Genotype-phenotype correlation and description of two novel mutations in Iranian patients with glycogen storage disease 1b (GSD1b)

Background: Glycogen storage disease (GSD) is a rare inborn error of the synthesis or degradation of glycogen metabolism. GSD1, the most common type of GSD, is categorized into GSD1a and GSD1b which caused by the deficiency of glucose-6-phosphatase (G6PC) and glucose-6-phosphate transporter (SLC37A4), respectively. The high rates of consanguineous marriages in Iran provide a desirable context to facilitate finding the homozygous pathogenic mutations. This study designates to evaluate the clinical and genetic characteristics of patients with GSD1b to assess the possible genotype-phenotype correlation. Results: Autozygosity mapping was performed on nineteen GSD suspected families to suggest the causative loci. The mapping was done using two panels of short tandem repeat (STR) markers linked to the corresponding genes. The patients with autozygous haplotype block for the markers flanking the genes were selected for direct sequencing. Six patients showed autozygosity in the candidate markers for SLC37A4. Three causative variants were detected. The recurrent mutation of c.10421043delCT (p.Leu348Valfs*53) and a novel missense mutation of c.365G > A (p.G122E) in the homozygous state were identified in the SLC37A4. In silico analysis was performed to predict the pathogenicity of the variants. A novel whole SLC37A4 gene deletion using long-range PCR and sequencing was confirmed as well. Severe and moderate neutropenia was observed in patients with frameshift and missense variants, respectively. The sibling with the whole gene deletion has shown both severe neutropenia and leukopenia. Conclusions: The results showed that the hematological findings may have an appropriate correlation with the genotype findings. However, for a definite genotype-phenotype correlation, specifically for the clinical and biochemical phenotype, further studies with larger sample sizes are needed. © 2020 The Author(s)

Fast Linear State Estimation for Unbalanced Distribution Systems Using Hybrid Measurements

Distribution system state estimation (DSSE) is traditionally solved iteratively using unsynchronized measurements provided by the SCADA system and/or smart meters. This article puts forward a decoupled linear state estimation (SE) method for unbalanced distribution systems. Contrary to conventional methods, the proposed linear DSSE (LDSSE) method can function with purely unsynchronized or hybrid synchronized/unsynchronized measurements. In the case of purely unsynchronized measurements, the voltage phase angles of the reference bus are acquired through local measurements. In the first stage, the proposed LDSSE method estimates the voltage phase angles in terms of network parameters and available measurements. These are referred to as pseudo-synchronized voltage phase angles, which establish a basis for deriving pseudo-synchronized voltage/current phasors. In the second stage, a set of linear equations are derived for each phase separately. Solving these equations results in estimates for voltage phasors. The linearity and decoupled nature of the proposed LDSSE method significantly reduces the computation time without impacting the accuracy of estimates. The superiority of the proposed LDSSE method over the existing methods is verified using extensive simulations conducted on several test feeders, delivering results 20 times faster than the nonlinear DSSE (NDSSE) on the 8500-bus test feeder

Genome-wide single nucleotide polymorphism-based autozygosity mapping facilitates identification of mutations in consanguineous families with epidermolysis bullosa

Autozygosity mapping (AM) is a technique utilised for mapping homozygous autosomal recessive (AR) traits and facilitation of genetic diagnosis. We investigated the utility of AM for the molecular diagnosis of heterogeneous AR disorders, using epidermolysis bullosa (EB) as a paradigm. We applied this technique to a cohort of 46 distinct EB families using both short tandem repeat (STR) and genome-wide single nucleotide polymorphism (SNP) array-based AM to guide targeted Sanger sequencing of EB candidate genes. Initially, 39 of the 46 cases were diagnosed with homozygous mutations using this method. Independently, 26 cases, including the seven initially unresolved cases, were analysed with an EB-targeted next-generation sequencing (NGS) panel. NGS identified mutations in five additional cases, initially undiagnosed due to the presence of compound heterozygosity, deep intronic mutations or runs of homozygosity below the set threshold of 2 Mb, for a total yield of 44 of 46 cases (95.7) diagnosed genetically. © 2018 John Wiley & Sons Ltd

Whole-Exome Sequencing Uncovers Novel Causative Variants and Additional Findings in Three Patients Affected by Glycogen Storage Disease Type VI and Fanconi�Bickel Syndrome

Glycogen storage diseases (GSDs) are the heterogeneous group of disorders caused by mutations in at least 30 different genes. Different types of GSDs, especially liver GSDs, take overlapping symptoms and can be clinically indistinguishable. This survey evaluated the use of whole-exome sequencing (WES) for the genetic analysis of the liver GSD-suspected patients in three unrelated families. An in-house filtering pipeline was used to assess rare pathogenic variants in GSD-associated genes, autosomal recessive/mendelian disorder genes (carrier status for genetic counseling subjects), and the ACMG�s list of 59 actionable genes. For the interpretation of the causative variants and the incidental/secondary findings, ACMG guidelines were applied. Additionally, we have explored PharmGKB class IA/IB pharmacogenetic variants. The segregation analysis was performed using Sanger sequencing for the novel causative variants. Bioinformatics analysis of the exome data in three individuals revealed three novel homozygous causative variants in the GSD-associated genes. The first variant, c.298307delATGATCAACC in PYGL gene has related to HERS disease (GSD VI). Both variants of c.1043dupT and c.613-1G > C in SLC2A2 gene have been associated with Fanconi-Bickel syndrome (GSDXI). Eight pathogenic/likely pathogenic medical actionable findings in Mendelian disease genes and 10 pharmacogenetic variants with underlying drug response phenotypes have been identified. No known/expected pathogenic variants were detected in the ACMG�s list of 59 actionable genes. The logical filtering steps can help in finding other medical actionable secondary/incidental findings as well as effectively identifying the causative variants in heterogeneous conditions such as GSDs. Three novel variants related to GSD genes recognized in liver GSD-suspected patients with early infantile and childhood-age onset. © Copyright © 2021 Eghbali, Fatemi, Salehpour, Abiri, Saei, Talebi, Olyaei, Yassaee and Modarressi

Molecular genetic diagnosis of Glanzmann syndrome in Iranian population; Reporting novel and recurrent mutations

Background: Glanzmann thrombasthenia (GT) is a rare autosomal recessive abnormality of platelet aggregation with quantitative and/or qualitative abnormality of αIIbβ3 integrin. The αIIbβ3 is a platelet fibrinogen receptor, which is required for platelet aggregation, firm adhesion, and also spreading. The disease is more prevalent in the populations with a higher rate of consanguineous marriages as in some Middle Eastern populations including Iraq, Jordan, and Iran. Different types of mutations in ITGA2B and ITGB3 genes have been previously reported to cause the disease. Result: In this study, 16 patients with the clinical diagnosis of GT were studied. Direct sequencing of the exons and exon-intron boundaries of the above genes revealed mutations in 14 patients (detection rate: 87.5). Briefly, out of fifteen types of identified mutations, 14 were novel. Seven mutations in the ITGB3 gene included 4 missense c.2T > C, c.155 G > T, c. 538 G > A, c.1990 G > T, one nonsense mutation c.1303 G > T, a small deletion c.1656-1658delCTC and a deletion of one nucleotide c.401delA. Mutations in the ITGA2B were 8 different mutations consisting 2 missense c.286 T > A, c.842 C > T, 2 deletions c.1899 del T, c.189-319-236del, an insertion c.1071-1072insG and one splice site mutations c.409-3 C > G, one synonymous mutation that might alter the normal splicing process c.1392 A > G and a nonsense mutation c.1555 C > T. The causative mutation in 2 patients remained unknown. Using long-range PCR and sequencing, we found a rather large deletion. The break point of this deletion covers 319 nt from the last part of the first intron and 48 nt from the beginning of the second exon of ITGA2B gene. The deletion was also detected in two unrelated patients with the same ethnicity. In addition, in silico analyses of novel mutations were performed. Conclusion: There was no recurrent mutation in the studied population. This may be due to either small sample size or the heterogeneity of the studied population. © 2019 The Author(s)

Development and validation of a novel panel of 16 STR markers for simultaneous diagnosis of β-thalassemia, aneuploidy screening, maternal cell contamination detection and fetal sample authenticity in PND and PGD/PGS cases

Prenatal diagnosis (PND) may be complicated with sample mix-up; maternal cell contamination, non-paternity and allele drop out at different stages of diagnosis. Aneuploidy screening if combined with PND for a given single gene disorder, can help to detect any common aneuploidy as well as aiding sample authenticity and other probable complications which may arise during such procedures. This study was carried out to evaluate the effectiveness of a novel panel of STR markers combined as a multiplex PCR kit (HapScreen� kit) for the detection of β-thalassemia, aneuploidy screening, ruling in/out maternal cell contamination (MCC), and sample authenticity. The kit uses 7 STR markers linked to β-globin gene (HBB) as well as using 9 markers for quantitative analysis of chromosomes 21, 18, 13, X and Y. Selection of the markers was to do linkage analysis with β-globin gene, segregation analysis and to perform a preliminary aneuploidy screening of fetal samples respectively. These markers (linked to the β-globin gene) were tested on more than 2185 samples and showed high heterozygosity values (68.4�91.4). From 2185 fetal cases we found 3 cases of non-paternity, 5 cases of MCC, one case of sample mix-up and one case of trisomy 21 which otherwise may have end up to misdiagnosis. This kit was also successfully used on 231 blastomeres for 29 cases of pre-implantation genetic diagnosis (PGD) and screening (PGS). The markers used for simultaneous analysis of haplotype segregation and aneuploidy screening proved to be very valuable to confirm results obtained from direct mutation detection methods (i.e. ARMS, MLPA and sequencing) and aneuploidy screening. © 2019, The Author(s)

Chemical profile and biological activities of essential oil from Artemisia vulgaris L. cultivated in Brazil

Essential oil from the leaves of Artemisia vulgaris L. (Compositae) cultivated in Brazil was investigated for its chemical composition and biological activities including antibacterial, antifungal, and anthelmintic. The constituents of essential oils isolated by hydro-distillation were examined by GC-MS and a total of 18 components were identified. The essential oil was dominated by oxygenated sesquiterpenes (44.4%), sesquiterpene hydrocarbons (33.3%), and oxygenated monoterpenes (16.6%). Caryophyllene (37.45%), germacrene D (16.17%), and humulene (13.66%) were the major components. The essential oils from A. vulgaris showed bactericidal and fungicidal properties against Staphylococcus aureus and Candida albicans, respectively. Anthelmintic activity against Haemonchus contortus was absent in this essential oil. Altogether above results indicate that essential oils from A. vulgaris can be used for various medicinal purposes.Sonia Malik, Ludmilla Santos Silva de Mesquita, Carolina Rocha Silva, José Wilson Carvalho de Mesquita, Emmeline de Sá Rocha, Jayakumar Bose, Rambod Abiri, Patricia de Maria Silva Figueiredo, and Livio M. Costa-Júnio