Article

Mapping segmental and sequence variations among laboratory mice using BAC array CGH.

Cancer Research Institute, University of California San Francisco, San Francisco, California 94143, USA.
Genome Research (impact factor: 13.61). 03/2005; 15(2):302-11. DOI:10.1101/gr.2902505 pp.302-11
Source: PubMed

ABSTRACT We used arrays of 2069 BACs (1303 nonredundant autosomal clones) to map sequence variation among Mus spretus (SPRET/Ei and SPRET/Glasgow) and Mus musculus (C3H/HeJ, BALB/cJ, 129/J, DBA/2J, NIH, FVB/N, and C57BL/6) strains. We identified 80 clones representing 74 autosomal loci of copy number variation (|log(2)ratio| >/= 0.4). These variant loci distinguish laboratory strains. By FISH mapping, we determined that 63 BACs mapped to a single site on C57BL/6J chromosomes, while 17 clones mapped to multiple chromosomes (n = 16) or multiple sites on one chromosome (n = 1). We also show that small ratio changes (Delta log(2)ratio approximately 0.1) distinguish homozygous and heterozygous regions of the genome in interspecific backcross mice, providing an efficient method for genotyping progeny of backcrosses.

0 0
 · 
0 Bookmarks
 · 
41 Views
  • Source
    Article: Pericentromeric duplications in the laboratory mouse.
    James W Thomas, Mary G Schueler, Tyrone J Summers, Robert W Blakesley, Jennifer C McDowell, Pamela J Thomas, Jacquelyn R Idol, Valerie V B Maduro, Shih-Queen Lee-Lin, Jeffrey W Touchman, Gerard G Bouffard, Stephen M Beckstrom-Sternberg, Eric D Green
    [show abstract] [hide abstract]
    ABSTRACT: Duplications have long been postulated to be an important mechanism by which genomes evolve. Interspecies genomic comparisons are one method by which the origin and molecular mechanism of duplications can be inferred. By comparative mapping in human, mouse, and rat, we previously found evidence for a recent chromosome-fission event that occurred in the mouse lineage. Cytogenetic mapping revealed that the genomic segments flanking the fission site appeared to be duplicated, with copies residing near the centromere of multiple mouse chromosomes. Here we report the mapping and sequencing of the regions of mouse chromosomes 5 and 6 involved in this chromosome-fission event as well as the results of comparative sequence analysis with the orthologous human and rat genomic regions. Our data indicate that the duplications associated with mouse chromosomes 5 and 6 are recent and that the resulting duplicated segments share significant sequence similarity with a series of regions near the centromeres of the mouse chromosomes previously identified by cytogenetic mapping. We also identified pericentromeric duplicated segments shared between mouse chromosomes 5 and 1. Finally, novel mouse satellite sequences as well as putative chimeric transcripts were found to be associated with the duplicated segments. Together, these findings demonstrate that pericentromeric duplications are not restricted to primates and may be a common mechanism for genome evolution in mammals.
    Genome Research 02/2003; 13(1):55-63. · 13.61 Impact Factor
  • Article: Large-scale genomic comparison using two-dimensional DNA gels.
    C L Sidman, D J Shaffer
    [show abstract] [hide abstract]
    ABSTRACT: Two-dimensional electrophoresis (2DE) of DNA fragments, in which separation occurs first by size and then by sequence variation, is a method enabling large-scale comparison of complex genomes. Combining 2DE with probing for various classes of repetitive genomic elements allows rapid and efficient comparison of thousands of fragments and millions of base-pairs of DNA distributed across most genomic regions. This approach is demonstrated here by analyzing the extent of genomic relatedness of different inbred strains of mice. Such strains are shown to differ from each other by approximately 0.2-1% of their nucleotides, above which level reproductive speciation occurs. The 2DE method of assessing the overall relationship between two genomes represents an appropriate tool for analyzing members of a single species, but is too sensitive for use in interspecies comparisons.
    Genomics 10/1994; 23(1):15-22. · 3.02 Impact Factor
Data provided are for informational purposes only. Although carefully collected, accuracy cannot be guaranteed. The impact factor represents a rough estimation of the journal's impact factor and does not reflect the actual current impact factor. Publisher conditions are provided by RoMEO. Differing provisions from the publisher's actual policy or licence agreement may be applicable.

Keywords

1303 nonredundant autosomal clones
 
74 autosomal loci
 
80 clones
 
backcrosses
 
copy number variation
 
efficient method
 
heterozygous regions
 
interspecific backcross mice
 
map sequence variation
 
multiple sites
 
Mus musculus
 
single site
 
small ratio changes
 
variant loci distinguish laboratory strains