scholarly journals Genetic Diversity ofSCN5AGene and Its Possible Association with the Concealed Form of Brugada Syndrome Development in Polish Group of Patients

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Beata Uziębło-Życzkowska ◽  
Grzegorz Gielerak ◽  
Paweł Siedlecki ◽  
Beata Pająk

Brugada Syndrome (BS) is an inherited channelopathy associated with a high incidence of sudden cardiac death. The paper presents the discovery of new genetic variants ofSCN5Agene which might be associated with the development of a concealed form of Brugada Syndrome. The study involved a group of 59 patients (37 men) with suspected concealed form of Brugada Syndrome. Pharmacological provocation with intravenous ajmaline administration was performed. Six patients with positive test results were subjected to molecular analysis ofSCN5Agene with MSSCP method. Additionally, MSSCP genotyping was performed for samples obtained from the family members with Brugada Syndrome, despite the fact that they had negative ajmaline challenge test results. Genetic examinations of theSCN5Agene at 6 positive patients showed 6 known polymorphisms, 8 new single nucleotide point (SNP) variants located at exons, and 12 new single nucleotide point variants located at introns. Among new SNPs localized inSCN5Agene exons three SNPs affected the protein sequence.

2021 ◽  
Author(s):  
Jialin Liu ◽  
Huimin Xie ◽  
Ting Lin ◽  
Congxiao Tie ◽  
Huolin Luo ◽  
...  

Abstract Soybean cultivars bred in the Huang-Huai-Hai region (HR) are rich in pedigree information. To data, few reports have exposed the genetic variants, population structure and genetic diversity of cultivars in this region by making use of genome-wide resequencing data. To depict genetic variation, population structure and composition characteristics of genetic diversity, a sample of soybean population that composed all by cultivars was constructed. We re-sequenced 181 soybean cultivar genomes with an average depth of 10.38x. In total, 11185589 single nucleotide polymorphisms (SNPs) and 2520208 insertion-deletions (InDels) were identified on all 20 chromosomes. A considerable number of putative variants existed in important genome regions that may have an incalculable influence on genes, which participated in momentous biological processes. PCA and population structure figured out that there was no obvious grouping trend. The LD semi-decay distances of the five sub-populations were 290kb, 380kb, 753kb, 182kb, and 227kb, respectively. Sub-population A (SA) had the highest value of nucleotide polymorphism (π). With the passage of time, the nucleotide polymorphism of SB and SC decreased gradually, however that of SD and SE, opposite to SB and SC, gave a rapid up-climbing trend, which meant a sharp increasing in genetic diversity during the latest 20 years, hinting that breeders may have different breeding goals in different breeding periods in HR. Analysis of the PIC statistics exhibited very similar results with π. The current study was to analyze the genetic variants and characterize the structure and genetic diversity of soybean cultivars bred in different decades in HR, and in the hope of providing a theoretical reference for other identical studies.


2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
GUSTAVO GRELONI ◽  
Federico Varela ◽  
Griselda Bratti ◽  
Guillermo Rosa Diez ◽  
Celia Dos Santos ◽  
...  

Abstract Background and Aims Advances in the past 2 decades have shown atypical hemolytic uremic syndrome (aHUS) to be a disorder of the alternative pathway of complement. Most aHUS cases involve sequence variations in genes encoding complement proteins The term pregnancy associated aHUS (P-aHUS) refer to the thrombotic microangiopathy (TMA) that result from uncontrolled complement activation during pregnancy or the postpartum period. P-aHUS is a devastating systemic disease, with high maternal mortality and morbidity rates, in the pre-eculizumab era. The term ‘C3 glomerulopathy’ (C3GN) encompasses a heterogeneous spectrum of immune-mediated nephropathies that share a common pathological feature, glomerular deposition of C3. This entity may progress to advanced stages of chronic kidney disease and shares a common genetic risk factors with aHUS. Even more, some authors even suggest that C3GN and aHUS represent two forms of a disease spectrum with a common pathogenic principle. Here, we report this rare association and describe the family genetic variants that could cause it Method We describe the clinical and laboratoy data of a patient with the association of aHUS and C3 Glomerulopathy. A genetic study was performed and her available relatives were also screened for mutations/polymorphisms in aHUS-associated complement genes. After extracting gDNA from whole blood (Wizard Genomic DNA Purification Kit, Promega), PCR products of coding sequences and intronic flanking regions of complement genes were sequenced by ABI PRISM 310 Genetic Analyzer (Applied Biosystems). In silico analysis for pathogenicity was completed with Polyphen2-HDIV, PhyloP/Phastcons (MutationTaster), SIFT and PANTHER. All the participants provided informed written consent Results In 3/2012 a 27-year-old patient, with no family history, started his current illness one month after his first natural birth, with acute renal failure and microangiopathic hemolytic anemia, demonstrating a severe TMA in a renal biopsy. Laboratory results showed low C3 serum levels, but C4 were normal, haptoglobine was undetectably low, and all ADAMTS13 parameters were normal. Her urine tests showed also glomerular hematuria and proteinuria in the nephrotic range. She was treated with plasmapheresis and fresh frozen plasma with hematological improvement, but hemodialysis was required for more than 3 months. Despite partial recovery of renal function, six months later reappeared anemia and developed severe arterial hypertension, congestive heart failure and progressive renal insufficiency. Diagnosis of aHUS was made and start treatment with eculizumab with progressive recovery of renal function in the following months. Nevertheless the C3 serum levels persisted low and the proteinuria and hematuria did not change even after long term treatment with eculizumab. Retrospectively, her urynalisis before the pregnant showed proteinuria and hematuria, and a revision of a renal biopsy revealed the presence of dominant C3 deposits in the immunofluorescence, and electrondense deposits in the electronic microscopy, suggesting the diagnostic of C3GN. In a genetic study two novel single nucleotide variants were founded (CFH c.575G>A, p.C192Y (exon 5) (NM_000186), predicted to be pathogenic by 4 of 5 available pathogenicity prediction programs; and CFI c.1189G>T, p.V397L (exon 11) (NM_000204), predicted pathogenic by 0 of 6 available pathogenicity prediction programs). (Figure 1) Conclusion We present here the family genetic bases of a patient who developed a C3GN and a aHUS with a different response to treatment with eculizumab. In this case we identified two novel genetic variants in the CFH and CFI genes in a patient with aHUS, who inherited one variant from each parent. Although the CFI variant is predicted to be benign, the CFH variant is predicted to be damaging. It is located in exon 5, which encodes a portion of the factor H protein implicated in binding to C3b


2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Chao Zhang ◽  
Yang Gao ◽  
Zhilin Ning ◽  
Yan Lu ◽  
Xiaoxi Zhang ◽  
...  

Abstract Despite the tremendous growth of the DNA sequencing data in the last decade, our understanding of the human genome is still in its infancy. To understand the implications of genetic variants in the light of population genetics and molecular evolution, we developed a database, PGG.SNV (https://www.pggsnv.org), which gives much higher weight to previously under-investigated indigenous populations in Asia. PGG.SNV archives 265 million SNVs across 220,147 present-day genomes and 1018 ancient genomes, including 1009 newly sequenced genomes, representing 977 global populations. Moreover, estimation of population genetic diversity and evolutionary parameters is available in PGG.SNV, a unique feature compared with other databases.


Author(s):  
R. Singla ◽  
A. Udyavar ◽  
A. Gupta ◽  
A. Bade ◽  
K. Munde ◽  
...  

The present case series discuss three patients who had brugada type 2/ type 3 like ECG pattern that was converted to type 1 pattern with oral flecanide challenge test. Brugada syndrome is associated with a high incidence of sudden cardiac death,   typical ECG pattern being ST-segment elevation in the right precordial leads with T wave inversion. Pharmacological provocation should only be performed when the baseline ECG is not diagnostic of Brugada Syndrome. PR prolongation in the baseline ECG is also a contraindication because of the risk of inducing AV block. Drug challenge is performed under strict monitoring of BP and 12-lead ECG and facilities for cardio version and resuscitation are available. Atypical RBBB pattern/type 2/3 Brugada pattern on ECG in patients of syncope or family history of sudden cardiac arrest is commonly encountered by a cardiologist. This can be performed to provoke type 1 brugada pattern on ECG. Diagnosed cases of Brugada may be treated with ICD with proper indication if needed and thus prevent sudden cardiac death.


2004 ◽  
Vol 40 ◽  
pp. 157-167 ◽  
Author(s):  
Maria Nilsson ◽  
Karin Dahlman-Wright ◽  
Jan-Åke Gustafsson

For several decades, it has been known that oestrogens are essential for human health. The discovery that there are two oestrogen receptors (ERs), ERalpha and ERbeta, has facilitated our understanding of how the hormone exerts its physiological effects. The ERs belong to the family of ligand-activated nuclear receptors, which act by modulating the expression of target genes. Studies of ER-knockout (ERKO) mice have been instrumental in defining the relevance of a given receptor subtype in a certain tissue. Phenotypes displayed by ERKO mice suggest diseases in which dysfunctional ERs might be involved in aetiology and pathology. Association between single-nucleotide polymorphisms (SNPs) in ER genes and disease have been demonstrated in several cases. Selective ER modulators (SERMs), which are selective with regard to their effects in a certain cell type, already exist. Since oestrogen has effects in many tissues, the goal with a SERM is to provide beneficial effects in one target tissue while avoiding side effects in others. Refined SERMs will, in the future, provide improved therapeutic strategies for existing and novel indications.


Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 144
Author(s):  
Nohra Castillo Rodríguez ◽  
Xingbo Wu ◽  
María Isabel Chacón ◽  
Luz Marina Melgarejo ◽  
Matthew Wohlgemuth Blair

Orphan crops, which include many of the tropical fruit species used in the juice industry, lack genomic resources and breeding efforts. Typical of this dilemma is the lack of commercial cultivars of purple passion fruit, Passiflora edulis f. edulis, and of information on the genetic resources of its substantial semiwild gene pool. In this study, we develop single-nucleotide polymorphism (SNP) markers for the species and show that the genetic diversity of this fruit crop has been reduced because of selection for cultivated genotypes compared to the semiwild landraces in its center of diversity. A specific objective of the present study was to determine the genetic diversity of cultivars, genebank accession, and landraces through genotyping by sequencing (GBS) and to conduct molecular evaluation of a broad collection for the species P. edulis from a source country, Colombia. We included control genotypes of yellow passion fruit, P. edulis f. flavicarpa. The goal was to evaluate differences between fruit types and compare landraces and genebank accessions from in situ accessions collected from farmers. In total, 3820 SNPs were identified as informative for this diversity study. However, the majority distinguished yellow and purple passion fruit, with 966 SNPs useful in purple passion fruits alone. In the population structure analysis, purple passion fruits were very distinct from the yellow ones. The results for purple passion fruits alone showed reduced diversity for the commercial cultivars while highlighting the higher diversity found among landraces from wild or semi-wild conditions. These landraces had higher heterozygosity, polymorphism, and overall genetic diversity. The implications for genetics and breeding as well as evolution and ecology of purple passion fruits based on the extant landrace diversity are discussed with consideration of manual or pollinator-assisted hybridization of this species.


2021 ◽  
Vol 22 (9) ◽  
pp. 4700
Author(s):  
Michelle M. Monasky ◽  
Emanuele Micaglio ◽  
Giuseppe Ciconte ◽  
Ilaria Rivolta ◽  
Valeria Borrelli ◽  
...  

Genetic testing in Brugada syndrome (BrS) is still not considered to be useful for clinical management of patients in the majority of cases, due to the current lack of understanding about the effect of specific variants. Additionally, family history of sudden death is generally not considered useful for arrhythmic risk stratification. We sought to demonstrate the usefulness of genetic testing and family history in diagnosis and risk stratification. The family history was collected for a proband who presented with a personal history of aborted cardiac arrest and in whom a novel variant in the SCN5A gene was found. Living family members underwent ajmaline testing, electrophysiological study, and genetic testing to determine genotype-phenotype segregation, if any. Patch-clamp experiments on transfected human embryonic kidney 293 cells enabled the functional characterization of the SCN5A novel variant in vitro. In this study, we provide crucial human data on the novel heterozygous variant NM_198056.2:c.5000T>A (p.Val1667Asp) in the SCN5A gene, and demonstrate its segregation with a severe form of BrS and multiple sudden deaths. Functional data revealed a loss of function of the protein affected by the variant. These results provide the first disease association with this variant and demonstrate the usefulness of genetic testing for diagnosis and risk stratification in certain patients. This study also demonstrates the usefulness of collecting the family history, which can assist in understanding the severity of the disease in certain situations and confirm the importance of the functional studies to distinguish between pathogenic mutations and harmless genetic variants.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sabrina Samad Shoily ◽  
Tamim Ahsan ◽  
Kaniz Fatema ◽  
Abu Ashfaqur Sajib

AbstractDiabetes mellitus is a complex and heterogeneous metabolic disorder which is often pre- or post-existent with complications such as cardiovascular disease, hypertension, inflammation, chronic kidney disease, diabetic retino- and nephropathies. However, the frequencies of these co-morbidities vary among individuals and across populations. It is, therefore, not unlikely that certain genetic variants might commonly contribute to these conditions. Here, we identified four single nucleotide polymorphisms (rs5186, rs1800795, rs1799983 and rs1800629 in AGTR1, IL6, NOS3 and TNFA genes, respectively) to be commonly associated with each of these conditions. We explored their possible interplay in diabetes and associated complications. The variant allele and haplotype frequencies at these polymorphic loci vary among different super-populations (African, European, admixed Americans, South and East Asians). The variant alleles are particularly highly prevalent in different European and admixed American populations. Differential distribution of these variants in different ethnic groups suggests that certain drugs might be more effective in selective populations rather than all. Therefore, population specific genetic architectures should be considered before considering a drug for these conditions.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gavin W. Wilson ◽  
Mathieu Derouet ◽  
Gail E. Darling ◽  
Jonathan C. Yeung

AbstractIdentifying single nucleotide variants has become common practice for droplet-based single-cell RNA-seq experiments; however, presently, a pipeline does not exist to maximize variant calling accuracy. Furthermore, molecular duplicates generated in these experiments have not been utilized to optimally detect variant co-expression. Herein, we introduce scSNV designed from the ground up to “collapse” molecular duplicates and accurately identify variants and their co-expression. We demonstrate that scSNV is fast, with a reduced false-positive variant call rate, and enables the co-detection of genetic variants and A>G RNA edits across twenty-two samples.


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