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1. Author Correction: Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

Author

Meadows, Jennifer R. S., Kidd, Jefrey M., Wang, Guo-Dong, Parker, Heidi G., Schall, Peter Z., Bianchi, Matteo, Christmas, Matthew J., Bougiouri, Katia, Buckley, Reuben M., Hitte, Christophe, Nguyen, Anthony K., Wang, Chao, Jagannathan, Vidhya, Niskanen, Julia E., Frantz, Laurent A. F., Arumilli, Meharji, Hundi, Sruthi, Lindblad-Toh, Kerstin, Ginja, Catarina, Agustina, Kadek Karang, André, Catherine, Boyko, Adam R., Davis, Brian W., Drögemüller, Michaela, Feng, Xin-Yao, Gkagkavouzis, Konstantinos, Iliopoulos, Giorgos, Harris, Alexander C., Hytönen, Marjo K., Kalthof, Daniela C., Liu, Yan-Hu, Lymberakis, Petros, Poulakakis, Nikolaos, Pires, Ana Elisabete, Racimo, Fernando, Ramos-Almodovar, Fabian, Savolainen, Peter, Venetsani, Semina, Tammen, Imke, Triantafyllidis, Alexandros, vonHoldt, Bridgett, Wayne, Robert K., Larson, Greger, Nicholas, Frank W., Lohi, Hannes, Leeb, Tosso, Zhang, Ya-Ping, and Ostrander, Elaine A.

Published
2023
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2. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

Author

Meadows, Jennifer R. S., Kidd, Jeffrey M., Wang, Guo-Dong, Parker, Heidi G., Schall, Peter Z., Bianchi, Matteo, Christmas, Matthew J., Bougiouri, Katia, Buckley, Reuben M., Hitte, Christophe, Nguyen, Anthony K., Wang, Chao, Jagannathan, Vidhya, Niskanen, Julia E., Frantz, Laurent A. F., Arumilli, Meharji, Hundi, Sruthi, Lindblad-Toh, Kerstin, Ginja, Catarina, Agustina, Kadek Karang, André, Catherine, Boyko, Adam R., Davis, Brian W., Drögemüller, Michaela, Feng, Xin-Yao, Gkagkavouzis, Konstantinos, Iliopoulos, Giorgos, Harris, Alexander C., Hytönen, Marjo K., Kalthoff, Daniela C., Liu, Yan-Hu, Lymberakis, Petros, Poulakakis, Nikolaos, Pires, Ana Elisabete, Racimo, Fernando, Ramos-Almodovar, Fabian, Savolainen, Peter, Venetsani, Semina, Tammen, Imke, Triantafyllidis, Alexandros, vonHoldt, Bridgett, Wayne, Robert K., Larson, Greger, Nicholas, Frank W., Lohi, Hannes, Leeb, Tosso, Zhang, Ya-Ping, and Ostrander, Elaine A.

Published
2023
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3. A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs

Author

Guyon Richard, Rakotomanga Michaelle, Azzouzi Naoual, Coutanceau Jean Pierre, Bonillo Celine, D’Cotta Helena, Pepey Elodie, Soler Lucile, Rodier-Goud Marguerite, D’Hont Angelique, Conte Matthew A, van Bers Nikkie EM, Penman David J, Hitte Christophe, Crooijmans Richard PMA, Kocher Thomas D, Ozouf-Costaz Catherine, Baroiller Jean, and Galibert Francis

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. Results We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. Conclusion The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.

Published
2012
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4. Revisiting the missing protein-coding gene catalog of the domestic dog

Author

Galibert Francis, Ostrander Elaine A, André Catherine, Vaysse Amaury, Thézé Julien, Derrien Thomas, and Hitte Christophe

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Among mammals for which there is a high sequence coverage, the whole genome assembly of the dog is unique in that it predicts a low number of protein-coding genes, ~19,000, compared to the over 20,000 reported for other mammalian species. Of particular interest are the more than 400 of genes annotated in primates and rodent genomes, but missing in dog. Results Using over 14,000 orthologous genes between human, chimpanzee, mouse rat and dog, we built multiple pairwise synteny maps to infer short orthologous intervals that were targeted for characterizing the canine missing genes. Based on gene prediction and a functionality test using the ratio of replacement to silent nucleotide substitution rates (dN/dS), we provide compelling structural and functional evidence for the identification of 232 new protein-coding genes in the canine genome and 69 gene losses, characterized as undetected gene or pseudogenes. Gene loss phyletic pattern analysis using ten species from chicken to human allowed us to characterize 28 canine-specific gene losses that have functional orthologs continuously from chicken or marsupials through human, and 10 genes that arose specifically in the evolutionary lineage leading to rodent and primates. Conclusion This study demonstrates the central role of comparative genomics for refining gene catalogs and exploring the evolutionary history of gene repertoires, particularly as applied for the characterization of species-specific gene gains and losses.

Published
2009
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5. Genetic diversity of canine olfactory receptors

Author

Hitte Christophe, André Catherine, Dréano Stéphane, Vaysse Amaury, Rimbault Maud, Tacher Sandrine, Robin Stéphanie, and Galibert Francis

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Evolution has resulted in large repertoires of olfactory receptor (OR) genes, forming the largest gene families in mammalian genomes. Knowledge of the genetic diversity of olfactory receptors is essential if we are to understand the differences in olfactory sensory capability between individuals. Canine breeds constitute an attractive model system for such investigations. Results We sequenced 109 OR genes considered representative of the whole OR canine repertoire, which consists of more than 800 genes, in a cohort of 48 dogs of six different breeds. SNP frequency showed the overall level of polymorphism to be high. However, the distribution of SNP was highly heterogeneous among OR genes. More than 50% of OR genes were found to harbour a large number of SNP, whereas the rest were devoid of SNP or only slightly polymorphic. Heterogeneity was also observed across breeds, with 25% of the SNP breed-specific. Linkage disequilibrium within OR genes and OR clusters suggested a gene conversion process, consistent with a mean level of polymorphism higher than that observed for introns and intergenic sequences. A large proportion (47%) of SNP induced amino-acid changes and the Ka/Ks ratio calculated for all alleles with a complete ORF indicated a low selective constraint with respect to the high level of redundancy of the olfactory combinatory code and an ongoing pseudogenisation process, which affects dog breeds differently. Conclusion Our demonstration of a high overall level of polymorphism, likely to modify the ligand-binding capacity of receptors distributed differently within the six breeds tested, is the first step towards understanding why Labrador Retrievers and German Shepherd Dogs have a much greater potential for use as sniffer dogs than Pekingese dogs or Greyhounds. Furthermore, the heterogeneity in OR polymorphism observed raises questions as to why, in a context in which most OR genes are highly polymorphic, a subset of these genes is not? This phenomenon may be related to the nature of their ligands and their importance in everyday life.

Published
2009
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6. Coat colour in dogs: identification of the Merle locus in the Australian shepherd breed

Author

Denis Bernard, Galibert Francis, Derrien Thomas, Vilboux Thierry, Dréano Stéphane, Hitte Christophe, Corre Sébastien, Hédan Benoit, Galibert Marie-Dominique, and André Catherine

Subjects
Veterinary medicine, SF600-1100
Abstract

Abstract Background Coat colours in canines have many natural phenotypic variants. Some of the genes and alleles involved also cause genetic developmental defects, which are also observed in humans and mice. We studied the genetic bases of the merle phenotype in dogs to shed light on the pigmentation mechanisms and to identify genes involved in these complex pathways. The merle phenotype includes a lack of eumelanic pigmentation and developmental defects, hearing impairments and microphthalmia. It is similar to that observed in microphthalmia mouse mutants. Results Taking advantage of the dog as a powerful genetic model and using recently available genomic resources, we investigated the segregation of the merle phenotype in a five-generation pedigree, comprising 96 sampled Australian shepherd dogs. Genetic linkage analysis allowed us to identify a locus for the merle phenotype, spanning 5.5 megabases, at the centromeric tip of canine chromosome 10 (CFA10). This locus was supported by a Lod score of 15.65 at a recombination fraction θ = 0. Linkage analysis in three other breeds revealed that the same region is linked to the merle phenotype. This region, which is orthologous to human chromosome 12 (HSA12 q13-q14), belongs to a conserved ordered segment in the human and mouse genome and comprises several genes potentially involved in pigmentation and development. Conclusion This study has identified the locus for the merle coat colour in dogs to be at the centromeric end of CFA10. Genetic studies on other breeds segregating the merle phenotype should allow the locus to be defined more accurately with the aim of identifying the gene. This work shows the power of the canine system to search for the genetic bases of mammalian pigmentation and developmental pathways.

Published
2006
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7. An integrated 4249 marker FISH/RH map of the canine genome

Author

Mahairas Gregory G, Guyon Richard, Hudson Ruth, Kirkness Ewen F, Parker Heidi G, Evanno Gwenaelle, Scott Allyson, Sabacan Leah, Cadieu Edouard, Thomas Rachael, Lorentzen Travis D, Hitte Christophe, Breen Matthew, Gelfenbeyn Boris, Fraser Claire M, André Catherine, Galibert Francis, and Ostrander Elaine A

Subjects
canine, dog, radiation hybrid, microsatellites, ESTs, BAC-ends, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The 156 breeds of dog recognized by the American Kennel Club offer a unique opportunity to map genes important in genetic variation. Each breed features a defining constellation of morphological and behavioral traits, often generated by deliberate crossing of closely related individuals, leading to a high rate of genetic disease in many breeds. Understanding the genetic basis of both phenotypic variation and disease susceptibility in the dog provides new ways in which to dissect the genetics of human health and biology. Results To facilitate both genetic mapping and cloning efforts, we have constructed an integrated canine genome map that is both dense and accurate. The resulting resource encompasses 4249 markers, and was constructed using the RHDF5000-2 whole genome radiation hybrid panel. The radiation hybrid (RH) map features a density of one marker every 900 Kb and contains 1760 bacterial artificial chromosome clones (BACs) localized to 1423 unique positions, 851 of which have also been mapped by fluorescence in situ hybridization (FISH). The two data sets show excellent concordance. Excluding the Y chromosome, the map features an RH/FISH mapped BAC every 3.5 Mb and an RH mapped BAC-end, on average, every 2 Mb. For 2233 markers, the orthologous human genes have been established, allowing the identification of 79 conserved segments (CS) between the dog and human genomes, dramatically extending the length of most previously described CS. Conclusions These results provide a necessary resource for the canine genome mapping community to undertake positional cloning experiments and provide new insights into the comparative canine-human genome maps.

Published
2004
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9. Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps

Author

Murphy, William J., Larkin, Denis M., Bourque, Guillaume, Tesler, Glenn, Auvil, Loretta, Beever, Jonathan E., Chowdhary, Bhanu P., Galibert, Francis, Gatzke, Lisa, Hitte, Christophe, Meyers, Stacey N., Milan, Denis, Ostrander, Elaine A., Pape, Greg, Parker, Heidi G., Raudsepp, Terje, Rogatcheva, Margarita B., Schook, Lawrence B., Skow, Loren C., Welge, Michael, Womack, James E., O'Brien, Stephen J., Pevzner, Pavel A., and Lewin, Harris A.

Published
2005

10. A 1-Mb Resolution Radiation Hybrid Map of the Canine Genome

Author

Guyon, Richard, Lorentzen, Travis D., Hitte, Christophe, Kim, Lisa, Cadieu, Edouard, Parker, Heidi G., Quignon, Pascale, Lowe, Jennifer K., Renier, Corinne, Gelfenbeyn, Boris, Vignaux, Françoise, DeFrance, Hawkins B., Gloux, Stephanie, Mahairas, Gregory G., André, Catherine, Galibert, Francis, and Ostrander, Elaine A.

Published
2003

12. Genomic and archaeological evidence suggests a dual origin of domestic dogs

Author

Frantz, Laurent A. F., Mullin, Victoria E., Pionnier-Capitan, Maud, Lebrasseur, Ophélie, Ollivier, Morgane, Perri, Angela, Linderholm, Anna, Mattiangeli, Valeria, Teasdale, Matthew D., Dimopoulos, Evangelos A., Tresset, Anne, Duffraisse, Marilyne, McCormick, Finbar, Bartosiewicz, László, Gál, Erika, Nyerge, Éva A., Sablin, Mikhail V., Bréhard, Stéphanie, Mashkour, Marjan, Benjam, Adrian, Gillet, Benjamin, Hughes, Sandrine, Chassaing, Olivier, Hitte, Christophe, Vigne, Jean-Denis, Dobney, Keith, Hänni, Catherine, Bradley, Daniel G., and Larson, Greger

Published
2016

13. Figure S2 from Discovery of Human-Similar Gene Fusions in Canine Cancers

Author

Ulvé, Ronan, primary, Rault, Mélanie, primary, Bahin, Mathieu, primary, Lagoutte, Laetitia, primary, Abadie, Jérôme, primary, De Brito, Clotilde, primary, Coindre, Jean-Michel, primary, Botherel, Nadine, primary, Rousseau, Audrey, primary, Wucher, Valentin, primary, Cadieu, Edouard, primary, Thieblemont, Catherine, primary, Hitte, Christophe, primary, Cornevin, Laurence, primary, Cabillic, Florian, primary, Bachelot, Laura, primary, Gilot, David, primary, Hennuy, Benoit, primary, Guillaudeux, Thierry, primary, Le Goff, Arnaud, primary, Derrien, Thomas, primary, Hédan, Benoît, primary, and André, Catherine, primary

Published
2023
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14. Table S2 from Discovery of Human-Similar Gene Fusions in Canine Cancers

Author

Ulvé, Ronan, primary, Rault, Mélanie, primary, Bahin, Mathieu, primary, Lagoutte, Laetitia, primary, Abadie, Jérôme, primary, De Brito, Clotilde, primary, Coindre, Jean-Michel, primary, Botherel, Nadine, primary, Rousseau, Audrey, primary, Wucher, Valentin, primary, Cadieu, Edouard, primary, Thieblemont, Catherine, primary, Hitte, Christophe, primary, Cornevin, Laurence, primary, Cabillic, Florian, primary, Bachelot, Laura, primary, Gilot, David, primary, Hennuy, Benoit, primary, Guillaudeux, Thierry, primary, Le Goff, Arnaud, primary, Derrien, Thomas, primary, Hédan, Benoît, primary, and André, Catherine, primary

Published
2023
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19. MTM1 mutation associated with X-linked myotubular myopathy in Labrador Retrievers

Author

Beggs, Alan H., Böhm, Johann, Snead, Elizabeth, Kozlowski, Marek, Maurer, Marie, Minor, Katie, Childers, Martin K., Taylor, Susan M., Hitte, Christophe, Mickelson, James R., Guo, Ling T., Mizisin, Andrew P., Buj-Bello, Anna, Tiret, Laurent, Laporte, Jocelyn, Shelton, G. Diane, and Kunkel, Louis M.

Published
2010

20. A canine Arylsulfatase G (ARSG) mutation leading to a sulfatase deficiency is associated with neuronal ceroid lipofuscinosis

Author

Abitbol, Marie, Thibaud, Jean-Laurent, Olby, Natasha J., Hitte, Christophe, Puech, Jean-Philippe, Maurer, Marie, Pilot-Storck, Fanny, Hédan, Benoit, Dréano, Stéphane, Brahimi, Sandra, Delattre, Delphine, André, Catherine, Gray, Françoise, Delisle, Françoise, Caillaud, Catherine, Bernex, Florence, Panthier, Jean-Jacques, Aubin-Houzelstein, Geneviève, Blot, Stéphane, Tiret, Laurent, and Rine, Jasper

Published
2010

21. Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets

Author

Prouteau, Anais, Mottier, Stephanie, Primot, Aline, Cadieu, Edouard, Bachelot, Laura, Botherel, Nadine, Cabillic, Florian, Houel, Armel, Cornevin, Laurence, Kergal, Camille, Corre, Sebastien, Abadie, Jerome, Hitte, Christophe, Gilot, David, Lindblad-Toh, Kerstin, Andre, Catherine, Derrien, Thomas, Hedan, Benoit, Prouteau, Anais, Mottier, Stephanie, Primot, Aline, Cadieu, Edouard, Bachelot, Laura, Botherel, Nadine, Cabillic, Florian, Houel, Armel, Cornevin, Laurence, Kergal, Camille, Corre, Sebastien, Abadie, Jerome, Hitte, Christophe, Gilot, David, Lindblad-Toh, Kerstin, Andre, Catherine, Derrien, Thomas, and Hedan, Benoit

Abstract

Simple Summary In humans, mucosal melanoma (MM) is a rare and aggressive cancer. The canine model is frequently and spontaneously affected by MM, thus facilitating the collection of samples and the study of its genetic bases. Thanks to an integrative genomic and transcriptomic analysis of 32 canine MM samples, we identified two molecular subgroups of MM with a different microenvironment and structural variant (SV) content. We demonstrated that SVs are associated with recurrently amplified regions, and identified new candidate oncogenes (TRPM7, GABPB1, and SPPL2A) for MM. Our findings suggest the existence of two MM molecular subgroups that could benefit from dedicated therapies, such as immune checkpoint inhibitors or targeted therapies, for both human and veterinary medicine. Mucosal melanoma (MM) is a rare, aggressive clinical cancer. Despite recent advances in genetics and treatment, the prognosis of MM remains poor. Canine MM offers a relevant spontaneous and immunocompetent model to decipher the genetic bases and explore treatments for MM. We performed an integrative genomic and transcriptomic analysis of 32 canine MM samples, which identified two molecular subgroups with a different microenvironment and structural variant (SV) content. The overexpression of genes related to the microenvironment and T-cell response was associated with tumors harboring a lower content of SVs, whereas the overexpression of pigmentation-related pathways and oncogenes, such as TERT, was associated with a high SV burden. Using whole-genome sequencing, we showed that focal amplifications characterized complex chromosomal rearrangements targeting oncogenes, such as MDM2 or CDK4, and a recurrently amplified region on canine chromosome 30. We also demonstrated that the genes TRPM7, GABPB1, and SPPL2A, located in this CFA30 region, play a role in cell proliferation, and thus, may be considered as new candidate oncogenes for human MM. Our findings suggest the existence of two MM molecular

Published
2022
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25. Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets

Author

Prouteau, Anais, primary, Mottier, Stephanie, additional, Primot, Aline, additional, Cadieu, Edouard, additional, Bachelot, Laura, additional, Botherel, Nadine, additional, Cabillic, Florian, additional, Houel, Armel, additional, Cornevin, Laurence, additional, Kergal, Camille, additional, Corre, Sébastien, additional, Abadie, Jérôme, additional, Hitte, Christophe, additional, Gilot, David, additional, Lindblad-Toh, Kerstin, additional, André, Catherine, additional, Derrien, Thomas, additional, and Hedan, Benoit, additional

Published
2022
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26. Meat source, sacrificial item and companion: A comparative look at the genomics of dogs in pre-Hispanic Mexico and Peru, and its legacy in modern populations

Author

Manin, Aurélie, Hitte, Christophe, Debruyne, Régis, Lin, A., Joncour, Pauline, Bréhard, Stéphanie, Lefevre, Christine, Goepfert, Nicolas, Ollivier, Morgane, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

27. Thousands of years of human-dog relationships: uncovering adaptation to dietary changes of dogs, resulting from the transition to farming

Author

Ollivier, Morgane, Hitte, Christophe, Barloy-Hubler, Frédérique, Balasse, Marie, Brassard, Colline, deborah, diquelou, Debruyne, Régis, Herrel, Anthony, Bréhard, Stéphanie, Bălăşescu, Adrian, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), and Mécanismes Adaptatifs et Evolution (MECADEV)

Subjects
[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

29. Drosophila translational elongation factor-1[gamma] is modified in response to DOA kinase activity and is essential for cellular viability

Author

Yujie Fan, Schlierf, Michael, Gaspar, Ana Cuervo, Dreux, Catherine, Kpebe, Arlette, Chaney, Linda, Mathieu, Aurelie, Hitte, Christophe, Gremy, Olivier, Sarot, Emeline, Horn, Mark, Yunlong Zhao, Kinzy, Terri Goss, and Rabinow, Leonard

Subjects
Drosophila -- Physiological aspects, Drosophila -- Genetic aspects, Gene mutations -- Research, Phosphorylation -- Research, Protein-protein interactions -- Analysis, Biological sciences
Published
2010

30. Canine oral melanoma genomic and transcriptomic study defines two molecular subgroups with different therapeutical targets

Author

Prouteau, Anais, primary, Mottier, Stephanie, additional, Primot, Aline, additional, Cadieu, Edouard, additional, Bachelot, Laura, additional, Botherel, Nadine, additional, Cabillic, Florian, additional, Houel, Armel, additional, Cornevin, Laurence, additional, Kergal, Camille, additional, Corre, Sebastien, additional, Abadie, Jerome, additional, Hitte, Christophe, additional, Gilot, David, additional, Lindblad-Toh, Kerstin, additional, Andre, Catherine, additional, Derrien, Thomas, additional, and Hedan, Benoit, additional

Published
2021
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31. Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome

Author

Jagannathan, Vidhya, primary, Hitte, Christophe, additional, Kidd, Jeffrey M., additional, Masterson, Patrick, additional, Murphy, Terence D., additional, Emery, Sarah, additional, Davis, Brian, additional, Buckley, Reuben M., additional, Liu, Yan-Hu, additional, Zhang, Xiang-Quan, additional, Leeb, Tosso, additional, Zhang, Ya-Ping, additional, Ostrander, Elaine A., additional, and Wang, Guo-Dong, additional

Published
2021
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33. Genome sequence, comparative analysis and haplotype structure of the domestic dog

Author

Lindblad-Toh, Kerstin, Wade, Claire M., Mikkelsen, Tarjei S., Karlsson, Elinor K., Jaffe, David B., Kamal, Michael, Clamp, Michele, Chang, Jean L., Kulbokas, III, Edward J., Zody, Michael C., Mauceli, Evan, Xie, Xiaohui, Breen, Matthew, Wayne, Robert K., Ostrander, Elaine A., Ponting, Chris P., Galibert, Francis, Smith, Douglas R., deJong, Pieter J., Kirkness, Ewen, Alvarez, Pablo, Biagi, Tara, Brockman, William, Butler, Jonathan, Chin, Chee-Wye, Cook, April, Cuff, James, Daly, Mark J., DeCaprio, David, Gnerre, Sante, Grabherr, Manfred, Kellis, Manolis, Kleber, Michael, Bardeleben, Carolyne, Goodstadt, Leo, Heger, Andreas, Hitte, Christophe, Kim, Lisa, Koepfli, Klaus-Peter, Parker, Heidi G., Pollinger, John P., Searle, Stephen M. J., Sutter, Nathan B., Thomas, Rachael, Webber, Caleb, Baldwin, Jennifer, Abebe, Adal, Abouelleil, Amr, Aftuck, Lynne, Ait-zahra, Mostafa, Aldredge, Tyler, Allen, Nicole, An, Peter, Anderson, Scott, Antoine, Claudel, Arachchi, Harindra, Aslam, Ali, Ayotte, Laura, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Benamara, Mostafa, Berlin, Aaron, Bessette, Daniel, Blitshteyn, Berta, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Brown, Adam, Cahill, Patrick, Calixte, Nadia, Camarata, Jody, Cheshatsang, Yama, Chu, Jeffrey, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Dawoe, Tenzin, Daza, Riza, Decktor, Karin, DeGray, Stuart, Dhargay, Norbu, Dooley, Kimberly, Dooley, Kathleen, Dorje, Passang, Dorjee, Kunsang, Dorris, Lester, Duffey, Noah, Dupes, Alan, Egbiremolen, Osebhajajeme, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Ferreira, Patricia, Fisher, Sheila, FitzGerald, Mike, Foley, Karen, Foley, Chelsea, Franke, Alicia, Friedrich, Dennis, Gage, Diane, Garber, Manuel, Gearin, Gary, Giannoukos, Georgia, Goode, Tina, Goyette, Audra, Graham, Joseph, Grandbois, Edward, Gyaltsen, Kunsang, Hafez, Nabil, Hagopian, Daniel, Hagos, Birhane, Hall, Jennifer, Healy, Claire, Hegarty, Ryan, Honan, Tracey, Horn, Andrea, Houde, Nathan, Hughes, Leanne, Hunnicutt, Leigh, Husby, M., Jester, Benjamin, Jones, Charlien, Kamat, Asha, Kanga, Ben, Kells, Cristyn, Khazanovich, Dmitry, Kieu, Alix Chinh, Kisner, Peter, Kumar, Mayank, Lance, Krista, Landers, Thomas, Lara, Marcia, Lee, William, Leger, Jean-Pierre, Lennon, Niall, Leuper, Lisa, LeVine, Sarah, Liu, Jinlei, Liu, Xiaohong, Lokyitsang, Yeshi, Lokyitsang, Tashi, Lui, Annie, Macdonald, Jan, Major, John, Marabella, Richard, Maru, Kebede, Matthews, Charles, McDonough, Susan, Mehta, Teena, Meldrim, James, Melnikov, Alexandre, Meneus, Louis, Mihalev, Atanas, Mihova, Tanya, Miller, Karen, Mittelman, Rachel, Mlenga, Valentine, Mulrain, Leonidas, Munson, Glen, Navidi, Adam, Naylor, Jerome, Nguyen, Tuyen, Nguyen, Nga, Nguyen, Cindy, Nguyen, Thu, Nicol, Robert, Norbu, Nyima, Norbu, Choe, Novod, Nathaniel, Nyima, Tenchoe, Olandt, Peter, O'Neill, Barry, O'Neill, Keith, Osman, Sahal, Oyono, Lucien, Patti, Christopher, Perrin, Danielle, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Rachupka, Anthony, Raghuraman, Sujaa, Rameau, Rayale, Ray, Verneda, Raymond, Christina, Rege, Filip, Rise, Cecil, Rogers, Julie, Rogov, Peter, Sahalie, Julie, Settipalli, Sampath, Sharpe, Theodore, Shea, Terrance, Sheehan, Mechele, Sherpa, Ngawang, Shi, Jianying, Shih, Diana, Sloan, Jessie, Smith, Cherylyn, Sparrow, Todd, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Stone, Sabrina, Sykes, Sean, Tchuinga, Pierre, Tenzing, Pema, Tesfaye, Senait, Thoulutsang, Dawa, Thoulutsang, Yama, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Venkataraman, Vijay, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Yang, Shuli, Yang, Xiaoping, Young, Geneva, Yu, Qing, Zainoun, Joanne, Zembek, Lisa, Zimmer, Andrew, and Lander, Eric S.

Abstract

Author(s): Kerstin Lindblad-Toh (corresponding author) [1]; Claire M Wade [1, 2]; Tarjei S. Mikkelsen [1, 3]; Elinor K. Karlsson [1, 4]; David B. Jaffe [1]; Michael Kamal [1]; Michele Clamp [...]

Published
2005
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39. Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Author

Halo, Julia V., primary, Pendleton, Amanda L., additional, Shen, Feichen, additional, Doucet, Aurélien J., additional, Derrien, Thomas, additional, Hitte, Christophe, additional, Kirby, Laura E., additional, Myers, Bridget, additional, Sliwerska, Elzbieta, additional, Emery, Sarah, additional, Moran, John V., additional, Boyko, Adam R., additional, and Kidd, Jeffrey M., additional

Published
2020
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41. PTPN11 mutations in canine and human disseminated histiocytic sarcoma

Author

Hédan, Benoit, primary, Rault, Mélanie, additional, Abadie, Jérôme, additional, Ulvé, Ronan, additional, Botherel, Nadine, additional, Devauchelle, Patrick, additional, Copie‐Bergman, Christiane, additional, Cadieu, Edouard, additional, Parrens, Marie, additional, Alten, Julia, additional, Zalcman, Emmanuelle L., additional, Cario, Gunnar, additional, Damaj, Gandhi, additional, Mokhtari, Karima, additional, Le Loarer, Francois, additional, Coulomb‐Lhermine, Aurore, additional, Derrien, Thomas, additional, Hitte, Christophe, additional, Bachelot, Laura, additional, Breen, Matthew, additional, Gilot, David, additional, Blay, Jean Y., additional, Donadieu, Jean, additional, and André, Catherine, additional

Published
2020
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43. Mobility and adaptation of dogs in agricultural societies: when the study of the animal reflects the history of human

Author

Ollivier, Morgane, Tresset, Anne, Bălăşescu, Adrian, Bréhard, Stéphanie, Boroneanţ, Adina, Hitte, Christophe, Vigne, J.-D., Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Romanian Academy, Institut de Génétique et Développement de Rennes (IGDR), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Bréhard, Stéphanie

Subjects
[SHS.ARCHEO] Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

46. Construction of a 2- Mb resolution BAC microarray for CGH analysis of canine tumors

Author

Thomas, Rachel, Scott, Allyson, Langford, Cordelia F., Fosmire, Susan P., Jubala, Cristan M., Lorentzen, Travis D., Hitte, Christophe, Karlsson, Elinor K., Kirkness, Ewen, Ostrander, Elaine, Gailbert, Francis, Lindblad-Toh, Kerstin, Modiano, Jaime F., and Breen, Matthew

Subjects
Genomes -- Research, Nucleic acid hybridization -- Research, Cytogenetics -- Research, Dogs -- Genetic aspects, Dogs -- Diseases, Health
Abstract

A study is conducted on the similarities shared between many human and dog diseases using a wide range of molecular cytogenetic techniques. A comprehensive canine comparative genome hybridization (CGH) array that has 1158 canine BAC clones ordered throughout the genome with an average interval of 2-Mb is studied.

Published
2005

49. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants.

Author

Kinsey, Nathan A., Belanger, Janelle M., Oberbauer, Anita M., Aguirre, Gustavo, André, Catherine, Bannasch, Danika, Becker, Doreen, Davis, Brian, Drögemüller, Cord, Ekenstedt, Kari, Faller, Kiterie, Forman, Oliver, Friedenberg, Steven, Furrow, Eva, Giger, Urs, Hitte, Christophe, Hytönen, Marjo, Jagannathan, Vidhya, Leeb, Tosso, and Lingaas, Frode

Subjects
WHOLE genome sequencing, DOGS, HOMOZYGOSITY, CANIDAE, GENOMES
Abstract

Deficient homozygosity of a variant maintained in a population suggests that the variant may be embryonic lethal. We examined whole genome sequence data from 675 canids to investigate for variants with missing homozygosity and high predicted impact. Our analysis identified 45 variants, in 32 genes. However, further scrutiny of the sequence reads revealed that all but one of these variants were artifacts of the variant calling process when using CanFam3.1, a widely utilized canine reference genome. We demonstrate that the use of multiple, newer reference genomes could reduce artifacts and lead to more accurate variant identification. [ABSTRACT FROM AUTHOR]

Published
2022
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