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

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.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.Array comparative genomic hybridization (array CGH) [1] and single nucleotide polymorphism (SNP) array [2] are array-based karyotyping techniques which can help determine the genome abnormalities causing genetic disorders and the acquired genome copy number changes in cancer cells. They provide higher resolution than traditional karyotyping. However, the use of these and other DNA-based approaches for analysis is sometimes limited by the availability of suitable tissue samples, particularly for retrospective cancer genome analysis.Fixed cytogenetic specimens are often stored after analysis, and are a potential source of total genomic DNA for array karyotyping and other DNA analysis techniques. Bone marrow specimens are commonly used to determine karyotype abnormalities in hematological malignancies. If unprocessed bone marrow is stored at 4°C during this time, it may be up to a month old before a karyotype is known and the decision to carry out array karyotyping is made. Anecdotally, it has been assumed that DNA extracted from these types of specimen is too degraded for analysis. Here we show that, on the contrary, an array karyotyping result can be obtained from these specimens.The process of fixing and storing cells in 3:1 methanol/acetic acid introduces the possibility of acid nicking and de