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Open Access Highly Accessed Methodology

CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens

Ruth N MacKinnon12*, Carly Selan3, Adrian Zordan1, Meaghan Wall1, Harshal Nandurkar24 and Lynda J Campbell12

Author Affiliations

1 Victorian Cancer Cytogenetics Service, St Vincent's Hospital (Melbourne), Fitzroy, Vic, Australia

2 Department of Medicine (St Vincent's Hospital, Melbourne), University of Melbourne, Australia

3 Immunology Research Centre, St. Vincent's Hospital, Melbourne, Australia

4 Department of Haematology, St Vincent's Hospital, Melbourne, Australia

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Molecular Cytogenetics 2012, 5:10  doi:10.1186/1755-8166-5-10

Published: 2 February 2012

Abstract

Background

The analysis of nucleic acids is limited by the availability of archival specimens and the quality and amount of the extracted material. Archived cytogenetic preparations are stored in many laboratories and are a potential source of total genomic DNA for array karyotyping and other applications. Array CGH using DNA from fixed cytogenetic preparations has been described, but it is not known whether it can be used for SNP arrays. Diagnostic bone marrow specimens taken during the assessment of hematological malignancies are also a potential source of DNA, but it is generally assumed that DNA must be extracted, or the specimen frozen, within a day or two of collection, to obtain DNA suitable for further analysis. We have assessed DNA extracted from these materials for both SNP array and array CGH.

Results

We show that both SNP array and array CGH can be performed on genomic DNA extracted from cytogenetic specimens stored in Carnoy's fixative, and from bone marrow which has been stored unfrozen, at 4°C, for at least 36 days. We describe a procedure for extracting a usable concentration of total genomic DNA from cytogenetic suspensions of low cellularity.

Conclusions

The ability to use these archival specimens for DNA-based analysis increases the potential for retrospective genetic analysis of clinical specimens. Fixed cytogenetic preparations and long-term refrigerated bone marrow both provide DNA suitable for array karyotyping, and may be suitable for a wider range of analytical procedures.

Keywords:
SNP array; array CGH; bone marrow; archived specimens; old archived specimens; DNA extraction; DNA analysis; U937