CIDR - Mouse Custom SNP Genotyping

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Mouse Custom SNP Genotyping

CIDR performs custom SNP genotyping using Illumina technology on a BeadLab system. From 96 to 60,000 investigator-chosen SNPs can be assayed per sample. Depending on the number of custom SNPs desired and the sample number to be assayed, the chemistry used is either GoldenGate or Infinium I or II. The custom SNP study service is appropriate for a variety of project designs including fine mapping follow-up of a genome scan linkage study as well as positional or functional candidate gene studies. Mouse custom genotyping services can be applied for at the same time as Linkage Scan Services or independent of a previous CIDR linkage scan.

In general, it is preferable for investigators to have all samples collected before applying to CIDR. In the event that all samples are not in hand by the application due date, the application will be accepted for review as long as the PI provides data regarding phenotypic characterization.

SNP Customization
    • Investigator-defined density and location
    • Selection by investigator, assistance available
    • Genotypes for 480 strains and >13,000 Illumina-validated SNPs are publicly available at www.well.ox.ac.uk/mouse/INBREDS/. This website also provides SNP selection tools.
    • Two chemistry options:
        • GoldenGate:
          360 sample minimum
          SNP number per sample
         – Choice of 96, 384, 1536 or multiples of 1536
        • iSelect Infinium:
          1,080 sample minimum
          SNP number per sample
         – Ranges from ~7,000 to ~60,000 attempted SNPs

Statistical Genetics Consultation
Statistical genetics services are not available for mouse projects. Map Manager QT and QX software packages for mouse mapping are available free of charge at http://www.mapmanager.org/.