ArticleBMC genomics2021
A new mouse SNP genotyping assay for speed congenics: combining flexibility, affordability, and power.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 15 citations in OpenAlex.
- Article
- The updated mouse universal genotyping array bioinformatic pipeline improves genetic QC in laboratory mice.G3 (Bethesda, Md.) · 2024Article
- Establishment and Application of a Novel Genetic Detection Panel for SNPs in Mongolian Gerbils.Genes · 2024Article
- Basophil-Derived IL-4 and IL-13 Protect Intestinal Barrier Integrity and Control Bacterial Translocation during Malaria.ImmunoHorizons · 2024Article
- Mast cell-derived IL-10 protects intestinal barrier integrity during malaria in mice and regulates parasite transmission toInfection and immunity · 2024Article
- Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep (PeerJ · 2024Article
- Genetic and Molecular Quality Control of Genetically Engineered Mice.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A potential new tool to enhance translational success rate in stroke research by backcrossing techniques in transgenic mice.Neural regeneration research · 2023Article
- Establishment of a Reproducible Ischemic Stroke Model in Nestin-GFP Mice with High Survival Rates.International journal of molecular sciences · 2021Article
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
backgroundSpeed congenics is an important tool for creating congenic mice to investigate gene functions, but current SNP genotyping methods for speed congenics are expensive. These methods usually rely on chip or array technologies, and a different assay must be developed for each backcross strain combination. "Next generation" high throughput DNA sequencing technologies have the potential to decrease cost and increase flexibility and power of speed congenics, but thus far have not been utilized for this purpose.
resultsWe took advantage of the power of high throughput sequencing technologies to develop a cost-effective, high-density SNP genotyping assay that can be used across many combinations of backcross strains. The assay surveys 1640 genome-wide SNPs known to be polymorphic across > 100 mouse strains, with an expected average of 549 ± 136 SD diagnostic SNPs between each pair of strains. We demonstrated that the assay has a high density of diagnostic SNPs for backcrossing the BALB/c strain into the C57BL/6J strain (807-819 SNPs), and a sufficient density of diagnostic SNPs for backcrossing the closely related substrains C57BL/6N and C57BL/6J (123-139 SNPs). Furthermore, the assay can easily be modified to include additional diagnostic SNPs for backcrossing other closely related substrains. We also developed a bioinformatic pipeline for SNP genotyping and calculating the percentage of alleles that match the backcross recipient strain for each sample; this information can be used to guide the selection of individuals for the next backcross, and to assess whether individuals have become congenic. We demonstrated the effectiveness of the assay and bioinformatic pipeline with a backcross experiment of BALB/c-IL4/IL13 into C57BL/6J; after six generations of backcrosses, offspring were up to 99.8% congenic.
conclusionsThe SNP genotyping assay and bioinformatic pipeline developed here present a valuable tool for increasing the power and decreasing the cost of many studies that depend on speed congenics. The assay is highly flexible and can be used for combinations of strains that are commonly used for speed congenics. The assay could also be used for other techniques including QTL mapping, standard F2 crosses, ancestry analysis, and forensics.
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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.