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  • The 16th International Mouse Genome Conference (2002)
    Tessarollo L 1 Shen H 1 Akagi K 2 Morse III H 1 Ward J 3 Malley J 4 Naiman D 5 Nakamura T 6 Ortiz M 6 Keller J 1 Jenkins N Institutions 1 National Cancer Institute 2 National Institute of Allergy and Infectious Diseases 3 National Institutes of Health 4 Johns Hopkins University 5 Japanese Foundation for Cancer Research 6 SAIC Frederick Retroviral insertional mutagenesis in inbred mouse strains with a high spontaneous incidence of retrovirally induced hematopoietic disease provides a potent cancer gene discovery tool To demonstrate the power of retroviral insertional mutagenesis for cancer gene discovery in the post genome sequence era we used a high throughput inverse PCR method to clone and sequence 1336 retroviral integration sites from murine hematopoietic tumors and then mapped 1199 of these sequences on the mouse genome using the Celera and or public mouse sequence databases These studies identified 153 loci that are targets of viral integration in more than one tumor and therefore likely to encode a disease gene Twenty eight of these loci encode genes that are known or suspected human cancer genes while another nine encode homologs of human cancer genes Many other loci encode excellent disease

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file187.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    VARIATION IN THE MOUSE GENOME K Lindblad Toh Whitehead Institute Co Authors Wade C Zody MC Kirby A Kulbolkas EJ Lander ES Daly MJ Institutions Whitehead Institute MIT Center for Genome Research Many commonly used inbred laboratory mouse strains are widely known to have originated from a mixed but limited founder population in a small number of labs However the dramatic effect this breeding history may have had on patterns of genetic variation among these strains has not previously been explored Here we present an analysis of the fine structure of variation using data from both long finished sequences and genome wide shotgun sequencing When the recently assembled C57BL 6J genome sequence is aligned with sequence from other strains we observe long segments of either extremely high 1 SNP 200 250 bp or extremely low 1 SNP 20 000 bp polymorphism rate In all strain to strain comparisons examined roughly one third of the genome falls into long high SNP rate regions consistent with estimated divergence rates between M m domesticus and either M m musculus or M m castaneus This suggests that the genomes of these inbred strains are as previously suggested mosaic with half of the genome falling

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file188.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    Center We have been working to establish the comprehensive mouse full length cDNA collection and sequence database to cover as many genes as we can named Riken mouse genome encyclopedia More than 1 000 000 clones prepared from 163 tissues were end sequenced to classify into 128 000 clusters and 60 000 representative clones were fully sequenced As a conclusion the 60 000 sequences contained 35 000 unique sequences with more than 24 000 clear protein encoding genes Using these results functional analysis of specific proteins such as motor protein secreted protein cytokine were carried out and gave new discovery to proteome research Many new imprinted genes were found and new candidates of transcription factors were listed up for further specific analysis as well Furthermore mouse is the first higher organism that is analyzed both in full length cDNA sequence and in Genome sequence and it enabled us to compare these two set of data and do genome wide substantial analysis The next generation of life science is clearly based on all of the genome information and resources Based on our cDNA clones we developed the additional system to explore gene function We developed cDNA microarray system to print all

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file189.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    Takada T 1 Jones EP 2 Fischer Lindahl K Institutions 1 University of Texas Southwestern Medical Center 2 Howard Hughes Medical Institute and University of Texas Southwestern Medical Center We are finishing the sequence of the 129 SvJ mouse Mhc or H2 class I region on Chr 17 and the human sequence is already completed Here we present a large scale comparison of the Mhc from the two species to define the limits of mouse as model organism and to understand the evolution of the Mhc We describe differences at the level of 1 genomic organization 2 orthologous and paralogous gene families 3 single gene insertions and deletions and 4 gene structure The only major organizational difference between the rodent and human Mhc is the presence of a 45 kb insert with class I genes in the proximal part of the mouse Mhc The orthology between the central 1 Mb of the human and mouse Mhc is long established Our sequencing extends this to the distal 2 Mb region The Mhc is a mosaic of stretches formed by conserved and non conserved genes Surprisingly the 1 9 Mb stretches that encode the class I and class II genes which epitomize

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file190.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    1 Schuler G and the NCBI Annotation Team Institutions 1 National Center for Biotechnology Information Bethesda MD 2 The Jackson Laboratory Bar Harbor ME The Mouse Genome Sequencing Consortium MGSC has released a Whole Genome Shotgun WGS based assembly of the mouse genome MGSCv3 In an effort to assess this resource we have been comparing the assembly to non sequenced based maps as well at to clone based sequences Preliminary results indicate that this assembly covers 90 of the mouse genome and shows good agreement with the WIBR genetic map However this coverage is not completely uniform In a comparison to finished BAC sequence NT contigs overall greater than 95 of the bases in the NT contigs were covered but the coverage varied from 56 99 when looking at individual contigs In addition only 35 of the expected 56 loci of the non ecotropic MLV family could be identified in this assembly Searching the trace archive for these loci yielded the expected number of hits suggesting that moderately repetitive sequences could be difficult to assemble using WGS methodology We are moving toward an integrated assembly of BAC sequenced combined with WGS contigs Preliminary results in this effort suggest that with BAC sequence only covering approximately 25 of the genome sequence for 35 of gaps in the MGSCv3 with map information can be found in BAC sequence The integration of these two sequence resources will likely improve the overall representation of the genome In addition we are annotating the MGSCv3 assembly The first round of annotation placed 23 419 STSs 27 354 SNPs and 101 665 clones onto the genome In addition 46 370 gene models were produced compared to 46 038 gene models for Human build 29 8198 of 8454 RefSeqs could be used as evidence for producing a gene

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file191.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    3 Schmoyer D 3 Baes F 3 Jackson B 4 Jones B the Tennessee Mouse Genome Consortium and the Integrative Neuroscience Initiative on Alcoholism Stress Program Project Institutions 1 Baylor University 2 University of Tennessee 3 Oak Ridge National Laboratory 4 University of Tennessee and Oak Ridge National Laboratory The genome sequences from several chordates are being completed the bioinformatics largely exists in the research community to discover the protein coding potential of those genomes However the bioinformatics to elucidate gene regulation encoded in genomes and gene regulatory networks is not so developed New bioinformatics new model organism resources new experimental approaches and new collaborations are needed if the community is to understand the gene networks that help create phenotypes of interest A research team at ORNL and the University of Tennessee are developing some needed bioinformatics The overall projects include 1 supplying several web services and collaborative bioinformatics that supports large consortia of experimental researchers and 2 developing comparative bioinformatics and new data mining environments that can ultimately help understand the nature and evolution of gene regulatory networks Collaborative projects under way at ORNL the University of Tennessee the Tennessee Mouse Genome Consortium www tnmouse org and the new

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file192.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    2 Peyrefiwte S 3 Botcherby MRM 4 Gautier P 5 Hummerich H 4 Cross S 4 van Heyningen V 4 Edgar R 3 Leaves N 3 Greystrong J 3 Greenham L 3 Jones S 3 Maggott K 3 Manjunath S 3 Russell E 3 Strachan G 1 Strivens M 3 North P 3 Boal E 3 Cobley V 3 Hunter G 3 Kimberley G 3 Cave Berry L 2 Mathews L 2 Simms S 2 Gregory S 2 Evans R 2 Hubbard T 2 Durbin R 1 Cadman M 1 McKeone R 1 Southwell A 1 Sellick C 5 Iravani M 4 White S 6 Little P 4 Jackson I 2 Rogers J 3 Campbell RD 1 Brown SDM Institutions 1 MRC UK Mouse Genome Centre and Mammalian Genetics Unit 2 Wellcome Trust Sanger Institute 3 MRC UK HGMP Resource Centre 4 MRC Human Genetics Unit 5 Imperial College 6 School of Biochemistry Molecular Genetics University of New South Wales The MRC UK Mouse sequencing programme has adopted a regional and functional approach focussing on the delivery of finished contiguous sequence for four substantial regions on chromosomes 2 4 13 and X The detailed manual annotation of this finished genomic sequence will improve the efficiency of mutation scanning and the identification of genes underlying mutations of interest within these regions The region of mouse chromosome 13 being sequenced is encompassed by the Chromosome 13 deletion Del 13 Svea36H hereafter referred to as Del36H This region was chosen for sequencing for a number of reasons but in particular because it is a target of an ENU mutagenesis programme underway at Harwell This programme is using the deletion to uncover recessive phenotypes resulting from point mutations generated across the Del36H region The Del36H region spans approximately 14Mb of genomic DNA and is

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file193.shtml (2016-02-17)
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  • The 16th International Mouse Genome Conference (2002)
    Blake J Richardson J Kadin J Mouse Genome Informatics Curation and Software Teams Institutions The Jackson Laboratory The release of the publicly accessible genome sequence for the C57BL 6J strain of laboratory mouse represents a significant landmark in genome biology The mouse stands as one of the premier model organism for understanding human biology and disease processes The availability of high quality well annotated genome sequence data for both mouse and human will serve as platforms on which biological research will be based for decades to come Key to using the mouse genome sequence effectively will be how well the genes and other features identified in the genome sequence are integrated with the rich biological information about the laboratory mouse represented in well curated knowledgebases such as the Mouse Genome Informatics MGI database http www informatics jax org Indeed model organism databases have a unique role to play in connecting sequence and biology and with the long term curation of these connections The MGI database provides extensive information about mouse genes alleles and phenotypes Quantitative Trait Loci QTL strain polymorphisms functional annotations using the Gene Ontology vocabularies developmental gene expression patterns and curated mammalian homology especially for rat and human

    Original URL path: http://www.imgs.org/Archive/abstracts/2002abstracts/file194.shtml (2016-02-17)
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