Whole genome sequencing identifies low frequency mutations: GP6,TET2 and JAK2 of VTE in Chinese Han familial cohort

<bold>Rationale:</bold> Genetic factors are crucial in VTE risk, notably in unprovoked early-onset cases and those with a family history. While GWAS on common variants has advanced our understanding of VTE genetics, the field still needs high-quality whole-genome sequencing, particularly from family studies, to uncover the impact of low-frequency variants. <bold>Methods:</bold> We sequenced 216 individuals across 35 Han Chinese VTE pedigrees, validating filtered variants (MAF < 5%) via Sanger sequencing in a 99-case cohort of high-heritability (family history or unprovoked, early-onset(<50y)) VTE. To demonstrate the impact of key novel mutations, we conducted qPCR and Western Blot analyses in HEK293T cells. <bold>Results:</bold> Within the 35 pedigrees, three novel mutations—GP6 (c.G1094A:p.R365H), TET2 (c.G3451T:p.E1151X), and JAK2 (c.G380A:p.G127D)—were identified in two unrelated pedigrees each. These mutations have a minor allele frequency (MAF) of less than 5% in East Asian populations according to public databases. Replication in 99 high-heritability VTE cases revealed these mutations in 6, 2, and 6 cases, respectively. qPCR and WB results suggested that the mutations of GP6 and TET2 markedly changed gene and protein expression compared to wild type (WT). Network and enrichment analyses indicated that candidate genes in our study affect the main pathway of complement and coagulation cascades. <bold>Conclusion:</bold> This WGS study revealed a diverse genetic landscape and GP6, TET2, and JAK2 might as novel risk factors in East-Asia VTE patients. Potential clinical utilities of the low frequency genetic risk factors deserve attention.