CGH and SNP Array Using DNA Extracted from Fixed Cytogenetic Preparations and Long-term Refrigerated Bone Marrow Specimens

Overview

Journal Mol Cytogenet

Publisher Biomed Central

Specialty Biochemistry

Date 2012 Feb 4

PMID 22300816

Citations 2

Authors

Ruth N MacKinnon

Carly Selan

Adrian Zordan

Meaghan Wall

Harshal Nandurkar

Lynda J Campbell

Affiliations

Soon will be listed here.

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.

Citing Articles

Detailed molecular cytogenetic characterisation of the myeloid cell line U937 reveals the fate of homologous chromosomes and shows that centromere capture is a feature of genome instability.

MacKinnon R, Peverall J, Campbell L, Wall M Mol Cytogenet. 2020; 13(1):50.

PMID: 33317567 PMC: 7737353. DOI: 10.1186/s13039-020-00517-y.

Fixed nuclei as alternative template of BIOMED-2 multiplex polymerase chain reaction for immunoglobulin gene clonality testing in B-cell malignancies.

Tang Y, Chen J, Wang J, Zheng K, Liao D, Liao X Am J Blood Res. 2016; 5(2):62-78.

PMID: 27069754 PMC: 4769348.

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