OC 56.4 - Targeted panel sequencing for identifying new rare genetic variants associated with venous thromboembolism (VTE): application to 128 patients with unprovoked VTE and negative thrombophilia screening

Background: The genetic heritability of venous thromboembolism (VTE) is high (35%-60%). Rare variants have been proposed to cause severe rare inherited VTE whose identification is facilitated by the development of next generation sequencing technologies.

Aims: The aim of the present study was to identify candidate rare variants that could explain unprovoked VTE in 128 patients aged below 60yrs and presenting with negative thrombophilia screening, most of which with a family history of VTE.

Methods: Patients were sequenced using a targeted DNA panel of 20 coagulation genes . Identified rare variants (Minor Allele Frequencies MAF≤0.1% in the general population) were then classified according to American College of Medical Genetics (ACMG) guidelines.

Results: The molecular screening of the regulatory and coding regions of the selected 20 genes (Table 1) identified 15 potentially pathogenic variants (ACMG Class 4&5) and 21 Class 3 variants of uncertain significance (VUS), most of them (31/36) being non synonymous ones. Among class 4-5 variants, 5 were located in inhibitors genes (SERPINC1, PROC, PROS1) and were identified in patients in whom thrombophilia screening had been performed under anticoagulant treatment preventing one from measuring inhibitors in their plasma samples. In addition, 10 class 4-5 variants were identified in F2, F5, F7, F10, FGA, TFPI among which 7 have never been reported in public database. Finally, 4 VUS were identified in SERPINC1 and 7 in PROS1, all in patient samples without deficiency of the corresponding protein. The PROS1 Heerlen S501P variant was present in 3 patients (MAF=0.012) at a much higher frequency than that reported in the gnomAD database (MAF=0.003).

Conclusion(s): This study allowed the discovery of potentially strongly VTE-associated variants despite a negative thrombophilia screening and suggests that target panel sequencing could help identifying molecular defects in natural coagulation inhibitors in patients under anticoagulant treatment. Functional validation of newly identified variants remained to be performed.