Our main simulations used in-sample LD computed directly from the target samples. Although we have publicly released summary LD information for British-ancestry UK Biobank samples as part of this study, there are many settings in which researchers conducting fine-mapping cannot obtain in-sample LD, and instead use LD information from an external LD reference panel29. We performed extensive simulations to assess how fine-mapping performance is impacted by LD mismatch between the target sample and the LD reference panel. We specifically considered (1) non-overlapping target and reference samples; (2) sample sizes of the target sample and reference panel; (3) differences in ancestry; (4) presence of related individuals in the target sample; and (5) SNPs available for analysis in the target sample and reference panel.
