Targeted next-generation sequencing reveals novel and known variants of thrombophilia associated genes in Saudi patients with venous thromboembolism.

BACKGROUND: Thrombophilia is a substantial source of indisposition and mortality in several countries, including Arab populations. Deep venous thrombosis (DVT) with or without pulmonary embolism (PE) is the prevalent clinical manifestation of thrombophilia. While many genetic risk factors for DVT are known, almost all associated with hemostasis, many genetic factors remain unexplained. Nowadays, Next Generation Sequencing (NGS) offers a potential solution that allows several candidate genes to be analyzed simultaneously at a reasonable expense. METHODS: We performed variant screening in the thrombophilia associated genes in Factor V Leiden (FVL) mutation-negative patients using Ion Torrent Next-generation sequencing (NGS). Ion AmpliSeq panel for 18 genes was designed. Twenty-nine unrelated patients with idiopathic VTE were recruited for NGS. RESULTS: We were able to identify 19 variants (1 novel and 18 previously reported) in 10 out of 18 targeted genes. Pathogenic variants were identified in 22 patients demonstrating mutation detection rates of 76%. Previously reported variants in the F5, MTHFR, PROS1, PROC, F8, F9, SERPINA10, SERPIND1, and HRG genes were recognized in 21 patients. More than one variant in the targeted genes was detected in some of the patients with VTE. We identified SERPINA10 recurrent variant p.(R88*) in seven patients representing 32% of VTE cases. Additionally, we report one novel variant c.356G > T, p.(G119V) in the F7 gene, considered to be pathogenic in this study. CONCLUSIONS: Our studies finding illustrates the ability of targeted next-generation sequencing to uncover uncommon/unknown genetic variants that may predispose to thrombophilia. The finding of the novel variant in the F7 gene extends the spectrum of variants affecting thrombosis. While a comparatively small number of subjects have been included in our cohort, the findings summarize the possible genetic features of thrombophilia.

Identification of six novel factor viii gene variants using next generation sequencing and molecular dynamics simulation.

Hemophilia A is an X-linked recessive hemorrhagic disorder caused by variants in the F8 gene. To identify known and novel causative variants in hemophilia A, we have carried out genetic analysis among Saudi patients. Twenty-one patients, who were negative for inv-1/inv-22, were selected for analysis by next generation sequencing, thereafter confirmed by Sanger sequencing. In addition, the functionality and structural changes in the variant proteins were assessed using Molecular dynamics (MD) simulation and compared with wild-type and native proteins. In the samples we analyzed, we found 10 variants in 12 individuals; among them, five were novel and five were previously reported. The novel variants were located at positions: c.6130_6131insC, c.5815G>C, c.5493C>G, c.3734_3740delinsATTTCT and c.3744A>T. With the exception of one variant which was silent, the MD simulation revealed that the observed variants were causing severe structural changes when compared to the native protein and resulted in a loss of the protein's function. The MD analysis is in line with clinical data of patients who had <1% Factor VIII levels (severe hemophilia) with episodic bleeding, and were on more than one treatment. Moreover, some patients presented with chronic joint disability. These results will enrich the spectrum of variants and enlarge the factor VIII protein's database in the Saudi Arabian population.

IMPORTED MALARIA TO MAKKAH DISTRICT, SAUDI ARABIA: IS THERE ANY RISK OF LOCAL TRANSMISSION?

In Makkah, Saudi Arabia, there is an impending risk of imported malaria. This risk comes from the fact that millions of people, in majority from tropical and subtropical countries where malaria is endemic, visit the country to perform Hajj and Umrah every year. Moreover, millions of expatriates from endemic countries come to Makkah for work. Likewise, many Saudi citizens travel to endemic areas overseas for business and pleasure. We performed a retrospective analysis of all reported malaria cases in Makkah region, Saudi Arabia for years 2014 and 2015. In addition, sorting of mosquito populations in Makkah region was undertaken. Based on national data regarding reported malaria cases, 235 malaria cases were recorded in years 2014 and 2015. Of the reported cases 232 were non-Saudi and only 3 cases were Saudi. Those recorded Saudi cases were just returning from a travel to an endemic area. Most of the cases (79.6%) were P. falciprum and the remaining was P. vivax. Infected male represent 62% and female represent 38%. Age of the majority of reported cases (71.5%) lie between 31 and 50 years. Most of reported cases were from Chad, Pakistan, Nigeria and Sudan. Sorting of mosquito populations revealed the absence of malaria vectors in Makkah District.