title: Unexpected complexity in the haplotypes of commonly used inbred strains of laboratory mice.
abstract: Investigation of sequence variation in common inbred mouse strains has revealed a segmented pattern in which 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 mouse strains over a 4.8-megabase 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.
authors.affiliation: Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.
authors.forename: B
authors.initials: B
authors.lastname: Yalcin
authors.forename: J
authors.initials: J
authors.lastname: Fullerton
authors.forename: S
authors.initials: S
authors.lastname: Miller
authors.forename: D A
authors.initials: DA
authors.lastname: Keays
authors.forename: S
authors.initials: S
authors.lastname: Brady
authors.forename: A
authors.initials: A
authors.lastname: Bhomra
authors.forename: A
authors.initials: A
authors.lastname: Jefferson
authors.forename: E
authors.initials: E
authors.lastname: Volpi
authors.forename: R R
authors.initials: RR
authors.lastname: Copley
authors.forename: J
authors.initials: J
authors.lastname: Flint
authors.forename: R
authors.initials: R
authors.lastname: Mott
mesh_terms: D000483:Alleles; D000818:Animals; D001007:Anxiety / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics*; D051379:Mice; D008815:Mice, Inbred Strains / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D017422:Sequence Analysis, DNA