International Mammalian Genome Society

The 15th International Mouse Genome Conference (2001)

POSTER 50 - Chromosome 17 SNPs and haplotype mapping

Dr Leonard Schalkwyk
SGDP Research Centre, Institute of Psychiatry
De Crespigny Park
London SE5 8AF

Co-Authors: Palczewski S, Fernandes C
Institutions: SGDP Research Centre, Institute of Psychiatry

The classical mouse inbred strains are derived from diverse stocks held by fanciers and scientists who shared animals.  Different strains will thus share some ancestral haplotypes, and there has been some recent success in mapping loci based on strain comparison (Grupe et al 2001; Lyon et al 2000), and it is unknown how extensive the shared haplotype fragments are. Ideal for this kind of mapping would be a dense SNP map, but there are currently few SNPs between classical inbred strains.  Starting with BAC end sequences from TIGR, we are screening for chromo-some 17 SNPs by DHPLC in the strains A/J,AKR/J,BALB/cJ,C3H/Hej,C57BL/10J, C57BL/6J,DBA/2J,IS/CamEi,IS/CamRK,RIII/DmMob,RIIIS/J and PWD.  86% of primers pairs designed using primer3 function under standardised conditions (improved primer picking is under development), and of these 80.5% showed polymorphism by DHPLC of which 23% were PWD-only alleles (summary of 80 primer pairs). Confirmation of these candidates by sequencing reveals that many have multiple, generally parallel, SNPs.

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