👤 E V Filatova

A variety of techniques for DNA sequencing, such as specific gene sequencing, whole genome sequencing, or exome sequencing, are currently used to detect single nucleotide variations (SNVs). Although RNA-seq can be used to identify SNVs, studies that employ this approach are uncommon, and those that do often rely on outdated mapping methods or methods that are more suitable for genomic and exomic alignment. In this work, our aim is to apply modern RNA-seq specific alignment method in order to identify SNV in a cohort of HCMP patients, and characterize those SNV to gain insight into possible mechanisms of HCMP pathogenesis. The algorithm of identification of SNV based on transcriptomic sequencing data has been developed and evaluated. The algorithm was evaluated and the optimal quality threshold was determined based on allelic discrimination for the rs397516037 mutation (MYBPC3 c.3697 C > T) among patients. A total of 42,809 SNVs with a quality of 75 or higher were identified in 48 transcriptomes of hypertrophic cardiomyopathy (HCMP) myocardial tissue. Verification of missense and nonsense variants in key HCMP genes using Sanger sequencing confirmed the accuracy of the pipeline results. To identify variants potentially associated with HCMP pathogenesis, a filtration process was conducted based on minor allele frequency, substitution prediction score and ClinVar outcome. 214 missense mutations and 6 nonsense mutations were selected. Together with nonsense mutations, 19 mutations meeting the strictest SIFT and PolypPhen criteria were identified as potential factors influencing HCMP pathogenesis. We have developed and validated a method for identifying SNVs based on transcriptomic data, which can be used to identify putative pathogenic variants. We identified mutations in key HCMP genes MYBPC3 and MYH7 in a cohort of patients. We also found potentially pathologic mutations in genes ANXA6 and FEM1 A and obtained data supporting the role of NEBL in myocardial diseases. This method would be useful in analyzing transcriptomic data available in the Gene Expression Omnibus, but should be used with caution as we have tested it on a specific disease. Show less

Multiple osteochondromas (MO) is a rare autosomal dominant skeletal disorder characterized by the development of multiple benign tumors known as osteochondromas. The condition is predominantly caused by loss-of-function variants in the Show less

This study is aimed at investigating the clinical and genetic characteristics of 244 unrelated probands diagnosed with multiple osteochondromas (MO). The diagnosis of MO typically involves identifying multiple benign bone tumors known as osteochondromas (OCs) through imaging studies and physical examinations. However, cases with both OCs and enchondromas (ECs) may indicate the more rare condition metachondromatosis (MC), which is assumed to be distinct disease. Previous cohort studies of MO found heterozygous loss-of-function (LoF) variants only in the Show less

Aim      To determine specific clinical characteristics caused by a combination of the rs397516037 pathogenic variant in the myosin-binding protein C (MTBPC3) and the rs749628307 polymorphic variant in the vinculin (VCL) gene in a Russian family of carriers and to evaluate the contribution of the rs749628307 polymorphic variant in the VCL gene to the development of hypertrophic cardiomyopathy (HCMP).Material and methods  The family under study included one healthy person and 3 patients with HCMP. A targeted analysis of proband's exome was performed. A structural alignment for both forms of the VCL protein, the canonical form and the form with p.Arg230His substitution, was performed.Results The pathogenic rs397516037 variant and the potentially pathogenic rs749628307 variant were detected in the proband and several family members. A possibly damaging variant rs749628307 was detected in the proband and several family members evaluated in this study. The structural alignment confirmed that the rs749628307 variant did not alter the protein structure significantly and could not cause an impairment or loss of the protein function.Conclusion      This study demonstrated that apparently the rs749628307 variant in the VCL gene does not affect the protein structure in a pathogenetically significant way, neither does it affect the severity and form of the clinical manifestations of HCMP; therefore, it cannot be considered as pathogenic. Show less