Chromosome-specific DNA repeats: rapid identification in silico and validation using fluorescence  in situ hybridization.
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.
Department of Molecular and Cell Biology, University of California, Berkeley (UCB), Berkeley, CA 94720, USA. jhhsu@berkeley.edu.
Joanne H
JH
Hsu
Hui
H
Zeng
Kalistyn H
KH
Lemke
Aris A
AA
Polyzos
Jingly F
JF
Weier
Mei
M
Wang
Anna R
AR
Lawin-O'Brien
Heinz-Ulrich G
HU
Weier
Benjamin
B
O'Brien
D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D002885:Chromosomes, Human, Pair 16 / Q000235:genetics*; D002999:Clone Cells; D003198:Computer Simulation; D015342:DNA Probes / Q000378:metabolism; D004276:DNA, Satellite / Q000235:genetics; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D015203:Reproducibility of Results; D012730:Sex Chromosomes / Q000235:genetics; D014314:Trisomy / Q000235:genetics
D015342:DNA Probes; D004276:DNA, Satellite