Macromolecular Chemistry | Bioinformatics | Medical Genetics
Construction of a workflow for genome-wide variation analysis of formalin fixed paraffin embedded tumor samples
Zelha Nil*, Yesim Aydin-Son, Mukerrem Safali, Fikret Arpaci, Ufuk Gunduz
*Corresponding author: Zelha Nil
Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
F1000Posters 2012, 3: 290 (poster) [English]
Poster [988.68 KB]
7th International Symposium on Health Informatics and Bioinformatics 2012, 19 - 22 Apr 2012, 32
Formalin fixed paraffin embedded (FFPE) tissues are the most available material for routine diagnostics in pathology laboratories worldwide. They can be used for both microscopic examinations and molecular diagnostic assays after microscopy. Molecular assays, such as PCR and high throughput microarrays, have the potential to be used as routine diagnostic and prognostic tests. Those assays require high quality DNA. However, DNA extracted from FFPE material is problematic due to chemical modifications caused by formalin and continued degradation over time.
In this research, FFPE samples from lung tissue of 10 patients with pulmonary metastatic osteosarcoma was used in order to provide a microarray data analysis workflow for application of FFPE-derived DNA samples in reliable copy number and loss of heterozygosity (LOH) predictions.
The present study demonstrates a feasible approach to use archival FFPE samples for the assessment of copy number aberration and LOH.
Identification of such regions may also be helpful in investigations of potential diagnostic and prognostic markers in tumors.
No relevant competing interests disclosed.
Middle East Technical University , 10
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