Effect of linkage between vWA and D12S391 in kinship analysis

Ideally for use in forensic analyses, genetic markers on the same chromosome should be more than 50 Mb in physical distance to ensure full recombination and thus independent inheritance. The forensic community has given attention to two STR markers, D12S391 and vWA, that are 6.3 megabases (Mb) apart on chromosome 12. Recent studies have shown no significant linkage disequilibrium between vWA and D12S391 in U.S. and worldwide populations, although genetic linkage has been identified. It is important to evaluate the impact of linkage effects on kinship analysis. In this study, we aimed to determine a more precise measurement of the recombination frequency between vWA and D12S391 based on a larger number of informative meiosis than has been studied previously. We estimated the recombination frequency (θ) to 0.089 (95% CI 0.044-0.158). Using pedigrees simulated under specific kinship scenarios where recombination was expected to affect the likelihood ratio (LR), we evaluated the impact on LR values of including or ignoring linkage between vWA and D12S391. For all pedigree scenarios considered, on average, LR values ignoring linkage were slightly underestimated than when linkage was considered. However, in the incest scenario considered, LR values could be overestimated up to 25-30 times when linkage was ignored. We demonstrate that the effect of ignoring linkage in the likelihood ratio calculation can be considerable. These results suggest that linkage should be considered during kinship analysis when vWA and D12S391 are tested for pedigrees where a recombination could impact the LR value.