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Characterization of a strain-specific CD-1 reference genome reveals potential inter- and intra-strain functional
Yoon Hee Jung1, Hsiao-Lin V Wang1, Samir Ali2
1Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
BMC Genomics
|August 3, 2023
Summary
Researchers mapped millions of genetic variants in CD-1 mice, creating a strain-specific reference genome. This improves the accuracy and reduces bias in genomic studies using CD-1 mice.
Area of Science:
- Genomics
- Mouse Models
- Bioinformatics
Background:
- CD-1 mice are widely used in toxicology and biomedical research.
- Outbred stocks offer practical advantages like cost-effectiveness and breeding efficiency.
- Understanding CD-1 genetic variability enhances its utility in research.
Purpose of the Study:
- To identify genome-wide genetic variants in CD-1 mice.
- To construct a CD-1-specific reference genome.
- To improve the accuracy of genomic data analysis in CD-1 mice.
Main Methods:
- Deep genomic DNA sequencing of CD-1 mice.
- Identification of single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and transposable elements.
- Validation of variants using multiple sequencing data types and existing SNP data.
Main Results:
- Millions of previously unidentified genetic variants were discovered in CD-1 mice.
- A strain-specific CD-1 reference genome was constructed.
- Genetic variations were found to potentially alter transcription factor binding and gene translation.
Conclusions:
- Millions of CD-1 variants were identified, which could impact research findings.
- A CD-1-specific reference genome was developed to enhance genomic data alignment.
- This resource improves accuracy and reduces bias in studies utilizing CD-1 mice.
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