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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

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 possi...

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Autores principales: de Jong, Danielle, Verbeke, Sofie LJ, Meijer, Danielle, Hogendoorn, Pancras CW, Bovee, Judith VMG, Szuhai, Károly
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024235/
https://www.ncbi.nlm.nih.gov/pubmed/21205301
http://dx.doi.org/10.1186/1756-0500-4-1
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author de Jong, Danielle
Verbeke, Sofie LJ
Meijer, Danielle
Hogendoorn, Pancras CW
Bovee, Judith VMG
Szuhai, Károly
author_facet de Jong, Danielle
Verbeke, Sofie LJ
Meijer, Danielle
Hogendoorn, Pancras CW
Bovee, Judith VMG
Szuhai, Károly
author_sort de Jong, Danielle
collection PubMed
description 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.
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spelling pubmed-30242352011-01-21 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 de Jong, Danielle Verbeke, Sofie LJ Meijer, Danielle Hogendoorn, Pancras CW Bovee, Judith VMG Szuhai, Károly BMC Res Notes Technical Note 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. BioMed Central 2011-01-04 /pmc/articles/PMC3024235/ /pubmed/21205301 http://dx.doi.org/10.1186/1756-0500-4-1 Text en Copyright ©2011 Szuhai et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<url>http://creativecommons.org/licenses/by/2.0</url>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Technical Note
de Jong, Danielle
Verbeke, Sofie LJ
Meijer, Danielle
Hogendoorn, Pancras CW
Bovee, Judith VMG
Szuhai, Károly
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
title 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
title_full 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
title_fullStr 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
title_full_unstemmed 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
title_short 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
title_sort 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
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024235/
https://www.ncbi.nlm.nih.gov/pubmed/21205301
http://dx.doi.org/10.1186/1756-0500-4-1
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