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Mouse Whole Genome
SNP Genotyping
Linkage Scans
&
Congenic / Consomic Line Construction
CIDR has replaced its
Mouse Microsatellite (STRP) Service and is now performing SNP
genotyping for linkage scans and congenic/consomic line construction using Illumina's
BeadArray technology on a BeadLab system. With this technology, 96 samples
are assayed for up to 1,536 SNP loci in a single experiment. Investigators also have a new option of applying for follow-up fine mapping using our Mouse Custom SNP Genotyping Service at the same time as they apply for a linkage scan.
CIDR uses the Ilumina Medium Density Mouse Linkage Panel. The fixed content panel is comprised of 1,449 SNPs chosen from the Wellcome-CTC Mouse Strain SNP Genotype Set ( www.well.ox.ac.uk/mouse/INBREDS, Valder et al., 2006). For the design of this fixed-content product, genotype data from ten inbred strains (129S1/SvlmJ, AKR/J, BALB/cJ, C3H/H3J, C57BL/6J, CBA/J, DBA/2J, FVB/NJ, NOD/LtJ, and SJL/J) was considered. The assay contains approximately 3 SNPs per each 5 Mb interval across the genome such that at least one SNP in each interval is informative for 85% of the strain combinations. Table 1 shows the coverage (average physical) of the Medium Density Mouse Linkage product for 4 crosses that have been studied in 3 CIDR projects.
| Medium Density Mouse Linkage Panel: Coverage for 4 Crosses | ||
|---|---|---|
| Cross | Number of Informative SNPs (1,449 SNPs in assay) |
Coverage: Average Physical (Mb) |
| 129P3/J x C57BL/6J | 870 | 2.9 |
| CBA/J x JF1/Ms | 701 | 3.5 |
| NZW/LacJ x BTBR T + tf/J | 626 | 4 |
| BALB/cJ x C57BL/6J | 876 | 2.8 |
| Note: One project contained samples from two crosses. | ||
Table 2 demonstrates the robustness of the assay (99.52% of 1,441 samples across 3 projects were successfully genotyped and 98.4% of all informative SNPs produced high-quality data that was released).
| Sample and SNP Performance: SNP Linkage Projects (Mouse) | |||||||
|---|---|---|---|---|---|---|---|
| Sample Performance | SNP Performance | ||||||
| Attempted Samples |
Released Samples | Sample Success Rate |
Attempted SNPs * |
Released SNPs | SNP success rate |
||
| 240 | 239 | 99.58% | 870 | 854 | 98.2% | ||
| 1,040 | 1,034 | 99.42% | 1,027 | 1,005 | 97.9% | ||
| 168 | 168 | 100.00% | 883 | 876 | 99.2% | ||
| 1,448 | 1,441 | 99.52% | 2,780 | 2,735 | 98.4% | Total | |
| *Number of SNPs informative for the experiment | |||||||
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/.
References
Valdar, W., Solberg, L.C., Gauguier, D., Burnett, S., Klenerman, P., Cookson, W.O., et al.
(2006). Genome-Wide Genetic association of complex traits in heterogeneous stock mice.
Nature Genetics 38, 879-887.
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