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 R Show more
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RNA-seq can be used to identify SNVs, studies that employ this approach are uncommon, and those that do often rely on outdated mapping methods or methods that are more suitable for genomic and exomic alignment.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
Hypertrophic cardiomyopathy (HCM) is a common inherited cardiac disorder characterized by marked clinical and genetic heterogeneity. Ethnic groups underrepresented in studies may have distinctive char Show more
Hypertrophic cardiomyopathy (HCM) is a common inherited cardiac disorder characterized by marked clinical and genetic heterogeneity. Ethnic groups underrepresented in studies may have distinctive characteristics. We sought to evaluate the clinical and genetic landscape of Russian HCM patients. A total of 193 patients (52% male; 95% Eastern Slavic origin; median age 56 years) were clinically evaluated, including genetic testing, and prospectively followed to document outcomes. As a result, 48% had obstructive HCM, 25% had HCM in family, 21% were asymptomatic, and 68% had comorbidities. During 2.8 years of follow-up, the all-cause mortality rate was 2.86%/year. A total of 5.7% received an implantable cardioverter-defibrillator (ICD), and 21% had septal reduction therapy. A sequencing analysis of 176 probands identified 64 causative variants in 66 patients (38%); recurrent variants were Show less
Hypertrophic cardiomyopathy (HCM) is the most common inherited myocardial disease with significant genetic and phenotypic heterogeneity. To search for novel biomarkers, which could increase the accura Show more
Hypertrophic cardiomyopathy (HCM) is the most common inherited myocardial disease with significant genetic and phenotypic heterogeneity. To search for novel biomarkers, which could increase the accuracy of HCM diagnosis and improve understanding of its phenotype formation, we analyzed the levels of circulating miRNAs—stable non-coding RNAs involved in post-transcriptional gene regulation. Performed high throughput sequencing of miRNAs in plasma of HCM patients and controls pinpointed miR-499a-5p as one of 35 miRNAs dysregulated in HCM. Further investigation on enlarged groups of individuals showed that its level was higher in carriers of pathogenic/likely pathogenic (P/LP) variants in MYH7 gene compared to controls (fold change, FC = 8.9; p < 0.0001). Just as important, carriers of variants in MYH7 gene were defined with higher miRNA levels than carriers of variants in the MYBPC3 gene (FC = 14.1; p = 0.0003) and other patients (FC = 4.1; p = 0.0008). The receiver operating characteristic analysis analysis showed the ability of miR-499a-5p to identify MYH7 variant carriers with the HCM phenotype with area under the curve value of 0.95 (95% confidence interval: 0.88−1.03, p = 0.0004); sensitivity and specificity were 0.86 and 0.91 (cut-off = 0.0014). Therefore, miR-499a-5p could serve as a circulating biomarker of HCM, caused by P/LP variants in MYH7 gene. Show less