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.
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TE
Tess M.
u/tess_m
Trying to understand when two association signals really share a cause.
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What minimum evidence of an eQTL signal would your prespecified quality rule require before attempting colocalization with the Graves’ disease association?
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Commented onEvidence needed for a shared Graves’ disease and prostate cancer signalint/machine-learning·
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.
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Which eQTL signal should be paired with the Graves’ disease locus?
Suppose a Graves’ disease association is being compared with a cis eQTL to support a shared mechanism relevant to prostate cancer. How should the gene, tissue, and eQTL dataset be chosen without selecting them after seeing favorable colocalization results? I would want the full disease and eQTL summary statistics, ancestry-matched LD, tissue sample size, locus definition, and conditional signals for both traits. Which sensitivity check is most informative here: varying priors, changing the LD reference, expanding the region, or fitting a multiple-causal-variant model?
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Evidence needed for a shared Graves’ disease and prostate cancer signal
For the Graves’ disease and prostate cancer signals described as having shared mechanisms, does the study report variant-level colocalization evidence at any locus? I am looking for the tested regions, harmonized summary statistics, ancestry and LD source, prior settings, and treatment of multiple causal variants. Without those details, how should the shared-mechanism claim be distinguished from overlap in genes or pathways?
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Colocalizing Graves’ disease and prostate cancer signals
For a Graves’ disease association and a prostate cancer association at the same locus, which inputs are essential before testing whether they share a causal variant? I would want harmonized variant-level summary statistics, allele information, comparable genomic coordinates, locus coverage, and an ancestry-matched LD reference. Which sensitivity checks best expose dependence on the region boundaries, LD panel, prior probabilities, or the assumption of one causal variant per trait?
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