Characterization of Pathogenic Variants Associated with Hereditary Thrombocytopenias in Families from the Czech Republic

Introduction

Inherited thrombocytopenias (IT) are a heterogeneous group of 33 different forms of monogenic disorders caused by molecular defects affecting 40 genes at least. The pathogenic germline variants play an important role in the development and maintenance of hematopoietic system (megakaryopoesis and thrombopoesis). These changes lead to disruption of these processes and are presented as the thrombocytopenia phenotype (low platelet count, blood-examination). However, patients are occasionally misdiagnosed with the immune thrombocytopenia and unsuccessfully treated with steroid therapy and splenectomy. In some patients, accurate diagnosis of IT can only be established based on the results of molecular genetic testing. Furthermore, it has also been shown that some hematological conditions with Mendelian type of hereditability precede the development of hematooncological disease.

Patients and Methods

DNA samples from peripheral blood or buccal swabs of four unrelated families were isolated. The whole exome sequencing (WES) was performed using the NextSeq 500 Illumina instrument with adequate chemistry and sequencing libraries were prepared according to the SeqCap EZ Human Exome Probes v3 protocol. The generated data were processed using in-house bioinformatics pipelines. The detected pathogenic variants were confirmed by Sanger sequencing. Moreover, the novel variant was analyzed in silico using analytical procedures including protein modelling, too. Germline DNA analysis was performed on all available samples and somatic DNA analysis was done for the oncological patient. Within each family, the obtained pathogenic variants were compared between the individuals with IT phenotype and their disease-free relatives.

Results

The pathogenic variants were characterized in four families with different forms of IT. Moreover, the additional genetic variants were detected in three of them which predispose to the development of hematological malignancies. In the first family, a novel heterozygous variant c.320C>T; p.(Thr107Met) in TUBB1 gene is probably responsible for essential thrombocytopenia disease because all rare TUBB1 variants until now have been detected in patients with macrothrombocytopenia. The known pathogenic variant c.1402G>T; p.(Val468Phe) in JAK2 gene (10.9% frequency) was identified in a family member suffering from the myeloproliferative disease. In the second family, heterozygous pathogenic variants c.3076C>T; p.(Arg1026Trp) in ITGA2B gene and c.3188G>A; p.(Arg1063His) in JAK2 gene were detected, associated with platelet-type bleeding disorders and hereditary erythrocytosis with megakaryocytic atypia and predisposition for hematological malignancy, respectively. It is known that stomach tumor occurred in patient´s family before. In the third family, heterozygous pathogenic variant c.3493C>T; p.(Arg1165Cys) in MYH9 gene was identified in a patient with macrothrombocytopenia. This variant was associated with Sebastian syndrome, macrothrombocytopenia and granulocyte inclusions and predisposition to kidney failure, hearing loss, and cataracts. In the fourth family, ANKRD26-related thrombocytopenia with predisposition to myeloid malignancy was probably identified in a patient with detected heterogeneous known variant c.-140C>G in 5´ UTR of ANKRD26 gene. Moreover, the novel c.682C>T; p.(Arg228Trp) variant in SYTL3 gene with uncertain significance was detected in this patient.

Conclusions

The pathogenic variants were detected in unrelated affected families with macrothrombocytopenia, platelet-type bleeding disorders and hereditary erythrocytosis with megakaryocytic atypia, Sebastian syndrome, and ANKRD26-related thrombocytopenia. Moreover, the genetic variants predispose to myeloid malignancy were identified. Molecular genetic testing helped the clinicians to determine the correct diagnosis in these patients.

This study was supported by Ministry of Health of the Czech Republic (grant No 16-29447A), and TA CR (TE02000058).