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Chromosome-Specific DNA Repeats: Rapid Identification in Silico and Validation Using Fluorescence in Situ Hybridization
Department of Molecular and Cell Biology, University of California, Berkeley (UCB), Berkeley, CA 94720, USA
Life Sciences Division, E.O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
Department of Pathology, University of California, San Francisco (UCSF), CA 94143, USA
Department of Diabetes, City of Hope, 1500 Duarte Road, Duarte, CA 91010-3012, USA
Department of Fetal Medicine, Whipps Cross University Hospital, Barts Health NHS Trust, London E11 1NR, UK
William Harvey Research Institute, Queen Mary University London, Barts Health London, London EC1A 7BE, UK
Department of Anesthesiology, German Heart Institute, Berlin 13353, Germany
* Author to whom correspondence should be addressed.
Received: 2 December 2012; in revised form: 9 December 2012 / Accepted: 10 December 2012 / Published: 20 December 2012
Abstract: Chromosome enumeration in interphase and metaphase cells using fluorescence in situ hybridization (FISH) is an established procedure for the rapid and accurate cytogenetic analysis of cell nuclei and polar bodies, the unambiguous gender determination, as well as the definition of tumor-specific signatures. Present bottlenecks in the procedure are a limited number of commercial, non-isotopically labeled probes that can be combined in multiplex FISH assays and the relatively high price and effort to develop additional probes. We describe a streamlined approach for rapid probe definition, synthesis and validation, which is based on the analysis of publicly available DNA sequence information, also known as “database mining”. Examples of probe preparation for the human gonosomes and chromosome 16 as a selected autosome outline the probe selection strategy, define a timeline for expedited probe production and compare this novel selection strategy to more conventional probe cloning protocols.
Keywords: molecular cytogenetics; chromosomes; heterochromatin; DNA repeats; data mining; fluorescence in situ hybridization; bacterial artificial chromosomes; DNA probes
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Hsu, J.H.; Zeng, H.; Lemke, K.H.; Polyzos, A.A.; Weier, J.F.; Wang, M.; Lawin-O'Brien, A.R.; Weier, H.-U.G.; O'Brien, B. Chromosome-Specific DNA Repeats: Rapid Identification in Silico and Validation Using Fluorescence in Situ Hybridization. Int. J. Mol. Sci. 2013, 14, 57-71.
Hsu JH, Zeng H, Lemke KH, Polyzos AA, Weier JF, Wang M, Lawin-O'Brien AR, Weier H-UG, O'Brien B. Chromosome-Specific DNA Repeats: Rapid Identification in Silico and Validation Using Fluorescence in Situ Hybridization. International Journal of Molecular Sciences. 2013; 14(1):57-71.
Hsu, Joanne H.; Zeng, Hui; Lemke, Kalistyn H.; Polyzos, Aris A.; Weier, Jingly F.; Wang, Mei; Lawin-O'Brien, Anna R.; Weier, Heinz-Ulrich G.; O'Brien, Benjamin. 2013. "Chromosome-Specific DNA Repeats: Rapid Identification in Silico and Validation Using Fluorescence in Situ Hybridization." Int. J. Mol. Sci. 14, no. 1: 57-71.