Supplemental Material for Zhou et al., 2020

There has been extensive discussion of the “Replication Crisis” in many fields, including genome-wide association studies (<b>GWAS</b>). We explored replication in a mouse model using an advanced intercross line (<b>AIL</b>), which is a multigenerational intercross between two inbred strains. We re-genotyped a previously published cohort of LG/J x SM/J AIL mice (F₃₄; n=428) using a denser marker set and genotyped a new cohort of AIL mice (F_39-43; n=600) for the first time. We identified 36 novel genome-wide significant loci in the F₃₄and 25 novel loci in the F_39-43 cohort. The subset of traits that were measured in both cohorts (locomotor activity, body weight, and coat color) showed high genetic correlations, although the SNP heritabilities were slightly lower in the F_39-43cohort. For this subset of traits, we attempted to replicate loci identified in either F₃₄or F_39-43in the other cohort. Coat color was robustly replicated; locomotor activity and body weight were only partially replicated, which was inconsistent with our power simulations. We used a random effects model to show that the partial replications could not be explained by Winner’s Curse but could be explained by study-specific heterogeneity. Despite this heterogeneity, we performed a mega-analysis by combining F₃₄and F_39-43 cohorts (n=1,028), which identified four novel loci associated with locomotor activity and body weight. These results illustrate that even with the high degree of genetic and environmental control possible in our experimental system, replication was hindered by study-specific heterogeneity, which has broad implications for ongoing concerns about reproducibility.

许多领域都对"复制危机"展开了广泛讨论，包括全基因组关联研究（genome-wide association studies，GWAS）。我们利用高级互交系（advanced intercross line，AIL）——一种两个近交系之间的多代互交群体——在小鼠模型中探索了复制问题。我们使用更密集的标记集对先前发表的LG/J×SM/J AIL小鼠队列（F₃₄；n=428）重新进行基因分型，并首次对新的AIL小鼠队列（F_39-43；n=600）进行基因分型。我们在F₃₄队列中鉴定出36个新的全基因组显著位点，在F_39-43队列中鉴定出25个新位点。两个队列均测量的性状（运动活性、体重和毛色）显示出较高的遗传相关性，尽管F_39-43队列的SNP遗传力略低。针对这些性状，我们尝试在另一个队列中复制在其中一个队列中鉴定的位点：毛色实现了稳健复制，而运动活性和体重仅部分复制，这与我们的功效模拟结果不一致。通过随机效应模型分析，我们发现部分复制无法用胜者诅咒（Winner’s Curse）解释，但可归因于研究特异性异质性。尽管存在这种异质性，我们仍合并两个队列（n=1028）进行了mega分析，鉴定出4个与运动活性和体重相关的新位点。这些结果表明，即使在我们的实验系统中能够实现高度的遗传和环境控制，复制仍会受到研究特异性异质性的阻碍，这对当前关于可重复性的担忧具有广泛意义。