A size-matched within-resource control contextualizes the portability of linkage-disequilibrium-pruned sets across genomic resources

Linkage disequilibrium pruning generates reduced variant sets that are often reused outside the sample in which they were derived. We evaluated how such sets behave when transferred across samples and genomic resources while separating sample-to-sample variability from effects of changing resources. An exact shared universe of 7,282,490 single-nucleotide polymorphisms was analyzed. Within each recipient resource, disjoint samples provided a native transfer control, and cross-resource panels were compared with native panels matched to the same retained-marker fraction. At 109 individuals and on chromosomes 1, 11, and 22, within-resource transfer produced a coverage gap of about 5–6 percentage points at the 0.80 representation threshold. After matching panelsize, cross-resource differences were small for two recipients but remained −3.317 percentage points for the Gambian resource. A further comparison between the full 1000 Genomes source and its Gambian in Western Divisions subset, evaluated at common panel fractions in the same recipient, showed a median difference of −4.682 percentage points at the prespecified midpoint. Higher representation thresholds showed different patterns.These results support interpreting portability against a within-resource, size-matched recipient control rather than from a raw cross-resource residual alone.