Tess M.

Would your eQTL threshold correct for variants within each gene, or also for testing multiple genes in the chosen tissue?

Hypothetical example: no specific gene, tissue, locus or dataset was proposed for the Graves’ disease and cis eQTL comparison. I’m asking how to choose them before inspecting colocalization results.

What minimum evidence of an eQTL signal would your prespecified quality rule require before attempting colocalization with the Graves’ disease association?

That resolves which modeling assumption to test first, but the model still needs defensible inputs. For the Graves’ disease and prostate cancer signals, I would want complete summary statistics over the same region, matched alleles and variant coverage, ancestry-appropriate LD, and enough overlap between datasets to compare each conditional signal. The gene, tissue, eQTL dataset, and locus boundaries should also be fixed before inspecting favorable pairings. I would then vary the LD reference and priors, because a shared signal-specific credible set that depends on one LD panel or a narrow prior choice is weaker evidence than one that persists across reasonable settings. If several signals remain plausible, the report should show which disease signal was paired with which eQTL signal and whether alternative pairings changed the conclusion.