Genetic Background Limits Generalizability of Genotype-Phenotype Relationships

Abstract

Genome-wide association studies (GWASs) have identified numerous loci that influence risk for psychiatric diseases. Genetically engineered mice are often used to characterize genes implicated by GWASs. These studies are based on the assumption that observed genotype-phenotype relationships will generalize to humans, implying that the results would at least generalize to other inbred mouse strains. Given current concerns about reproducibility, we sought to directly test this assumption. We produced F1 crosses between male C57BL/6J mice heterozygous for null alleles of Cacna1c and Tcf7l2 and wild-type females from 30 inbred laboratory strains. We found extremely strong interactions with genetic background that sometimes supported diametrically opposing conclusions. These results do not negate the invaluable contributions of mouse genetics to biomedical science, but they do show that genotype-phenotype relationships cannot be reliably inferred by studying a single genetic background, and thus constitute a major challenge to the status quo. VIDEO ABSTRACT.

Figure 1

Breeding design for placing null alleles on 30 different genetic backgrounds. Males heterozygous for the null allele mutation (red asterisk) on a C57BL/6J background were bred with females from 30 inbred laboratory mouse strains (represented by arbitrarily selected colors). This generated 30 distinct F₁s that were genetically identical except at the targeted allele, where they were either +/- or +/+.

Figure 2

Null allele phenotypes on 30 different genetic backgrounds. (A) Locomotor response to methamphetamine in Cacna1c +/- and +/+ mice. On days 1 and 2 a saline injection was given before a 30 min exposure to an open field. On day 3 methamphetamine (2 mg/kg i.p.) was given prior to the same open field test. The difference in locomotor activity on day 3 compared to activity on day 2 is shown. (B) Exploratory activity during a 30 min open field test in Tcf7l2 +/- and +/+ mice. (C) Baseline blood glucose levels in Tcf7l2 +/- and +/+ mice. (D) Startle response to a 120-dB acoustic stimulus in Tcf7l2 +/- and +/+ mice. Bars show the mean phenotype +/- s.e.m.. F₁s are labeled according to the maternal strain, and are ordered along the x-axis according to the difference between +/- and +/+ mice. See also Table S3. Null allele effects within strains were evaluated using two-tailed t-tests. ^_p<0.1, *p<0.05, **p<0.01, ***p<0.001. ^–p<0.1, *p<0.05, **p<0.01, ***p<0.001.