Evidence map›Paper›PMID 39271181›Full record

ArticleG3 (Bethesda, Md.)2024

The updated mouse universal genotyping array bioinformatic pipeline improves genetic QC in laboratory mice.

Matthew W Blanchard, John Sebastian Sigmon, Jennifer Brennan, Chidima Ahulamibe, Michelle E Allen, Sam Ardery, Ralph S Baric, Timothy A Bell, Joseph Farrington, Dominic Ciavatta and 27 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in G3 (Bethesda, Md.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Article
  3. bioRxiv : the preprint server for biology · 2026
    Article
  4. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

37 authors.

Matthew W BlanchardDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.ORCID 0000-0003-3977-2115
John Sebastian SigmonDepartment of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA.
Jennifer BrennanMutant Mouse Resource and Research Center, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Chidima AhulamibeDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Michelle E AllenDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Sam ArderyGenetics and Molecular Biology Curriculum, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Ralph S BaricDepartment of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.
Timothy A BellDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Joseph FarringtonDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Dominic CiavattaDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Marta C Cruz CisnerosDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Madison DrushalDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Martin T FerrisDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.ORCID 0000-0003-1241-6268
Rebecca C FryDepartment of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.
Christiann GainesDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Bin GuDepartment of Neuroscience, The Ohio State University, Columbus, OH 43210, USA.ORCID 0000-0002-6846-5563
Mark T HeiseDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Pablo HockDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Richard Austin HodgesDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Mia HulginSystems Genetics Core Facility, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Tal KafriDepartment of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA.
Rachel M LynchDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Terry MagnusonDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Darla R MillerDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Caroline E Y MurphyDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
David Truong NguyenDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Kelsey E NollDepartment of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA.
Megan K ProulxDepartment of Microbiology, UMass Chan Medical School, Worchester, MA 01655, USA.ORCID 0000-0002-9524-8302
Christopher M SassettiDepartment of Microbiology, UMass Chan Medical School, Worchester, MA 01655, USA.
Sarah A SchoenrockDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Ginger D ShawDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Jeremy M SimonDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Clare M SmithDepartment of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA.ORCID 0000-0003-2601-0955
Miroslav StybloDepartment of Nutrition, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.
Lisa M TarantinoDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Joyce WooDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Fernando Pardo Manuel de VillenaDepartment of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.ORCID 0000-0002-5738-5795

Funding

Unlocking Zika Virus Immune Control and Pathogenesis with the Collaborative CrossU19AI100625 · NIAID · UNIV OF NORTH CAROLINA CHAPEL HILL · PI PARDO-MANUEL DE VILLENA, FERNANDO · 2012 to 2021
$36.6M
UNC-CH CENTER FOR ENVIRONMENTAL HEALTH &SUSCEPTIBILITYP30ES010126 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Hazel B Nichols · 2001 to 2026
$36.3M
Resource Section - Core 001U42OD010924 · OD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI TERRY R MAGNUSON · 2012 to 2026
$24.5M
The UNC Chapel Hill Superfund Research Program (UNC-SRP)P42ES031007 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Kathleen M Gray · 2020 to 2026
$22.2M
Systems Genetics of TuberculosisP01AI132130 · NIAID · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI BEHAR, SAMUEL M · 2017 to 2021
$11.2M
Systems Genetics of TuberculosisP01AI181898 · NIAID · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI CHRISTOPHER M SASSETTI · 2024 to 2026
$10.5M
Respiratory Virus Vaccine and Adjuvant Exploration - Equipment SupplementU01AI149644 · NIAID · UNIV OF NORTH CAROLINA CHAPEL HILL · PI BARIC, RALPH S · 2019 to 2023
$6.1M
Genetic Analysis of COVID-19 Susceptibility and Resistance Determinants in the Collaborative CrossR01AI157253 · NIAID · UNIV OF NORTH CAROLINA CHAPEL HILL · PI BARIC, RALPH S, HEISE, MARK T · 2020 to 2024
$3.8M
Genetic underpinning of diabetes associated with arsenic exposureR01ES029925 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI FRY, REBECCA, PARDO-MANUEL DE VILLENA, FERNANDO · 2019 to 2023
$3.3M
The circadian rhythm as a lentiviral vector restriction factorR01HL155986 · NHLBI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI KAFRI, TAL · 2020 to 2023
$3.0M
Genomic Resources for the Collaborative CrossU24HG010100 · NHGRI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI MCMILLAN, LEONARD, PARDO-MANUEL DE VILLENA, FERNANDO · 2018 to 2022
$1.8M
Rapid identification of cocaine sensitivity genes using a novel reduced complexity crossR21DA052171 · NIDA · UNIV OF NORTH CAROLINA CHAPEL HILL · PI TARANTINO, LISA M · 2020 to 2021
$430k
Mutant Mouse Resource and Research Centers U42OD010924NHGRI NIH HHS U24 HG010100NHLBI NIH HHS R01 HL155986NIAID NIH HHS P01 AI132130NIAID NIH HHS P01 AI181898NIAID NIH HHS R01 AI157253NIAID NIH HHS U01 AI149644NIAID NIH HHS U19 AI100625NIDA NIH HHS R21 DA052171NIEHS NIH HHS P30 ES010126NIEHS NIH HHS P42 ES031007NIEHS NIH HHS R01 ES029925NIH HHS U42 OD010924
6 · The paper itself

Abstract

The MiniMUGA genotyping array is a popular tool for genetic quality control of laboratory mice and genotyping samples from most 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 the array's performance and the associated report's usefulness by leveraging thousands of samples genotyped since the initial description of MiniMUGA. Here, we report our efforts to update and improve marker annotation, increase the number and the reliability of the consensus genotypes for classical inbred strains and substrains, and increase the number of constructs reliably 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 updated the layout of the report to simplify the interpretation and completeness of the analysis and added a section summarizing the ideogram in table format. 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.

Indexed as

Computational BiologyGenotyping TechniquesAllelesAnimalsGenotypeMiceOligonucleotide Array Sequence AnalysisQuality ControlReproducibility of Resultschromosomal sexdiagnostic SNPsgenetic backgroundgenetic constructsgenetic QCinbred strainsmicroarrayssubstrains

Identifiers

PMID39271181
PMCPMC11457065

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.