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Open Access Technical Note

Opening the archives for state of the art tumour genetic research: sample processing for array-CGH using decalcified, formalin-fixed, paraffin-embedded tissue-derived DNA samples

Danielle de Jong1, Sofie LJ Verbeke2, Danielle Meijer2, Pancras CW Hogendoorn2, Judith VMG Bovee2 and Károly Szuhai1*

Author Affiliations

1 Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2333ZC Leiden, The Netherlands

2 Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands

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BMC Research Notes 2011, 4:1  doi:10.1186/1756-0500-4-1

Published: 4 January 2011

Abstract

Background

Molecular genetic studies on rare tumour entities, such as bone tumours, often require the use of decalcified, formalin-fixed, paraffin-embedded tissue (dFFPE) samples. Regardless of which decalcification procedure is used, this introduces a vast breakdown of DNA that precludes the possibility of further molecular genetic testing. We set out to establish a robust protocol that would overcome these intrinsic hurdles for bone tumour research.

Findings

The goal of our study was to establish a protocol, using a modified DNA isolation procedure and quality controls, to select decalcified samples suitable for array-CGH testing. Archival paraffin blocks were obtained from 9 different pathology departments throughout Europe, using different fixation, embedding and decalcification procedures, in order to preclude a bias for certain lab protocols. Isolated DNA samples were subjected to direct chemical labelling and enzymatic labelling systems and were hybridised on a high resolution oligonucleotide chip containing 44,000 reporter elements.

Genomic alterations (gains and losses) were readily detected in most of the samples analysed. For example, both homozygous deletions of 0.6 Mb and high level of amplifications of 0.7 Mb were identified.

Conclusions

We established a robust protocol for molecular genetic testing of dFFPE derived DNA, irrespective of fixation, decalcification or sample type used. This approach may greatly facilitate further genetic testing on rare tumour entities where archival decalcified, formalin fixed samples are the only source.