Next-generation sequencing of 17 genes associated with venous thromboembolism reveals a deficit of non-synonymous variants in procoagulant genes

Eric Manderstedt, Christina Lind-Halldén, Peter Svensson, Bengt Zöller, C Halldén

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5 Citations (Scopus)


BACKGROUND:  The heritability of venous thromboembolism (VTE) is only partially explained by variants in 17 previously VTE-associated genes.

OBJECTIVE:  This article screens for additional rare variants in the 17 genes and investigates the relative contributions of pro- and anticoagulant genes to VTE.

PATIENTS AND METHODS:  Ninety-six VTE patients from the population-based Malmö Thrombophilia Study were analysed using an AmpliSeq strategy and Ion Torrent sequencing and the variant data were compared with data from public databases.

RESULTS:  A total of 102 non-synonymous and 76 synonymous variants were identified. Forty-six non-synonymous variants were present in the human gene mutation database. Anticoagulant and procoagulant genes showed 14 and 22 rare non-synonymous variants, respectively. Individual patients showed varying numbers of risk factors; 13 patients had non-synonymous mutations in SERPINC1, PROC and PROS1 genes and 42 had factor V Leiden or prothrombin mutations generating a total of 47 patients with at least one of these risk factors. Ten common VTE-associated variants showed low level enrichments and no correlation to the other risk factors. The enrichment of previously identified risk factors was similar to previous studies. Determination of the nsyn/syn ratio (number of non-synonymous variants per non-synonymous site, nsyn, to the number of synonymous variants per synonymous site, syn) showed, as expected in patients, an increase of non-synonymous relative to synonymous anticoagulant variants compared with controls (nsyn/syn, 0.95 vs. 0.68). In contrast, non-synonymous procoagulant variants (nsyn/syn, 0.31 vs. 0.63) showed a decrease. We suggest that the deficit of non-synonymous variants in procoagulant genes is a novel mechanism contributing to VTE.

Original languageEnglish
Pages (from-to)1441-1450
Number of pages9
JournalThrombosis and Haemostasis
Issue number9
Publication statusPublished - 2019

Swedish Standard Keywords

  • Biological Sciences (106)


  • venous thromboembolism - blood coagulation factors - anticoagulant - procoagulant - next-generation sequencing


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