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Molecular cytogenetics is the study of chromosome structure. Building off of classical cytogenetics approaches, molecular cytogenetics involves provides a close look at the chromosomes in a cell and can be used to reveal structural changes. This approach is based on fluorescence in situ hybridization (FISH) and is used to detect abnormalities in chromosome size and structure. Molecular cytogenetics has many applications in medicine and research, and is a useful diagnostic tool for genetic disorders and cancer.

FISH: in which DNA probes are labeled with different colored fluorescent tags to visualize one or more specific regions of the genome. FISH can either be performed as a direct approach to metaphase chromosomes or interphase nuclei. Alternatively, an indirect approach can be taken in which the entire genome can be assessed for copy number changes using virtual karyotyping. Virtual karyotypes are generated from arrays made of thousands to millions of probes, and computational tools are used to recreate the genome in silico.

Studies of meiosis
In eukaryotes, the Rad51 and Dmc1 proteins have a central role in meiosis. Teresawa et al. using immunofluorescence microscopy found that in Lilium longiflorum, Rad51 and Lim15 (an ortholog of Dmc1) co-localize on meiotic prophase I chromosomes where they form discrete foci. Using electron microscopic immunogold labeling localization, Anderson et al. found Rad51 and/or Lim15 proteins to be components of early meiotic nodules that are involved in recombination related events. The stages of meiosis in which the co-localization of the Rad51 and Lim15 proteins occurs are the leptotene and zygotene stages of meiosis, suggesting that meiotic recombination begins at the leptotene stage with the cooperation of these proteins and continues into zygotene. These proteins catalyze pairing of homologous chromosomes, DNA strand exchange, and recombinational repair of DNA damages.

Uses
Cancer cells often accumulate complex chromosomal structural changes, such as loss, duplication, inversion or movement of a segment. By using FISH, any changes to the chromosome will be made visible through changes to the fluorescent-labelled cancer chromosomes compared to healthy chromosomes. The findings of these cytogenetic experiments can shed light on the genetic causes for the cancer and locate potential therapeutic targets.

Molecular cytogenetics can also be used as a diagnostic tool for congenital syndromes in which the underlying genetic causes of the disease are unknown. Analysis of a patient's chromosome structure can reveal causative changes. New molecular biology methods developed in the past two decades such as next generation sequencing and RNA-seq have largely replaced molecular cytogenetics, but recently the use of derivatives of FISH such as multicolor FISH and multicolor banding (mBAND) have been growing in medical applications, too.

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