Genotype versus laboratory phenotype correlation of defects in natural anticoagulants in patients with venous thromboembolism.

Introduction: Plasma-based assays or multigene panel testing can be used for the diagnosis of inherited venous thromboembolism (VTE). Our recent multigene panel data showed strictly concordant results between genetic and phenotypic laboratory testing in only half of the patients. We evaluated in detail the correlation between genotype and laboratory phenotype for defects in natural anticoagulants.

Method: Gene panel test results were compared with standard thrombophilia laboratory assay data, including protein C, protein S and antithrombin plasma activity or antigen levels. We performed additional functional protein C and protein S clot-based assays and mass spectrometry (MS) for the detection of antithrombin molecular proteoforms.

Results: We detected PROC, PROS1 or SERPINC1 variants in 110 of 317 VTE patients of which 61% were (likely)pathogenic variants. Oligogenic inheritance was present in 33% of all patients. Correlation studies showed that not all variants were associated with reduced plasma activity levels, while 14%, 20% and 5% of our VTE patients without a genetic variant had reduced levels for protein C, protein S and antithrombin respectively. Additional clot-based assays could diagnose additional patients but not all. MS-based antithrombin assay was able to detect SERPINC1 missense variants in plasmas that were associated with normal antithrombin activity levels.

Conclusion: Thrombophilia screening using plasma-based assays can lead to potential diagnostic misclassification. In contrast, multigene panel testing is more sensitive but still associated with the detection of variants of uncertain significance. Additional studies are required to clarify the role of panel testing for inherited VTE and the impact of oligogenic inheritance.