VCCS HEL and U937 cell line study: fresh and fixed cells

This study aims to determine the chromosome content and organisation of two myeloid leukaemia cell lines, HEL and U937. This will be done not only with SNP array data to determine breakpoints and copy number of copy number aberrations, but also with FISH (multicolour FISH, multicolour banding, centromere and single locus FISH) to identify translocation partners, chromosome organistion, centromere content, and provide some information on genome evolution in the cell line. Although several HEL SNP array karyotypes have been published and are available online the information here shows that there are some differences, and the additional FISH tests provide a greater depth of information on genome organisation and derivation of the abnormal chromosomes. The U937 cell line was also studied using DNA from fresh and fixed specimens for comparison of the quality of the SNP array data. Data from cells fixed using standard cytogenetic fixative (3:1 methanol:acetic acid) were compared to data from cells processed directly from tissue culture. Three specimens were processed with the Illumina CytoSNP 12 platform. Two of these (U937) represent fresh and fixed specimen for comparison. All samples were processed while in log phase. The method used in this experiment is described in: Mackinnon RN, Selan C, Zordan A, Wall M et al. CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens. Mol Cytogenet 2012 Feb 2;5:10. PMID: 22300816