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GWAS Summary Statistics and the LD Reference Panel

Almost all downstream work (fine-mapping, coloc, LDSC) runs on summary statistics plus an LD panel. The pairing and its risks are the node.

Questions this Concept answers

Why is an external LD reference panel needed when only summary statistics are available?

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Stochastic Summary Statistics for Reference-Panel-Free LD Estimation in Genetics

Genomic summary statistics — per-variant regression coefficients and standard errors from GWAS — are combined with linkage disequilibrium (LD, the cross-variant correlation matrix) to enable meta-ana…