Genetic quality: a complex issue for experimental study reproducibility

Abstract

Laboratory animal research involving mice, requires consideration of many factors to be controlled. Genetic quality is one factor that is often overlooked but is essential for the generation of reproducible experimental results. Whether experimental research involves inbred mice, spontaneous mutant, or genetically modified strains, exercising genetic quality through careful breeding, good recordkeeping, and prudent quality control steps such as validation of the presence of mutations and verification of the genetic background, will help ensure that experimental results are accurate and that reference controls are representative for the particular experiment. In this review paper, we will discuss various techniques used for the generation of genetically altered mice, and the different aspects to be considered regarding genetic quality, including inbred strains and substrains used, quality check controls during and after genetic manipulation and breeding. We also provide examples for when to use the different techniques and considerations on genetic quality checks. Further, we emphasize on the importance of establishing an in-house genetic quality program.

The Revolution of Animal Genomics in Forensic Sciences

“…The development of genetic markers also finds an important application in the analysis of laboratory animals by ensuring the purity of breeding lines, good monitoring of model species, and the identification and variation of genes acting on specific traits [70][71][72][73][74].…”

An oocyte‐specific Cas9‐expressing mouse for germline CRISPR/Cas9‐mediated genome editing

“…Previous studies have generated Cas9‐expressing mouse models using randomly targeted transgenes driven by ubiquitous promoters, and subsequently used these models to mediate genome editing in zygotes (Ghassemi et al, 2021; Sakurai et al, 2016; Sakurai et al, 2020). However, multi‐copy random integration sites are usually not mapped, can affect the spatiotemporal expression patterns of transgenes, alter expression or function of other genes, and can lead to loss of transgene expression by epigenetic silencing (Bronson et al, 1996; Palmiter & Brinster, 1986; Yoshiki et al, 2022). Moreover, Cas9 expression from random integrated transgenes driven by ubiquitous promoters (Ghassemi et al, 2021; Sakurai et al, 2016; Sakurai et al, 2020) could cause prolonged genome editing within embryos that inherit the transgene, potentially increasing mosaicism and off‐target mutagenesis rates in those embryos.…”

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

“…Genotyping arrays have been a staple in mouse research for more than two decades and have been successfully adopted for genetic QC and colony maintenance (Petkov et al 2004; Yang et al 2011; Morgan et al 2015; Andrews et al 2021; Amos-Landgraf et al 2022). Five years after its introduction, the MiniMUGA array has been used for genotyping over 40,000 mouse samples and the manuscript describing the array and its capabilities has been cited widely (Sigmon et al 2020; Birling et al 2022; Bourdon and Montagutelli 2022; Yoshiki et al 2022; Smith et al 2022). Part of MiniMUGA’s success is due to its unique characteristics, including discrimination between commercial substrains, robust chromosomal sex determination, and detection of commonly used constructs.…”