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Pages: - Volume / Issue: 4 Sequence Number: - Start / End Page: 68 Identifier: ISSN: 1755-8794 (Electronic) 1755-8794 (Linking)