New JAX® Mouse Diversity Genotyping Array Service

JAX® NOTES Issue 513, Spring 2009

JAX® Services is now offering a revolutionary genotyping service featuring the innovative Mouse Diversity Genotyping Array produced by Affymetrix, a leading source of genetic technologies. The array was designed for high-density, genome-wide profiling of single nucleotide polymorphisms (SNPs).

Applications

The array has a wide range of uses, including the following:

  • Characterizing novel or existing mouse strains as part of association and quantitative trait loci (QTL) studies
  • Performing strain genetic quality control
  • Characterizing or comparing mouse DNA samples (e.g., from tumor tissues, cell lines, substrains or sister strains)

Service features

The array can simultaneously assay over 600,000 SNPs—over 100 times the capability of other commercially-available mouse genotyping arrays. The selected SNPs are spaced approximately 4.3kb across the genome, offering exceptional resolution, and are highly polymorphic among characterized mouse strains. The genotyping accuracy of the array is very high: an internal study of two strains has revealed that 99.7% of National Council of Biological Investigators (NCBI) db SNP database genotypes matched those of the array. The analysis software uses data combined from our proprietary set and your samples to obtain posterior estimates of cluster centers and variances. Personnel in our computational sciences group are expertly trained to use this software and have already assayed and analyzed over 750 samples with the array.

Two service levels offered

Initially, JAX is offering two levels of array service, Basic and Custom.

Basic Service:

  • An array for each sample
  • DNA quality control check
  • Sample preparation and array hybridizations with your DNA samples
  • Brief report consisting of methods and QC diagnostics
  • Delivery of raw data, library file, SNP genotype calls and list of SNPs polymorphic among samples

Custom Service—Basic Service plus the following customizable options:

  • Study design consultation
  • Comparisons between selected samples
  • Report consisting of methods, QC diagnostics and summary statistics for each sample and each comparison
  • Additional customized SNP data analysis, such as comparisons with previously-reported genotypes

Pricing

Basic Service:

  • A data analysis and project management fee of $1,250/project
  • $720/array for 10 or fewer arrays or $670/array for 11 or more arrays (fee covers the array, reagents, processing)

For Custom Service pricing or for more details, contact us at 1-800-422-6423, 1-207-288-5845, or jaxservices@jax.org. Alternatively, visit our website.