What are CIDR's project goals for mouse genotyping?
CIDR strives for 90% completeness of all mouse projects. This means that, excluding samples that fail > 25% of the time, the average missing data rate across all samples will be < 10%. CIDR also strives for a <1% genotyping error rate as measured by project-specific blind duplicate samples provided by the investigator.

What quality control measures are in place at CIDR?
The Center will run two C57BL/6J controls, four blind duplicates provided by the investigator, two parental strains for each cross provided by the investigator, two parental strains for each cross from JAX, two F1 DNAs provided by the investigator, and two blank PCR controls per 96-lane gel. Two independent technicians will review all allele calls and resolve any differences. All data will be checked for consistency using the known parental alleles.

What is the minimum number of samples acceptable for a proposed genome scan project?
A minimum of 82 animals is recommended; if fewer are submitted, the charge will still be based on 82.

How much DNA is required for a full genome screen?
10 µg of DNA is required for a 20 cM genome scan (~80-90 markers).

Can CIDR do fine mapping?
No. Genotyping services are restricted to a 20 cM scan using our standard set of ~300 murine STR markers.

Can genotyping be done on strains not included in the strain list typed by CIDR?
No. Genotyping is restricted to the 54 strains initially typed at CIDR for our complete marker set. Additional strains may be added later if the mouse community demonstrates the need.

What do the .1 and .2 endings on the marker names mean?
These values reflect the current version of the primer pairs used to amplify each marker. Some primer pairs were redesigned (.2) during development of the marker set to optimize performance.

Why are there differences between the product sizes posted by CIDR and the product sizes for the same strains characterized using primers from Research Genetics (primers defined originally for MIT markers)?
Few, if any of the product sizes using the CIDR primer set will be the same as those using primers from Research Genetics for the MIT markers. The CIDR primer set, which is marketed by Applied Biosystems, was (1) redesigned to be used in multiplex panels, and (2) "pig-tailed" to promote non-templated addition of A to the products.

Why do I still see differences in product sizes from those posted by CIDR when using the Applied Biosystems primer set?
You are probably running the markers on a different instrument platform. All the primer pairs at CIDR were developed and characterized on Applied Biosystems 377 sequencers. Running the products on a different platform will often result in different allele sizes. However, the size difference between strains should be constant.

Why aren't the primer sequences for the markers posted on your Web site?
The primer sequences are proprietary. The primers are available for purchase from Applied Biosystems.