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The Mouse Universal Genotyping Array: From Substrains to Subspecies.

Andrew P Morgan1, Chen-Ping Fu2, Chia-Yu Kao2

  • 1Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599.

G3 (Bethesda, Md.)
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Summary

The new GigaMUGA array offers advanced genotyping for mice, aiding genetic mapping and quality control in diverse populations. This powerful tool enhances research across laboratory strains and wild species.

Keywords:
genetic mappinginbred strainsmicroarrays

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Area of Science:

  • Genomics
  • Animal Genetics

Background:

  • Genotyping microarrays are crucial for genetic mapping, population genetics, and maintaining the genetic integrity of laboratory animal stocks.
  • The Mouse Universal Genotyping Array (MUGA) series has been a valuable resource, with previous generations supporting various genetic studies.

Purpose of the Study:

  • To develop and characterize GigaMUGA, the third-generation Mouse Universal Genotyping Array (MUGA).
  • To optimize GigaMUGA for genetic mapping in specific mouse populations (Collaborative Cross, Diversity Outbred) and for laboratory mouse substrain identification.

Main Methods:

  • Development of a 143,259-probe Illumina Infinium II array (GigaMUGA) for the house mouse (Mus musculus).
  • Inclusion of 141,090 single nucleotide polymorphism (SNP) probes and 2006 copy number variation (CNV) probes targeting polymorphic genomic regions.
  • Performance characterization using 500 diverse reference samples, including inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice.

Main Results:

  • GigaMUGA demonstrates high informativeness across a broad spectrum of genetically diverse samples, including laboratory substrains and other Mus species.
  • The array effectively identifies substrain-level genetic variation and is optimized for mapping in key mouse populations.
  • Detailed probe-level annotation and quality control recommendations are provided.

Conclusions:

  • GigaMUGA represents a significant advancement in mouse genotyping arrays, offering enhanced resolution and broader applicability.
  • The array is a valuable resource for genetic mapping, population genetics, and ensuring the genetic quality of mouse research models.
  • The comprehensive annotation and performance data facilitate the effective use of GigaMUGA in diverse research settings.