CIDR

Mouse Whole Genome

Linkage Scans

Using Illumina's Mouse Medium Density Linkage Panel, 96 samples are assayed together with GoldenGate chemistry. Under the NIH CIDR Program, a single application can be submitted for both linkage as well as follow up fine mapping using our custom SNP service.

The fixed content panel is comprised of 1,449 SNPs chosen from the Wellcome-CTC Mouse Strain SNP Genotype Set. Genotype data from 10 inbred strains was considered in the design of this fixed-content product:

129S1/SvlmJ	CBA/J
AKR/J	DBA/2J
BALB/cJ	FVB/NJ
C3H/H3J	NOD/LtJ
C57BL/6J	SJL/J

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. The table below shows the coverage (average physical) of the Mouse Medium Density Linkage product for 4 crosses that have been studied in 3 CIDR projects.

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.

Congenic / Consomic Line Construction

The Mouse Medium Density Panel can also be used to create congenic or consomic strains of mice. We genotype progeny from the N2 and N3 generations in succession. Results for the N2 samples can be used to guide the selection of the best breeders for the N3 generation. After N3 generation genotyping is complete, you should be in a position to complete the project using targeted genotyping of specific chromosomes and chromosomal regions.