Identification of risk factors contributing to venous thromboembolism by Ion Torrent sequencing using an AmpliSeq strategy

Abstract: Venous thromboembolism (VTE) is a common cardiovascular disease that frequently recurs and is associated with significant numbers of death annually. The influence of the hereditary risk factors is not yet firmly established but twin and family studies suggest that heritability is about 50%. Several genetic risk factors have been identified by genomeHwide association studies (GWAS) but they do not explain all of the missing heritability of VTE. NextHgeneration sequencing (NGS) has revolutionized the genetic analysis of disease and has been used to discover the genes underlying unsolved Mendelian disorders. It has also been used to identify rare alleles which may help explain the missing heritability for complex diseases. The study population of this study consisted of 32 randomly chosen VTE patients from the MATSHstudy (Malmö Thrombophilia Study). The seventeen genes that in earlier studies have been shown to be associated with VTE were examined and the identified VTEHrelated mutations were compared to the general population. The results showed that Ion TorrentHsequencing effectively provided good coverage and read depth in all of the sequenced genes. Optimization of the primer panels resulted in higher and more balanced coverage and the quality of the results in this study was on an overall high level. A total of 215 variants were detected – 62 in exons, 8 in splice and 145 in introns. One Mendelian mutation was detected in PROC and rare variants were found in F2 and FGG. The most common risk factor (F5 Leiden) was highly enriched with 25% in this study compared to 3% in a background population.