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Daniel H Geschwind - One of the best experts on this subject based on the ideXlab platform.

  • search for autism loci by combined analysis of autism Genetic Resource exchange and finnish families
    Annals of Neurology, 2006
    Co-Authors: Tero Ylisaukkooja, Maricela Alarcon, Rita M Cantor, Mari Auranen, Raija Vanhala, Elli Kempas, Lennart Von Wendt, Irma Jarvela, Daniel H Geschwind
    Abstract:

    Objective Several genome-wide screens have been performed in autism spectrum disorders resulting in the identification of numerous putative susceptibility loci. Analyses of pooled primary data should result in an increased sample size and the different study samples have a potential to strengthen the evidence for some earlier identified loci, reveal novel loci, and even to provide information of the general significance of the locus. The objective of this study was to search for potential susceptibility loci for autism, which are supported by two independent samples. Methods We performed a combined analysis of the primary genome scan data of the Autism Genetic Resource Exchange (AGRE) and Finnish autism samples to reveal susceptibility loci potentially shared by these study samples. Results In the initial combined data analysis, the best loci (p < 0.05) were observed at 1p12-q25, 3p24-26, 4q21-31, 5p15-q12, 6q14-21, 7q33-36, 8q22-24, 17p12-q21, and 19p13-q13. The combined analysis of Finnish and AGRE families showed the most promising shared locus on 3p24-26 with nonparametric logarithm of odds (NPL) score of 2.20 (p = 0.011). The combined data analysis did not provide increased linkage evidence for the earlier identified loci on 3q25-27 or 17p12-q21. However, the 17p12-q21 locus remained promising also in the combined sample (NPLall =2.38, p = 0.0076). Interpretation Our study of 314 autism families highlights the importance of further analyses on 3p24-26 locus involving comprehensive molecular Genetic analyses of oxytocin receptor gene (OXTR), a positional and functional candidate gene for autism. Ann Neurol 2005

  • the autism Genetic Resource exchange a Resource for the study of autism and related neuropsychiatric conditions
    American Journal of Human Genetics, 2001
    Co-Authors: Daniel H Geschwind, Janice Sowinski, Catherine Lord, Portia Iversen, Jonathan Shestack, Patrick Jones, Lee Ducat, Sarah J Spence
    Abstract:

    We gratefully acknowledge the families and individuals who have contributed their biomaterials, time, and financial Resources to AGRE, especially Marianne Toedtman, AGRE family recruiter; Ed Berry, phlebotomist; Andrew Smith, M.D., pediatric neurologist; Paul Law, M.D., M.P.H., for database development; and Nancy Jones, AGRE Web master. We specifically thank Sallie and Tom Bernard, for their generous financial support of AGRE, and the Schering-Plough Research Institute and Pfizer Inc., for their contributions to AGRE. We also thank Maricela Alarcon, Ph.D., for her error checking and advice; Jianjun Liu, Ph.D., for updating of the genotyping data; and scientists who have started to utilize AGRE, for their helpful comments and criticism. The members of the AGRE Steering Committee are: W. Ted Brown, New York State Institute for Basic Research in Developmental Disabilities, Staten Island; Maya Bucan, University of Pennsylvania, Philadelphia; Joseph Buxbaum, Mt. Sinai School of Medicine, New York; T. Conrad Gilliam, Columbia University Genome Center, New York; David A. Greenberg, Mt. Sinai School of Medicine, New York; David H. Ledbetter, University of Chicago, Chicago; Bruce L. Miller, University of California, San Francisco; Stanley F. Nelson, UCLA School of Medicine, Los Angeles; Jonathan Pevsner, Kennedy Krieger Institute, Baltimore; Jerome I. Rotter, Cedars-Sinai Medical Center, Los Angeles; Carol Samango-Sprouse, Children’s National Medical Center, Baltimore; Gerard D. Schellenberg, University of Washington and Veterans Affairs Medical Center, Seattle; Rudolph E. Tanzi, Massachusetts General Hospital, Boston; and Kirk C. Wilhelmsen, University of California, San Francisco.

Yohei Minakuchi - One of the best experts on this subject based on the ideXlab platform.

  • genomic and phenotypic characterization of a wild medaka population towards the establishment of an isogenic population Genetic Resource in fish
    G3: Genes Genomes Genetics, 2014
    Co-Authors: Mikhail Spivakov, Thomas O Auer, Ravindra Peravali, Ian Dunham, Dirk Dolle, Asao Fujiyama, Atsushi Toyoda, Tomoyuki Aizu, Yohei Minakuchi
    Abstract:

    Oryzias latipes (medaka) has been established as a vertebrate Genetic model for more than a century and recently has been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate medaka Genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Here we characterize the genomes of wild medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near-isogenic panel of wild lines. The population is free of significant detrimental population structure and has advantageous linkage disequilibrium properties suitable for the establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition, high-throughput genome sequencing of these medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese medaka existed as a larger older population that went through a relatively recent bottleneck approximately 10,000 years ago. In addition, we detect patterns of recent positive selection in the Southern population. These data indicate that the Genetic structure of the Kiyosu medaka samples is suitable for the establishment of a vertebrate near-isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at http://www.ebi.ac.uk/birney-srv/medaka-ref-panel.

  • genomic and phenotypic characterisation of a wild medaka population establishing an isogenic population Genetic Resource in fish
    arXiv: Genomics, 2013
    Co-Authors: Mikhail Spivakov, Thomas O Auer, Ravindra Peravali, Ian Dunham, Dirk Dolle, Asao Fujiyama, Atsushi Toyoda, Tomoyuki Aizu, Yohei Minakuchi, Felix Loosli
    Abstract:

    Background Oryzias latipes (Medaka) has been established as a vertebrate Genetic model for over a century, and has recently been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate Medaka Genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Results Here we characterise the genomes of wild Medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near isogenic panel of wild lines. The population is free of significant detrimental population structure, and has advantageous linkage disequilibrium properties suitable for establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition high throughput genome sequencing of these Medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern Medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese Medaka existed as a larger older population which went through a relatively recent bottleneck around 10,000 years ago. In addition we detect patterns of recent positive selection in the Southern population. Conclusions These data indicate that the Genetic structure of the Kiyosu Medaka samples are suitable for the establishment of a vertebrate near isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at this http URL

Dirk Dolle - One of the best experts on this subject based on the ideXlab platform.

  • genomic and phenotypic characterization of a wild medaka population towards the establishment of an isogenic population Genetic Resource in fish
    G3: Genes Genomes Genetics, 2014
    Co-Authors: Mikhail Spivakov, Thomas O Auer, Ravindra Peravali, Ian Dunham, Dirk Dolle, Asao Fujiyama, Atsushi Toyoda, Tomoyuki Aizu, Yohei Minakuchi
    Abstract:

    Oryzias latipes (medaka) has been established as a vertebrate Genetic model for more than a century and recently has been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate medaka Genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Here we characterize the genomes of wild medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near-isogenic panel of wild lines. The population is free of significant detrimental population structure and has advantageous linkage disequilibrium properties suitable for the establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition, high-throughput genome sequencing of these medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese medaka existed as a larger older population that went through a relatively recent bottleneck approximately 10,000 years ago. In addition, we detect patterns of recent positive selection in the Southern population. These data indicate that the Genetic structure of the Kiyosu medaka samples is suitable for the establishment of a vertebrate near-isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at http://www.ebi.ac.uk/birney-srv/medaka-ref-panel.

  • genomic and phenotypic characterisation of a wild medaka population establishing an isogenic population Genetic Resource in fish
    arXiv: Genomics, 2013
    Co-Authors: Mikhail Spivakov, Thomas O Auer, Ravindra Peravali, Ian Dunham, Dirk Dolle, Asao Fujiyama, Atsushi Toyoda, Tomoyuki Aizu, Yohei Minakuchi, Felix Loosli
    Abstract:

    Background Oryzias latipes (Medaka) has been established as a vertebrate Genetic model for over a century, and has recently been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate Medaka Genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Results Here we characterise the genomes of wild Medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near isogenic panel of wild lines. The population is free of significant detrimental population structure, and has advantageous linkage disequilibrium properties suitable for establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition high throughput genome sequencing of these Medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern Medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese Medaka existed as a larger older population which went through a relatively recent bottleneck around 10,000 years ago. In addition we detect patterns of recent positive selection in the Southern population. Conclusions These data indicate that the Genetic structure of the Kiyosu Medaka samples are suitable for the establishment of a vertebrate near isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at this http URL

Mikhail Spivakov - One of the best experts on this subject based on the ideXlab platform.

  • genomic and phenotypic characterization of a wild medaka population towards the establishment of an isogenic population Genetic Resource in fish
    G3: Genes Genomes Genetics, 2014
    Co-Authors: Mikhail Spivakov, Thomas O Auer, Ravindra Peravali, Ian Dunham, Dirk Dolle, Asao Fujiyama, Atsushi Toyoda, Tomoyuki Aizu, Yohei Minakuchi
    Abstract:

    Oryzias latipes (medaka) has been established as a vertebrate Genetic model for more than a century and recently has been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate medaka Genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Here we characterize the genomes of wild medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near-isogenic panel of wild lines. The population is free of significant detrimental population structure and has advantageous linkage disequilibrium properties suitable for the establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition, high-throughput genome sequencing of these medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese medaka existed as a larger older population that went through a relatively recent bottleneck approximately 10,000 years ago. In addition, we detect patterns of recent positive selection in the Southern population. These data indicate that the Genetic structure of the Kiyosu medaka samples is suitable for the establishment of a vertebrate near-isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at http://www.ebi.ac.uk/birney-srv/medaka-ref-panel.

  • genomic and phenotypic characterisation of a wild medaka population establishing an isogenic population Genetic Resource in fish
    arXiv: Genomics, 2013
    Co-Authors: Mikhail Spivakov, Thomas O Auer, Ravindra Peravali, Ian Dunham, Dirk Dolle, Asao Fujiyama, Atsushi Toyoda, Tomoyuki Aizu, Yohei Minakuchi, Felix Loosli
    Abstract:

    Background Oryzias latipes (Medaka) has been established as a vertebrate Genetic model for over a century, and has recently been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate Medaka Genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Results Here we characterise the genomes of wild Medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near isogenic panel of wild lines. The population is free of significant detrimental population structure, and has advantageous linkage disequilibrium properties suitable for establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition high throughput genome sequencing of these Medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern Medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese Medaka existed as a larger older population which went through a relatively recent bottleneck around 10,000 years ago. In addition we detect patterns of recent positive selection in the Southern population. Conclusions These data indicate that the Genetic structure of the Kiyosu Medaka samples are suitable for the establishment of a vertebrate near isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at this http URL

Jaehoo Jung - One of the best experts on this subject based on the ideXlab platform.

  • the mosaic genome of indigenous african cattle as a unique Genetic Resource for african pastoralism
    Nature Genetics, 2020
    Co-Authors: Kwondo Kim, Dong Ah Yoo, Taehyung Kwo, Tadelle Dessie, Okeyo Ally Mwai, Jisung Jang, Samsu Sung, Saetbyeol Lee, Ashi Salim, Jaehoo Jung
    Abstract:

    Cattle pastoralism plays a central role in human livelihood in Africa. However, the Genetic history of its success remains unknown. Here, through whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds representative of the main cattle groups, we identify a major taurine × indicine cattle admixture event dated to circa 750–1,050 yr ago, which has shaped the genome of today’s cattle in the Horn of Africa. We identify 16 loci linked to African environmental adaptations across crossbred animals showing an excess of taurine or indicine ancestry. These include immune-, heat-tolerance- and reproduction-related genes. Moreover, we identify one highly divergent locus in African taurine cattle, which is putatively linked to trypanotolerance and present in crossbred cattle living in trypanosomosis-infested areas. Our findings indicate that a combination of past taurine and recent indicine admixture-derived Genetic Resources is at the root of the present success of African pastoralism. Whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds identifies 16 loci linked to environmental adaptations among crossbred animals, including a highly divergent locus in African taurine cattle putatively linked to trypanotolerance.