LXS Genotypes Database (July 2005)

    Summary:

The LXS genotype file used by WebQTL consists of a set of 2659 carefully error-checked SNPs and microsatellites typed across all 77 strains. Download all LXS genotypes as a 478 Kb text file.

LXS strains were derived from a cross between the following 8 strains: A, AKR, BALB/c, C3H/2, C57BL, DBA/2, IS/Bi, and RIII. All of these strains were maintained at the Institute for Behavior Genetics, Bolder Colorado by Dr. Gerald McClearn and colleagues. C3H/2 is presumably the same as C3H/Crgl/2 (see paper by Green V (1981) Behavioral and Neural Biology 31:56). C57BL is presumably the same as C57BL/Crgl. IS/Bi is extinct.

See Williams, Bennett, Johnson and colleagues (2004) for more details on the LXS panel.

    About the genotypes used in these studies:

WebQTL mapping algorithms rely on an initial set of 330 microsatellites genotyped in 2002 and 2003 at UTHSC (labeled Mit). The current expanded marker set (n = 2659) have been selected from a total of 13377 SNPs genotyped in collaboration with Jonathan Flint, Richard Mott, Beth Bennett, Lu Lu, and Jing Gu. Closely linked genetic markers often have the same strain distribution pattern (SDP) across the LXS strains. For computational efficiency, we only use a single marker associated with each SDP.

All LXS strains are from the Institute of Behavioral Genetics, Boulder Colorado. They were generated by Beth Bennett, Tom Johnson, and colleagues over a ten-year period. All of these strains are beyond the 22 generation of serial sibling mating and are formally fully inbred.

    Reference:

Williams RW, Bennett B, Lu L, Gu J, DeFries JC, Carosone-Link P, Rikke B, Belknap JK, Johnson TE (2004) Genetic structure of the LXS panel of recombinant inbred mouse strains. Mammalian Genome 15:637-647

This text file was originally written by RW Williams, July 26, 2005.