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

  1. Antoine M. Snijders1,
  2. Norma J. Nowak3,
  3. Bing Huey2,
  4. Jane Fridlyand1,5,
  5. Sindy Law1,
  6. Jeffrey Conroy3,
  7. Taku Tokuyasu1,
  8. Kubilay Demir1,
  9. Readman Chiu4,
  10. Jian-Hua Mao1,
  11. Ajay N. Jain1,
  12. Steven J.M. Jones4,
  13. Allan Balmain1,
  14. Daniel Pinkel2, and
  15. Donna G. Albertson1,2,6
  1. 1 Cancer Research Institute, University of California San Francisco, San Francisco, California 94143, USA
  2. 2 Department of Laboratory Medicine, University of California San Francisco, San Francisco, California 94143, USA
  3. 3 Roswell Park Cancer Institute, Buffalo, New York 14263, USA
  4. 4 Genome Sequence Centre, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada V5Z-4E6

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 (|log2ratio| ≥ 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 (Δ log2ratio ∼ 0.1) distinguish homozygous and heterozygous regions of the genome in interspecific backcross mice, providing an efficient method for genotyping progeny of backcrosses.

Footnotes

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2902505.

  • [Supplemental material is available online at www.genome.org.]

  • ↵5 Present address: Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA.

  • ↵6 Corresponding author. E-mail albertson{at}cc.ucsf.edu; fax (415) 476-8218.

    • Accepted November 15, 2004.
    • Received June 16, 2004.
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  1. doi: 10.1101/gr.2902505 Genome Res. 15: 302-311 Cold Spring Harbor Laboratory Press

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