Mouse Diversity Array — frequently asked questions

Array

How does the Mouse Diversity Genotyping Array compare to other mouse SNP or genotyping arrays?

This array has over 120x more SNPs, with greater density and distribution throughout the genome, than any other publicly available mouse SNP array. The SNPs were selected to represent polymorphisms from a comprehensive set of common inbred laboratory and wild-derived mice. The Diversity Array also contains over 900,000 non-polymorphic probes for CNV analysis. See the array platform comparison table:

Supplier Product Name # SNP probes Average distance between SNPs # CNV probes

Affymetrix

GeneChip® Mouse  Mapping 5K SNP array

5,000

505,000 bases

0

Illumina

Mouse medium density linkage panel

1,449

1,700,000 bases

0

Affymetrix

Mouse Diversity Genotyping Array

623,000

4,300 bases

916,000

 

Is the Mouse Diversity Genotyping Array the mouse version of the Affymetrix Human 6.0 array?

No, although the two arrays have some common attributes. The Mouse Diversity Genotyping Array is the highest density mouse SNP array on the market with probes spaced at regular interval throughout the genome, like the human 6.0 array. However, the Diversity Array was also designed to maximize the capability to discriminate between mouse strains, something obviously not possible with the human array. Affymetrix provides an analysis console to support Human 6.0 data analysis. This console cannot be used for Mouse Diversity Genotyping Array data analysis at this time.

Can you point me to any publications which used this array? 

No publications are available yet, but a manuscript describing the Diversity array is in preparation by Drs. Pardo-Manuel de Villena and Churchill.

Service

Is The Jackson Laboratory certified by Affymetrix to perform services with Affymetrix arrays?

Yes, we have been trained and certified by Affymetrix to run these assays. The Jackson Laboratory is currently the only service provider for this array.

Can I send tissue samples?

Yes, we actually prefer to receive tissue samples and perform the genomic DNA extraction ourselves. We observe higher call rates when the DNA is extracted in our service. You can provide us with tail, spleen or liver samples. Tissue samples must be shipped on dry ice.

What are your turnaround times once I’m ready to send my tissues or my DNA?

Once we receive your DNA, you can expect to receive data files and a summary report in six weeks for the Basic Service and in seven weeks for the Custom Service. If you send tissues, please add three additional days to the turnaround time.

Do you have a preferred delivery service?

Yes, we advise you use FedEx or UPS to send your samples. We strongly advise against using DHL as this company does not deliver directly to The Jackson Laboratory.

Are special skills required for running or analyzing the data from the new Diversity Array?

The Mouse Diversity Genotyping Array is a commercially available custom array.  While it uses the standard human SNP 6.0 assay processing procedure, the informatics end is much less standard. It is recommended that customers consider whether they have the following experience and expertise to purchase and use this array:

  • SNP 6.0 assay experience
    • Customers should be capable and trained in running the SNP 6.0 assay
  • Informatics (Affymetrix Power Tools) experience
    • Customers should have in-house expertise to run command line tools
      • This analysis is standard in high-throughput labs
    • Customers will not be able to use Genotyping Console to QC or analyze their samples
  • Affymetrix has a minimum purchase requirement of two wafers

Customers not meeting the above criteria should consider JAX® Mouse Diversity Genotyping Array Service. We have microarray experience running over 750 Diversity arrays, data analysis expertise from scientists who helped designed the array, and our large set of prior data enables analysis and increases genotyping call rates of your samples.

Can I purchase the Mouse Diversity Genotyping Arrays directly from JAX?

JAX sells the chip as part of service projects only.

Microarray processing

Please see separate DNA Requirements FAQ Document for questions about DNA preparation and submission.

Study design and bioinformatic data analysis

Do I need to incorporate biological replicates into my study design?

For most applications, a single sample per strain is acceptable.  However, if you believe there is genetic variation within a strain or group of samples, biological replicates must be assayed.

Do I need to incorporate technical replicates into my study design?

For most applications, a single technical replicate per sample is acceptable.  However, depending on your study objectives, it may be a good idea to have technical replicates. You should first maximize the number of biological replicates in your experimental design before considering technical replicates.

What do you offer for CNV analysis? When will it be available?

We do not offer CNV analysis currently, but hope to do so in the near future. You will receive the raw data from the IGP probes, and can evaluate the raw data by comparing IGP probe intensities among separate samples. Once the JAX Services CNV data sets and analysis methods have been validated, customers may (for an additional cost) have JAX® Services analyze CNV results.

How reliable are the SNP calls?

In an internal study comparing two inbred strains, 99.7% of the called genotypes were correct.  Among the 114,625 polymorphisms detected, 112,759 SNPs that had genotypes for these strains in dbSNP.  99.7% (112,452) of the SNPs had the same genotypes between the Diversity array analysis results and dbSNP.  Among the 307 discordant SNPs, 301 were genotyped by Perlegen and the other five were computed genotypes from the Sanger Institute.  Additionally, our analysts use data combined from our proprietary set and your samples to obtain posterior estimates of cluster centers and variances to increase call rates for all genotypes.

How do I use/ interpret the data files?

The Diversity Array yields massive data and result files.  The result files are formatted so that they are useful to researchers who frequently deal with large-scale biological data.