Mouse Haplotype Structure

This page contains information related to the paper "Unexpected complexity in the haplotypes of commonly used inbred strains of laboratory mice" by Binnaz Yalcin, Jan Fullerton, Sue Miller, David Keays, Saffron Brady, Amarjit Bhomra, Andrew Jefferson, Emanuela Volpi, Richard Copley, Jonathan Flint, Richard Mott. (2004) PNAS 10.1073/pnas0401189101.

Investigation of sequence variation in common inbred mouse strains has revealed a segmented pattern where regions of high and low variant density are intermixed. Furthermore it has been suggested that allelic strain distribution patterns also occur in well-defined blocks and consequently could be used to map quantitative trait loci (QTL) in comparisons between inbred strains. We report a detailed analysis of polymorphism distribution in multiple inbred mouSse strains over a 5 Mb region containing a QTL influencing anxiety. Our analysis indicates that it is only partly true that the genomes of inbred strains exist as a patchwork of segments of sequence identity and difference. We show that the definition of haplotype blocks is not robust and that methods for QTL mapping may fail if they assume a simple block like structure.

  • List of variants as analysed in the paper (text)
  • Sequence of region (4.8Mb) (FASTA format)
  • Annotation of the 4.8 Mb region as analysed in the paper (text).
    The file format comprises three columns with the start, end and type of the region. The types are
    • sequenced - this region was sequenced at high quality in all 8 strains
    • CNS - Conserved Non-coding Sequence in human-mouse comparison (must be > 100bp and >70% identity)
    • Coding coding sequence (with name of gene for first exon only)
    • 5UTR, Promotor, Intron, 3UTR self-explanatory
  • Graphic of the region, (6-page pdf) showing the genes(Exons as orange bars, introns as red lines), CNS (pink bars) and sequenced (grey bars) regions. The strain distribution patterns of the variants are marked.
  • Final list of variants (xls)(text). [Note: the Final list differs slightly from the analysis file, reflecting our ongoing work on the data].
  • Description of the data format (doc)(text).
  • Jonathan Flint's Home Page
  • SDP blocks found using the algorithm described in the paper. File has two parts: first half lists the diallelic variants, the second half the SDP blocks found as the block transition parameter C varies from 0 to 10.
  • PERL implementation of the algorithm described in the paper

Contact Richard Mott for more details.

  
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