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  1. AU="Nguyen, David Truong"
  2. AU="Khazanchi, Rakesh Kumar"
  3. AU="Agrò, Felice E"
  4. AU="Bücker, Bettina"
  5. AU="Steussy, Bryan W"

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Article: The Updated Mouse Universal Genotyping Array Bioinformatic Pipeline Improves Genetic QC in Laboratory Mice.

Blanchard, Matthew W / Sigmon, John Sebastian / Brennan, Jennifer / Ahulamibe, Chidima / Allen, Michelle E / Baric, Ralph S / Bell, Timothy A / Farrington, Joeseph / Ciavatta, Dominic / Cruz Cisneros, Marta / Drushal, Madison / Ferris, Martin T / Fry, Rebecca / Gaines, Christiann / Gu, Bin / Heise, Mark T / Hodges, Richard Austin / Kafri, Tal / Lynch, Rachel /
Magnuson, Terry / Miller, Darla / Murphy, Caroline E Y / Nguyen, David Truong / Noll, Kelsey E / Proulx, Megan / Sassetti, Chris / Shaw, Ginger D / Simon, Jeremy M / Smith, Clare / Styblo, Myrek / Tarantino, Lisa / Woo, Joyce / Pardo Manuel de Villena, Fernando

bioRxiv : the preprint server for biology

2024  

Abstract: The MiniMUGA genotyping array is a popular tool for genetic QC of laboratory mice and genotyping of samples from most types of experimental crosses involving laboratory strains, particularly for reduced complexity crosses. The content of the production ... ...

Abstract The MiniMUGA genotyping array is a popular tool for genetic QC of laboratory mice and genotyping of samples from most types of experimental crosses involving laboratory strains, particularly for reduced complexity crosses. The content of the production version of the MiniMUGA array is fixed; however, there is the opportunity to improve array's performance and the associated report's usefulness by leveraging thousands of samples genotyped since the initial description of MiniMUGA in 2020. Here we report our efforts to update and improve marker annotation, increase the number and the reliability of the consensus genotypes for inbred strains and increase the number of constructs that can reliably be detected with MiniMUGA. In addition, we have implemented key changes in the informatics pipeline to identify and quantify the contribution of specific genetic backgrounds to the makeup of a given sample, remove arbitrary thresholds, include the Y Chromosome and mitochondrial genome in the ideogram, and improve robust detection of the presence of commercially available substrains based on diagnostic alleles. Finally, we have made changes to the layout of the report, to simplify the interpretation and completeness of the analysis and added a table summarizing the ideogram. We believe that these changes will be of general interest to the mouse research community and will be instrumental in our goal of improving the rigor and reproducibility of mouse-based biomedical research.
Language English
Publishing date 2024-03-03
Publishing country United States
Document type Preprint
DOI 10.1101/2024.02.29.582794
Database MEDical Literature Analysis and Retrieval System OnLINE

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