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Blanchard MW, Sigmon JS, Brennan J, Ahulamibe C, Allen ME, Baric RS, Bell TA, Farrington J, Ciavatta D, Cruz Cisneros M, Drushal M, Ferris MT, Fry R, Gaines C, Gu B, Heise MT, Hodges RA, Kafri T, Lynch R, Magnuson T, Miller D, Murphy CEY, Nguyen DT, Noll KE, Proulx M, Sassetti C, Shaw GD, Simon JM, Smith C, Styblo M, Tarantino L, Woo J, Pardo Manuel de Villena F. The Updated Mouse Universal Genotyping Array Bioinformatic Pipeline Improves Genetic QC in Laboratory Mice. bioRxiv 2024:2024.02.29.582794. [PMID: 38464063 PMCID: PMC10925293 DOI: 10.1101/2024.02.29.582794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
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 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.
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Sigmon JS, Blanchard MW, Baric RS, Bell TA, Brennan J, Brockmann GA, Burks AW, Calabrese JM, Caron KM, Cheney RE, Ciavatta D, Conlon F, Darr DB, Faber J, Franklin C, Gershon TR, Gralinski L, Gu B, Gaines CH, Hagan RS, Heimsath EG, Heise MT, Hock P, Ideraabdullah F, Jennette JC, Kafri T, Kashfeen A, Kulis M, Kumar V, Linnertz C, Livraghi-Butrico A, Lloyd KCK, Lutz C, Lynch RM, Magnuson T, Matsushima GK, McMullan R, Miller DR, Mohlke KL, Moy SS, Murphy CEY, Najarian M, O'Brien L, Palmer AA, Philpot BD, Randell SH, Reinholdt L, Ren Y, Rockwood S, Rogala AR, Saraswatula A, Sassetti CM, Schisler JC, Schoenrock SA, Shaw GD, Shorter JR, Smith CM, St Pierre CL, Tarantino LM, Threadgill DW, Valdar W, Vilen BJ, Wardwell K, Whitmire JK, Williams L, Zylka MJ, Ferris MT, McMillan L, Manuel de Villena FP. Content and Performance of the MiniMUGA Genotyping Array: A New Tool To Improve Rigor and Reproducibility in Mouse Research. Genetics 2020; 216:905-930. [PMID: 33067325 PMCID: PMC7768238 DOI: 10.1534/genetics.120.303596] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well-annotated genome, wealth of genetic resources, and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost-effective, informative, and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole-genome sequencing. Here, we describe the content and performance of a new iteration of the Mouse Universal Genotyping Array (MUGA), MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: (1) chromosomal sex determination, (2) discrimination between substrains from multiple commercial vendors, (3) diagnostic SNPs for popular laboratory strains, (4) detection of constructs used in genetically engineered mice, and (5) an easy-to-interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA, we genotyped 6899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays, both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived, and recombinant inbred lines. Here, we also report the detection of a substantial number of XO and XXY individuals across a variety of sample types, new markers that expand the utility of reduced complexity crosses to genetic backgrounds other than C57BL/6, and the robust detection of 17 genetic constructs. We provide preliminary evidence that the array can be used to identify both partial sex chromosome duplication and mosaicism, and that diagnostic SNPs can be used to determine how long inbred mice have been bred independently from the relevant main stock. We conclude that MiniMUGA is a valuable platform for genetic QC, and an important new tool to increase the rigor and reproducibility of mouse research.
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Affiliation(s)
- John Sebastian Sigmon
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Matthew W Blanchard
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Timothy A Bell
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jennifer Brennan
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - A Wesley Burks
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Kathleen M Caron
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Richard E Cheney
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Dominic Ciavatta
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Frank Conlon
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David B Darr
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - James Faber
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Craig Franklin
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri 65211
| | - Timothy R Gershon
- Department of Neurology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lisa Gralinski
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Bin Gu
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Christiann H Gaines
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Robert S Hagan
- Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Ernest G Heimsath
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Mark T Heise
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Pablo Hock
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Folami Ideraabdullah
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Nutrition, Gillings School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - J Charles Jennette
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Tal Kafri
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599
- Gene Therapy Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Anwica Kashfeen
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Mike Kulis
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, Maine 04609
| | - Colton Linnertz
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Alessandra Livraghi-Butrico
- Marsico Lung Institute/UNC Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - K C Kent Lloyd
- Department of Surgery, University of California Davis, Davis, California 95616
- School of Medicine, University of California Davis, California 95616
- Mouse Biology Program, University of California Davis, California 95616
| | | | - Rachel M Lynch
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Glenn K Matsushima
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Rachel McMullan
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Darla R Miller
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sheryl S Moy
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina 27599
- Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Caroline E Y Murphy
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Maya Najarian
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lori O'Brien
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Benjamin D Philpot
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
- Marsico Lung Institute/UNC Cystic Fibrosis Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Scott H Randell
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Yuyu Ren
- University of California San Diego, La Jolla, California 92093
| | | | - Allison R Rogala
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
- Division of Comparative Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Avani Saraswatula
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Jonathan C Schisler
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sarah A Schoenrock
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - John R Shorter
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Clare M Smith
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | | | - Lisa M Tarantino
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David W Threadgill
- University of California San Diego, La Jolla, California 92093
- Department of Biochemistry and Biophysics, Texas A&M University, Texas 77843
| | - William Valdar
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Barbara J Vilen
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599
| | | | - Jason K Whitmire
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lucy Williams
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Mark J Zylka
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Leonard McMillan
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Mutant Mouse Resource and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
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