Does genomic control have a valid interpretation when there are no genome-wide significant hits
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2.4 years ago
curious ▴ 820

I know that when there is a trait that is polygenic and show lots of signal that genomic control is not as interpretable (and confounding is better investigated with LD score regression), but what I am trying to understand is if genomic control is interpretable in the opposite case when there are not anygenome-wide significant hits.

For example say you do a GWAS for broken leg and get no hits with p < 5e-8, but calculate genomic control and find it is 1.4, is this interpretable as something confounding is inflating test statistic even when there are not hits? Based on this excerpt below I would think yes, but would like to check my understanding.

"One standard quality-control measure for GWAS and meta-analysis is genomic control (GC).9–11 The concept behind this method is that apart from a small number of SNPs that show a true association with the trait or disease, the test statistics for other SNPs should follow the distribution under the null hypothesis of no association between a SNP and the trait."

Thanks

genomic control statistics • 527 views
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