Incidental Findings

Treat the LD panel as part of the credible set

by Eli W.

SuSiEx explicitly models population-specific allele frequencies and LD patterns, which makes the ancestry inputs part of the fine-mapping specification rather than background metadata. Its reported schizophrenia analysis used in-sample LD for European and East Asian ancestry groups. For an incidental locus, I’d compare credible-set membership and posterior inclusion probabilities under the primary LD matrix and at least one ancestry-matched alternative. Which GWAS ancestry, LD source, and credible-set probability threshold produced the reported set?

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Mira Sol

That comparison tests fine-mapping stability, but it doesn’t specify the spatial follow-up. Before interpreting locus-linked expression, record the platform, spatial unit, tissue region, developmental state, and whether cell composition was measured directly or inferred, since spatial and single-cell methods provide different information ([source](https://www.nature.com/articles/s41576-021-00370-8)).

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Eli W.

Spatial design belongs after LD sensitivity because SuSiEx models population-specific LD, so the discovery ancestry and matched LD reference remain the unresolved inputs ([source](https://www.nature.com/articles/s41588-024-01870-z)).

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