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The Application of Zoo-Fish Technique for Analysis of Chromosomal Rearrangements in the Equidae Family. ANNALS OF ANIMAL SCIENCE 2012. [DOI: 10.2478/v10220-012-0001-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Application of Zoo-Fish Technique for Analysis of Chromosomal Rearrangements in the Equidae FamilyGenome analysis is necessary to trace evolutionary rearrangements and relationships between species. Initially, to this end, the tools of classical cytogenetics were used but along with the development of molecular cytogenetics methods it became possible to analyse the genome more thoroughly. One of the widely used methods is fluorescence in situ hybridization (FISH) and its different types. Zoo-FISH, or cross-species chromosome painting, which uses painting probes specific for whole chromosomes, enables detecting homologous synteny blocks, the occurrence of which is evidence that species share a common ancestry and are related. Zoo-FISH technique is complemented by FISH with probes specific to chromosome arms or repetitive sequences (telomeres, centromeres), which provide additional information about karyotype organization, as well as karyotype polymorphism and conservation. Another method used is FISH with gene-specific probes, which enable the localization of single loci, thus making it possible to determine linkages between genes and verify data obtained after using painting probes in Zoo-FISH technique. Because of its diverse karyotype and rapid karyotypic evolution, the Equidae family is an ideal object of study using a number of methods based on in situ hybridization, which, in turn, enables information to be obtained at many levels of DNA organization.
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Perelman P, Beklemisheva V, Yudkin D, Petrina T, Rozhnov V, Nie W, Graphodatsky A. Comparative Chromosome Painting in Carnivora and Pholidota. Cytogenet Genome Res 2012; 137:174-93. [DOI: 10.1159/000341389] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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Comstock KE, Lingaas F, Kirkness EF, Hitte C, Thomas R, Breen M, Galibert F, Ostrander EA. A high-resolution comparative map of canine Chromosome 5q14.3-q33 constructed utilizing the 1.5x canine genome sequence. Mamm Genome 2005; 15:544-51. [PMID: 15366374 DOI: 10.1007/s00335-004-2365-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A high-density map of the region of canine Chromosome 5 (CFA5) surrounding the evolutionary breakpoint between human Chromosomes 1p32 and 17pll was constructed by integrating a radiation hybrid map including 41 microsatellites, 10 BACs, and 59 genes and a linkage map including 18 markers. A collection of canine genomic survey sequences providing 1.5x coverage was used to identify dog orthologs of human genes, proving instrumental in the development of this map. Of particular interest is the canine BHD gene, within which we have previously described a single nucleotide polymorphism associated with Hereditary Multifocal Renal Cystadenocarcinoma and Nodular Dermatofibrosis (RCND) in German Shepherd dogs. The corresponding region of the human genome is particularly gene rich, containing genes involved in development, metabolism, and cancer that are likely to be of interest in future mapping studies. This current mapping effort on CFA5 expands the degree to which initial findings of linkage in canine families can be followed by successful positional cloning efforts and increases the value of the human genome sequence for defining candidate genes. Moreover, this study demonstrates the utility of genomic survey sequences when combined with accurate genome maps for rapid mapping of disease susceptibility loci.
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Affiliation(s)
- Kenine E Comstock
- Clinical and Human Biology Divisions, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave., D4-100, P.O. Box 19024, Seattle, Washington 98109-1024, USA
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Thomas R, Fiegler H, Ostrander EA, Galibert F, Carter NP, Breen M. A canine cancer-gene microarray for CGH analysis of tumors. Cytogenet Genome Res 2004; 102:254-60. [PMID: 14970712 DOI: 10.1159/000075758] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2003] [Accepted: 08/05/2003] [Indexed: 12/19/2022] Open
Abstract
As with many human cancers, canine tumors demonstrate recurrent chromosome aberrations. A detailed knowledge of such aberrations may facilitate diagnosis, prognosis and the selection of appropriate therapy. Following recent advances made in human genomics, we are developing a DNA microarray for the domestic dog, to be used in the detection and characterization of copy number changes in canine tumors. As a proof of principle, we have developed a small-scale microarray comprising 87 canine BAC clones. The array is composed of 26 clones selected from a panel of 24 canine cancer genes, representing 18 chromosomes, and an additional set of clones representing dog chromosomes 11, 13, 14 and 31. These chromosomes were shown previously to be commonly aberrant in canine multicentric malignant lymphoma. Clones representing the sex chromosomes were also included. We outline the principles of canine microarray development, and present data obtained from microarray analysis of three canine lymphoma cases previously characterized using conventional cytogenetic techniques.
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MESH Headings
- Animals
- Chromosomes, Artificial, Bacterial/genetics
- DNA, Neoplasm/genetics
- Dog Diseases/genetics
- Dogs/genetics
- Female
- Gene Expression Profiling/methods
- Gene Expression Profiling/statistics & numerical data
- Gene Expression Profiling/veterinary
- Gene Expression Regulation, Neoplastic/genetics
- Genes, Neoplasm/genetics
- In Situ Hybridization, Fluorescence/methods
- In Situ Hybridization, Fluorescence/statistics & numerical data
- In Situ Hybridization, Fluorescence/veterinary
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/veterinary
- Lymphoma, Non-Hodgkin/genetics
- Lymphoma, Non-Hodgkin/veterinary
- Male
- Metaphase/genetics
- Nucleic Acid Hybridization
- Oligonucleotide Array Sequence Analysis/methods
- Oligonucleotide Array Sequence Analysis/statistics & numerical data
- Oligonucleotide Array Sequence Analysis/veterinary
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/veterinary
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Affiliation(s)
- R Thomas
- Oncology Research Group, Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, UK
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Thomas R, Bridge W, Benke K, Breen M. Isolation and chromosomal assignment of canine genomic BAC clones representing 25 cancer-related genes. Cytogenet Genome Res 2004; 102:249-53. [PMID: 14970711 DOI: 10.1159/000075757] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2003] [Accepted: 09/02/2003] [Indexed: 11/19/2022] Open
Abstract
An extensive number of genes have been implicated in the initiation and progression of human cancers, aiding our understanding of the genetic aetiology of this highly heterogeneous disease. In order to facilitate extrapolation of such information between species, we have isolated and physically mapped the canine orthologues of 25 well-characterised human cancer-related genes. The identity of PCR products representing each canine gene marker was first confirmed by DNA sequencing analysis. Each product was then radiolabelled and used to screen a genomic BAC library for the domestic dog. The chromosomal location of each positive clone in the canine karyotype was determined by fluorescence in situ hybridisation (FISH) onto canine metaphase preparations. Of the 25 genes, the FISH localisation of 21 correlated fully with that expected on the basis of known regions of conserved synteny between the human and canine genomes. Three correlated less closely, and the chromosomal location of the remaining marker showed no apparent correlation with current comparative mapping data. In addition to generating useful comparative mapping information, this panel of markers will act as a valuable resource for detailed study of candidate genes likely to be involved in tumourigenesis, and also forms the basis of a canine cancer-gene genomic microarray currently being developed for the study of unbalanced genomic aberrations in canine tumours.
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Affiliation(s)
- R Thomas
- Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, UK
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Thomas R, Breen M, Binns MM. Chromosome assignment of six dog genes by FISH, and correlation with dog-human Zoo-FISH data. Anim Genet 2001; 32:148-51. [PMID: 11493263 DOI: 10.1046/j.1365-2052.2001.00731.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cross-species chromosome painting analyses have recently demonstrated the presence of regions of conserved synteny between the human and domestic dog genomes, aiding the search for candidate genes for inherited traits. Concerted efforts to subchromosomally assign substantial numbers of dog gene sequences are now needed in order to refine these comparative data, both in terms of marker density and resolution. We have developed novel PCR markers representing three dog genes (ALB, FOS, HNRPA2B1) for which no sequence or mapping data were previously available, to our knowledge. These, in addition to three gene markers previously described (ALDOA, RPE65, VCAM1), were used to isolate and chromosomally assign corresponding large insert genomic clones by fluorescence in situ hybridization (FISH). Chromosome assignments for these six dog genes are discussed in terms of those of the human orthologues, and correlated with existing comparative mapping information, identifying one apparent exception to existing Zoo-FISH data, and aiding refinement of the boundaries of conserved chromosome segments in both genomes.
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Affiliation(s)
- R Thomas
- Genetics Section, Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, CB8 7UU, UK.
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Chowdhary BP, Raudsepp T. Chromosome painting in farm, pet and wild animal species. METHODS IN CELL SCIENCE : AN OFFICIAL JOURNAL OF THE SOCIETY FOR IN VITRO BIOLOGY 2001; 23:37-55. [PMID: 11741143 DOI: 10.1007/978-94-010-0330-8_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
Among the advanced karyotype analysis approaches embraced by animal cytogenetics during the past decade, chromosome painting has had the greatest impact. Generation of chromosome specific paints is considered pivotal to his development. Additionally, ability to use these paints across species (referred to as Zoo-FISH or comparative painting) is undisputedly the most important breakthrough that has contributed to our ability to compare karyotypes of a wide range of evolutionarily highly diverged chromosome painting, and makes them aware of the tools/resources available to carry out this research in a variety of animal species. An overview of the current status of comparative chromosome painting results across closely as well as distantly related species is presented. Findings from different studies show how some segmental syntenies are more conserved as compared to others. The comparisons provide insight into the likely constitution of a vertebrate/mammalian ancestral karyotype and help understand some of the intricacies about karyotype evolution. Importance of comparative painting in setting the stage for rapid development of gene maps in a number of economically important species is elaborated.
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Affiliation(s)
- B P Chowdhary
- Department of Veterinary Anatomy and Public Health, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843-4458, USA.
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Breen M, Thomas R, Binns MM, Carter NP, Langford CF. Reciprocal chromosome painting reveals detailed regions of conserved synteny between the karyotypes of the domestic dog (Canis familiaris) and human. Genomics 1999; 61:145-55. [PMID: 10534400 DOI: 10.1006/geno.1999.5947] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The domestic dog is increasingly being recognized as a useful model for human disease. The aim of this study was to conduct the first detailed whole-genome comparison of human and dog using bidirectional heterologous chromosome painting (reciprocal Zoo-FISH) analysis. We used whole-chromosome paint probes produced from degenerate oligonucleotide-primed PCR amplification of high-resolution bivariate flow-sorted human and dog chromosomes. No fewer than 68 evolutionarily conserved segments were identified between the dog and the human karyotypes. The use of elongated metaphase chromosomes for both species allowed the boundaries of each evolutionarily conserved segment to be determined to subband resolution. The distribution of conserved segments is discussed, as are the applications of these data in refining the current status of the dog genome map.
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Affiliation(s)
- M Breen
- Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, CB8 7UU, United Kingdom.
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