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Hubert Vaudry - One of the best experts on this subject based on the ideXlab platform.

  • Linkage Mapping of the [Pro 2 ]Somatostatin-14 Gene in Zebrafish: Evolutionary Perspectives
    Annals of the New York Academy of Sciences, 2005
    Co-Authors: Hervé Tostivint, Marc Ekker, J. Michael Conlon, Lucille Joly, Isabelle Lihrmann, Hubert Vaudry
    Abstract:

    Radiation Hybrid Mapping assigned the zebrafish [Pro(2)]somatostatin-14 (also termed somatostatin 2; SS2) gene to linkage group 23 of the zebrafish genome, close to the marker nadl1.2. Comparative genomic analysis revealed conserved syntenies of the SS2 gene locus with part of the human 1p36 region, where the cortistatin gene is located. This observation strongly suggests that the SS2 gene in nonmammalian species and the cortistatin gene in mammals are orthologous.

  • Linkage Mapping of the [Pro2]Somatostatin‐14 Gene in Zebrafish: Evolutionary Perspectives
    Annals of the New York Academy of Sciences, 2005
    Co-Authors: Hervé Tostivint, Marc Ekker, J. Michael Conlon, Lucille Joly, Isabelle Lihrmann, Hubert Vaudry
    Abstract:

    Radiation Hybrid Mapping assigned the zebrafish [Pro 2 ]somato-statin-14 (also termed somatostatin 2; SS2) gene to linkage group 23 of the zebrafish genome, close to the marker nadll.2. Comparative genomic analysis revealed conserved syntenies of the SS2 gene locus with part of the human lp36 region, where the cortistatin gene is located. This observation strongly suggests that the SS2 gene in nonmammalian species and the cortistatin gene in mammals are orthologous.

Lucille Joly - One of the best experts on this subject based on the ideXlab platform.

  • Linkage Mapping of the [Pro 2 ]Somatostatin-14 Gene in Zebrafish: Evolutionary Perspectives
    Annals of the New York Academy of Sciences, 2005
    Co-Authors: Hervé Tostivint, Marc Ekker, J. Michael Conlon, Lucille Joly, Isabelle Lihrmann, Hubert Vaudry
    Abstract:

    Radiation Hybrid Mapping assigned the zebrafish [Pro(2)]somatostatin-14 (also termed somatostatin 2; SS2) gene to linkage group 23 of the zebrafish genome, close to the marker nadl1.2. Comparative genomic analysis revealed conserved syntenies of the SS2 gene locus with part of the human 1p36 region, where the cortistatin gene is located. This observation strongly suggests that the SS2 gene in nonmammalian species and the cortistatin gene in mammals are orthologous.

  • Linkage Mapping of the [Pro2]Somatostatin‐14 Gene in Zebrafish: Evolutionary Perspectives
    Annals of the New York Academy of Sciences, 2005
    Co-Authors: Hervé Tostivint, Marc Ekker, J. Michael Conlon, Lucille Joly, Isabelle Lihrmann, Hubert Vaudry
    Abstract:

    Radiation Hybrid Mapping assigned the zebrafish [Pro 2 ]somato-statin-14 (also termed somatostatin 2; SS2) gene to linkage group 23 of the zebrafish genome, close to the marker nadll.2. Comparative genomic analysis revealed conserved syntenies of the SS2 gene locus with part of the human lp36 region, where the cortistatin gene is located. This observation strongly suggests that the SS2 gene in nonmammalian species and the cortistatin gene in mammals are orthologous.

  • Radiation Hybrid Mapping of the zebrafish genome.
    Proceedings of the National Academy of Sciences of the United States of America, 1999
    Co-Authors: Neil A. Hukriede, Lucille Joly, Michael Tsang, Jennifer Miles, Patricia Tellis, Jonathan A. Epstein, William B. Barbazuk, Barry H. Paw, John H. Postlethwait
    Abstract:

    The zebrafish is an excellent genetic system for the study of vertebrate development and disease. In an effort to provide a rapid and robust tool for zebrafish gene Mapping, a panel of Radiation Hybrids (RH) was produced by fusion of irradiated zebrafish AB9 cells with mouse B78 cells. The overall retention of zebrafish sequences in the 93 RH cell lines that constitute the LN54 panel is 22%. Characterization of the LN54 panel with 849 simple sequence length polymorphism markers, 84 cloned genes and 122 expressed sequence tags allowed the production of an RH map whose total size was 11,501 centiRays. From this value, we estimated the average breakpoint frequency of the LN54 RH panel to correspond to 1 centiRay = 148 kilobase. Placement of a group of 235 unbiased markers on the RH map suggests that the map generated for the LN54 panel, at present, covers 88% of the zebrafish genome. Comparison of marker positions in RH and meiotic maps indicated a 96% concordance. Mapping expressed sequence tags and cloned genes by using the LN54 panel should prove to be a valuable method for the identification of candidate genes for specific mutations in zebrafish.

Francis Galibert - One of the best experts on this subject based on the ideXlab platform.

  • 1 Survey Sequencing and Radiation Hybrid Mapping to Construct Comparative Maps
    2015
    Co-Authors: Christophe Hitte, Ewen F. Kirkness, Elaine A. Ostr, Francis Galibert
    Abstract:

    Abstract: Radiation Hybrid (RH) Mapping has become one of the most well established techniques for economically and efficiently navigating genomes of interest. The success of the technique relies on random chromosome breakage of a target genome, which is then captured by recipient cells missing a pre-selected marker. Selection for Hybrid cells that have DNA fragments bearing the marker of choice, plus a random set of DNA fragments from the initial irRadiation, generates a set of cell lines that recapitulates the genome of the target organism several-fold. Markers or genes of interest are analyzed by PCR using DNA isolated from each cell line. Statistical tools are applied to determine both the linear order of markers on each chromosome, and the confidence of each placement. The resolution of the resulting map relies on many factors, most notably the degree of breakage from the initial Radiation as well as the number of Hybrid clones and mean retention value. A high resolution RH map of a genome derived from low pass or survey sequencing (coverage from 1 to 2x) can provide essentially the same comparative data on gene order that is derived from high-coverage (greater than 7x) genome sequencing. When combined with Fluorescence in Situ Hybridization (FISH), RH maps are complete and ordered blueprints for each chromosome. They give information about the relative order and spacing of genes and markers, and allow investigators to move between target and reference genomes, such as those of mouse or human, with ease although the approach is not limited to mammal ha l-

  • Contribution of Radiation Hybrids to genome Mapping in domestic animals.
    Cytogenetic and genome research, 2009
    Co-Authors: Thomas Faraut, Christophe Hitte, S. De Givry, Y. Lahbib-mansais, Mireille Morisson, David J. Milan, Thomas Schiex, Bertrand Servin, Alain Vignal, Francis Galibert
    Abstract:

    Radiation Hybrid Mapping has emerged in the end of the 1990s as a successful and complementary approach to map genomes, essentially because of its ability to bridge the gaps between genetic and clone-based physical maps, but also using comparative Mapping approaches, between ‘gene-rich’ and ‘gene-poor’ maps. Since its early development in human, Radiation Hybrid Mapping played a pivotal role in the process of Mapping animal genomes, especially mammalian ones. We review here all the different steps involved in Radiation Hybrid Mapping from the constitution of panels to the construction of maps. A description of its contribution to whole genome maps with a special emphasis on domestic animals will also be presented. Finally, current applications of Radiation Hybrid Mapping in the context of whole genome assemblies will be described.

  • Survey sequencing and Radiation Hybrid Mapping to construct comparative maps
    Methods in molecular biology (Clifton N.J.), 2008
    Co-Authors: Christophe Hitte, Elaine A Ostrander, Ewen F. Kirkness, Francis Galibert
    Abstract:

    Radiation Hybrid (RH) Mapping has become one of the most well-established techniques for economically and efficiently navigating genomes of interest. The success of the technique relies on random chromosome breakage of a target genome, which is then captured by recipient cells missing a preselected marker. Selection for Hybrid cells that have DNA fragments bearing the marker of choice, plus a random set of DNA fragments from the initial irRadiation, generates a set of cell lines that recapitulates the genome of the target organism several-fold. Markers or genes of interest are analyzed by PCR using DNA isolated from each cell line. Statistical tools are applied to determine both the linear order of markers on each chromosome, and the confidence of each placement. The resolution of the resulting map relies on many factors, most notably the degree of breakage from the initial Radiation as well as the number of Hybrid clones and mean retention value.A high-resolution RH map of a genome derived from low pass or survey sequencing (coverage from 1 to 2 times) can provide essentially the same comparative data on gene order that is derived from high-coverage (greater than x7) genome sequencing. When combined with fluorescence in situ Hybridization, RH maps are complete and ordered blueprints for each chromosome. They give information about the relative order and spacing of genes and markers, and allow investigators to move between target and reference genomes, such as those of mouse or human, with ease although the approach is not limited to mammal genomes.

  • Radiation Hybrid Mapping of cataract genes in the dog.
    Molecular vision, 2006
    Co-Authors: L.s. Hunter, Francis Galibert, Catherine André, Duska J. Sidjanin, Jennifer L. Johnson, Barbara Zangerl, Ewen F. Kirkness, Elijah J. Talamas, Gregory M. Acland, Gustavo D. Aguirre
    Abstract:

    Purpose: To facilitate the molecular characterization of naturally occurring cataracts in dogs by providing the Radiation Hybrid location of 21 cataract-associated genes along with their closely associated polymorphic markers. These can be used for segregation testing of the candidate genes in canine cataract pedigrees. Methods: Twenty-one genes with known mutations causing hereditary cataracts in man and/or mouse were selected and mapped to canine chromosomes using a canine:hamster Radiation Hybrid RH5000 panel. Each cataract gene ortholog was mapped in relation to over 3,000 markers including microsatellites, ESTs, genes, and BAC clones. The resulting independently determined RH-map locations were compared with the corresponding gene locations from the draft sequence of the canine genome. Results: Twenty-one cataract orthologs were mapped to canine chromosomes. The genetic locations and nearest polymorphic markers were determined for 20 of these orthologs. In addition, the resulting cataract gene locations, as determined experimentally by this study, were compared with those determined by the canine genome project. All genes mapped within or near chromosomal locations with previously established homology to the corresponding human gene locations based on canine:human chromosomal synteny. Conclusions: The location of selected cataract gene orthologs in the dog, along with their nearest polymorphic markers, serves as a resource for association and linkage testing in canine pedigrees segregating inherited cataracts. The recent development of canine genomic resources make canine models a practical and valuable resource for the study of human hereditary cataracts. Canine models can serve as large animal models intermediate between mouse and man for both gene discovery and the development of novel cataract therapies.

  • CRH_Server: an online comparative and Radiation Hybrid Mapping server for the canine genome
    Bioinformatics (Oxford England), 2004
    Co-Authors: Christophe Hitte, Catherine André, Elaine A Ostrander, Thomas Derrien, Francis Galibert
    Abstract:

    Summary: CRH_Server is an on line Comparative and Radiation Hybrid Mapping Server dedicated to canine genomics. CRH_Server allows users to compute their own RH data using the current canine RH map, and allows comparative dog/human Mapping analyses. Finally, it suggests multiple options for storage and queries of the dog RH database. Availability: http://idefix.univ-rennes1.fr:8080/Dogs/rh-server.html Supplementary information: All information is available at http://idefix.univ-rennes1.fr:8080/Dogs/help_rh-server.html

Hervé Tostivint - One of the best experts on this subject based on the ideXlab platform.

  • Linkage Mapping of the [Pro 2 ]Somatostatin-14 Gene in Zebrafish: Evolutionary Perspectives
    Annals of the New York Academy of Sciences, 2005
    Co-Authors: Hervé Tostivint, Marc Ekker, J. Michael Conlon, Lucille Joly, Isabelle Lihrmann, Hubert Vaudry
    Abstract:

    Radiation Hybrid Mapping assigned the zebrafish [Pro(2)]somatostatin-14 (also termed somatostatin 2; SS2) gene to linkage group 23 of the zebrafish genome, close to the marker nadl1.2. Comparative genomic analysis revealed conserved syntenies of the SS2 gene locus with part of the human 1p36 region, where the cortistatin gene is located. This observation strongly suggests that the SS2 gene in nonmammalian species and the cortistatin gene in mammals are orthologous.

  • Linkage Mapping of the [Pro2]Somatostatin‐14 Gene in Zebrafish: Evolutionary Perspectives
    Annals of the New York Academy of Sciences, 2005
    Co-Authors: Hervé Tostivint, Marc Ekker, J. Michael Conlon, Lucille Joly, Isabelle Lihrmann, Hubert Vaudry
    Abstract:

    Radiation Hybrid Mapping assigned the zebrafish [Pro 2 ]somato-statin-14 (also termed somatostatin 2; SS2) gene to linkage group 23 of the zebrafish genome, close to the marker nadll.2. Comparative genomic analysis revealed conserved syntenies of the SS2 gene locus with part of the human lp36 region, where the cortistatin gene is located. This observation strongly suggests that the SS2 gene in nonmammalian species and the cortistatin gene in mammals are orthologous.

David R. Cox - One of the best experts on this subject based on the ideXlab platform.

  • Selected locus and multiple panel models for Radiation Hybrid Mapping.
    American journal of human genetics, 1996
    Co-Authors: Kathryn L Lunetta, Michael Boehnke, Kenneth Lange, David R. Cox
    Abstract:

    Abstract We develop two new types of models for whole-genome Radiation Hybrid Mapping using the general multipoint framework. The first, selected locus models, are appropriate for Mapping markers in the region of a selectable locus that was used in creation of the Hybrids. The models allow for strong retention of the selectable locus, with retention rates decreasing with increasing distance from the selectable locus in both directions. We illustrate the application of these models with 10 chromosome 17 sequence-tagged site (STS) markers and the thymidine kinase (TK) locus typed on a whole-genome Hybrid panel in which TK was used in the selection process. The second set of models are appropriate when loci typed on two or more independent panels are to be used to build maps. Maps can be built assuming interlocus distances are independent or proportional between the panels, and the hypothesis of proportional distances can be tested. We illustrate the application of these models by using 27 chromosome 21 STS markers typed on two Hybrid panels created with Radiation doses of approximately 10,000 and approximately 50,000 Rads.

  • statistical methods for polyploid Radiation Hybrid Mapping
    Genome Research, 1995
    Co-Authors: Kenneth Lange, Michael Boehnke, David R. Cox, Kathryn L Lunetta
    Abstract:

    Radiation Hybrid Mapping is a somatic cell technique for ordering genetic loci along a chromosome and estimating physical distances between adjacent loci. This paper presents a model of fragment generation and retention for data involving two or more copies of the chromosome of interest per clone. Such polyploid data can be generated by initially irradiating normal diploid cells or by pooling haploid or diploid clones. The current model assumes that fragments are generated in the ancestral cell of a clone according to an independent Poisson breakage process along each chromosome. Once generated, fragments are independently retained in the clone with a common retention probability. On the basis of this and less restrictive retention models, statistical criteria such as minimum obligate breaks, maximum likelihood ratios, and Bayesian posterior probabilities can be used to decide locus order. Distances can be estimated by maximum likelihood. Likelihood computation is particularly challenging, and computing techniques from the theory of hidden Markov chains prove crucial. Within this context it is possible to incorporate typing errors. The statistical tools discussed here are applied to 14 loci on the short arm of human chromosome 4.

  • Experimental design and error detection for polyploid Radiation Hybrid Mapping.
    Genome research, 1995
    Co-Authors: Kathryn L Lunetta, Michael Boehnke, Kenneth Lange, David R. Cox
    Abstract:

    In this paper we consider issues of experimental design and error detection and correction for polyploid Radiation Hybrid Mapping. Using analytic methods and computer simulation, we first consider the combinations of fragment retention rate, ploidy, and marker spacing that provide the best chance to order markers. We find that in general, combinations of ploidy and chromosome-specific retention rates that lead to a per-Hybrid retention rate of -50% result in the greatest power to order markers. We also find that analyzing polyploid Radiation Hybrids as if they were haploid does not compromise the ability to order markers but does result in less accurate intermarker distance estimates. Second, we examine the effect of typing errors on two-locus information, ability to order multiple loci, and estimation of intermarker distances and total map length. Even low levels of error result in large losses of information about breakage probabilities, markedly reduce ability to order loci, and inflate estimates of intermarker distances and total map length. We compare the ordering accuracy that results from duplicate typing of Hybrids to that of single typing twice as many Hybrids and find that duplicate typing results in a higher probability of identifying the true order as one of the best orders, but that single typing of twice as many Hybrids results in stronger support for the true order. For low error rates, framework maps constructed from the larger single-typed panels are only slightly less likely to be correct and include substantially more markers than the smaller double-typed panels. Third, we develop a method to calculate the distribution of the number of obligate chromosome breaks for a polyploid Radiation Hybrid under a given locus order and discuss how this method may be used to identify Hybrids with suspiciously large numbers of chromosome breaks.

  • Radiation Hybrid Mapping.
    Proceedings of the National Academy of Sciences of the United States of America, 1991
    Co-Authors: S Lawrence, Newton E. Morton, David R. Cox
    Abstract:

    Abstract A theory is developed to predict marker retention and conditional retention or loss in Radiation Hybrids. Applied to multiple pairwise analysis of a human chromosome 21 data set, this theory fits much better than proposed alternatives and gives a physical map consistent with other evidence and robust with respect to errors to typing. Radiation Hybrids have great promise to provide order and physical location at two levels of resolution, spanning the techniques of linkage and restriction fragments and not limited to polymorphic loci.

  • Statistical methods for multipoint Radiation Hybrid Mapping.
    American journal of human genetics, 1991
    Co-Authors: Michael Boehnke, Kenneth Lange, David R. Cox
    Abstract:

    On the basis of the earlier work of Goss and Harris, Cox et al. introduced Radiation Hybrid (RH) Mapping, a somatic cell genetic technique for constructing fine-structure maps of human chromosomes. Radiation Hybrid Mapping uses X-ray breakage of chromosomes to order a set of genetic loci and to estimate distances between them. To analyze RH Mapping data Cox et al. derived statistical methods that employ information on sets of two and four loci, to build an overall locus order. Here we describe alternative nonparametric and maximum-likelihood methods for the analysis of RHs that use information on many loci simultaneously, including information on partially typed Hybrids. Combination of these multipoint methods provides a statistically more efficient solution to the locus-ordering problem. We illustrate our approach by applying it to RH Mapping data on 14 markers in 99 Radiation Hybrids for the proximal long arm of human chromosome 21.