Iranian Journal of Reproductive Medicine, Jan 9, 2023
Background: Citrullinemia type 1 is an autosomal recessive disease resulting in ammonia accumulat... more Background: Citrullinemia type 1 is an autosomal recessive disease resulting in ammonia accumulation in the blood, and if uncontrolled may progress to coma or death in the early months after birth. Cases presentation: 7 families from Southwest Iran having one or more children in their families or relatives, who died in the early months after birth due to citrullinemia type 1 visited for genetic counseling and prenatal diagnosis. Whole-exome sequencing was performed on peripheral blood specimens and chorionic villus samples. Sanger sequencing confirmed the genetic results. Both parents were identified as carriers for the exon 15 c.1168G>A mutation in each family. The fetus in 6 out of 7 families was homozygote for A substitution on the argininosuccinate synthetase 1 gene. Conclusion: The presence of a common mutation in the argininosuccinate synthetase 1 gene in all affected families of Southwest Iran shows a possible population cluster in this area. Key words: Argininosuccinate synthetase, Chorionic villus sampling, Point mutation.
International Journal of Reproductive BioMedicine (IJRM)
Background: Citrullinemia type 1 is an autosomal recessive disease resulting in ammonia accumulat... more Background: Citrullinemia type 1 is an autosomal recessive disease resulting in ammonia accumulation in the blood, and if uncontrolled may progress to coma or death in the early months after birth. Cases presentation: 7 families from Southwest Iran having one or more children in their families or relatives, who died in the early months after birth due to citrullinemia type 1 visited for genetic counseling and prenatal diagnosis. Whole-exome sequencing was performed on peripheral blood specimens and chorionic villus samples. Sanger sequencing confirmed the genetic results. Both parents were identified as carriers for the exon 15 c.1168G>A mutation in each family. The fetus in 6 out of 7 families was homozygote for A substitution on the argininosuccinate synthetase 1 gene. Conclusion: The presence of a common mutation in the argininosuccinate synthetase 1 gene in all affected families of Southwest Iran shows a possible population cluster in this area. Key words: Argininosuccinate s...
We define a class of first-order formulas $\mathsf{P}^{\ast }$ which exactly contains formulas $\... more We define a class of first-order formulas $\mathsf{P}^{\ast }$ which exactly contains formulas $\varphi$ such that satisfaction of $\varphi$ in any classical structure attached to a node of a Kripke model of intuitionistic predicate logic deciding atomic formulas implies its forcing in that node. We also define a class of $\mathsf{E}$-formulas with the property that their forcing coincides with their classical satisfiability in Kripke models which decide atomic formulas. We also prove that any formula with this property is an $\mathsf{E}$-formula. Kripke models of intuitionistic arithmetical theories usually have this property. As a consequence, we prove a new conservativity result for Peano arithmetic over Heyting arithmetic.
Quarterly of the Horizon of Medical Sciences, 2020
Aims Morquio syndrome is a mucopolysaccharidosis (type 4) that has autosomal recessive inheritanc... more Aims Morquio syndrome is a mucopolysaccharidosis (type 4) that has autosomal recessive inheritance. Moreover, it is caused by defects in the two genes; GALNS (Murcio A) and GLB1 (Murcio B). The prevalence rate of this condition is estimated to be about 1 per 200000 live births globally. Besides, Middle Eastern cases shape the greatest ratio, due to higher rates of consanguineous marriages. The most frequent clinical manifestations of the disease include skeletal abnormalities, hearing and vision problems, decreased physical growth, and cardiac malformations. Methods & Materials This study investigated the pathogenic mutations in two Iranian individuals. Both cases were the result of consanguineous marriages with mucopolysaccharidosis type 4 (A or B types, each). Following of genomic DNA extraction, Whole Exome Sequencing was conducted for the study patients. Then, for the validation of observed pathogenic mutations, sanger sequencing was performed for the patients. Findings Two expl...
Objective: 45, X is a very rare condition that usually results from Y/autosomal translocations or... more Objective: 45, X is a very rare condition that usually results from Y/autosomal translocations or insertions. Here we present an infertile azoospermic man who had 45, X t(Yp;15) karyotype and deletion of AZF (azoospermia factor) gene region. Case report: A 35-year-old infertile azoospermic man with a typical male appearance came for infertility genetic counseling. He was infertile for more than ten years and had short height. High-resolution of metaphase chromosomes of 50 peripheral white blood cells were analyzed for karyotyping. Fluorescence in situ hybridization (FISH) analysis and Polymerase chain reaction (PCR) were done for SRY and AZF gene localization. Karyotyping and FISH analysis revealed 45, X t(Yp;15) karyotype and no mosaicism. More investigation on the Y chromosome revealed no deletion in the SRY region, but AZF a/b/c were deleted. It was revealed that Yp's subtelomeric region but not Yq was translocated to chromosome 15. Conclusion: This study shows that despite t...
Although it has been about 30 years since the discovery of circular RNAs (circRNAs) in mammalian ... more Although it has been about 30 years since the discovery of circular RNAs (circRNAs) in mammalian cells, these subtypes of RNAs’ capabilities have come into focus in recent years. The unique structure and various functional roles of circRNAs in many cellular processes have aroused researchers’ interest and raised many questions about whether circRNAs can facilitate the diagnosis and treatment of diseases. To answer these questions, we will illustrate the main known functions and regulatory roles of circRNAs in the cell after presenting a brief history of the discovery of circRNAs and the main proposed theories of the biogenesis of circRNAs. Afterward, the practical application of circRNAs as biomarkers of different pathophysiological conditions will be discussed, mentioning some examples and challenges in this area. We also consider one of the main questions that human beings have always been faced, “the origin of life,” and its possible connection to circRNAs. Finally, focusing on t...
Spinal muscular atrophies (SMAs) are a heterogeneous group of neuromuscular diseases characterize... more Spinal muscular atrophies (SMAs) are a heterogeneous group of neuromuscular diseases characterized by loss of motor neurons, muscle weakness, hypotonia and muscle atrophy, with different modes of inheritance; however, the survival motor neuron 1 (SMN1) gene is predominantly involved. The aims of the current study were to clarify the genetic basis of SMA and determine the mutation spectrum of SMN1 and other associated genes, in order to provide molecular information for more accurate diagnosis and future prospects for treatment. We performed a comprehensive analysis of 5q SMA in 1765 individuals including 528 patients from 432 unrelated families with at least one child with suspected clinical presentation of SMA. Copy number variations of the SMN1 and SMN2 genes and linkage analysis were performed using multiplex ligation-dependent probe amplification (MLPA) and short tandem repeat (STR) markers linked to the SMN1 gene. Cases without mutation in the SMA locus on 5q were analyzed for the DNAJB2, IGHMBP2, SIGMAR1 and PLEKHG5 genes using linked STR markers. Sanger sequencing of whole genes was performed for cases with homozygous haplotypes. Whole-genome sequencing (WGS) and whole-exome analysis was conducted for some of the remaining cases. Mutations in the SMN1 gene were identified in 287 (66.43%) families including 269 patients (62.26%) with homozygous deletion of the entire SMN1 gene. Only one of the patients had a homozygous point mutation in the SMN1 gene. Among the remaining families, three families showed mutations in either the DNAJB2, SIGMAR1 or PLEKHG5 genes, which were linked using STR analysis and Sanger sequencing. From 10 families who underwent WGS, we found six homozygous point mutations in six families for either the TNNT1, TPM3, TTN, SACS or COL6A2 genes. Two mutations in the PLA2G6 gene were also found in another patient as compound heterozygous. This rather large cohort allowed us to identify genotype patterns in Iranian 5q SMA patients. The process of identifying 11 mutations (9 novel) in 9 different genes among non-5q SMA patients shows the diversity of genes involved in non-5q SMA in Iranians. Genotyping of patients with SMA is essential for prenatal and preimplantation genetic diagnosis (PGD), and may be very helpful for guiding treatment, with the advent of new, more effective, albeit very expensive, therapies. Also, combining linkage analysis was shown to be beneficial in many ways, including sample authenticity and segregation analysis, and for ruling out maternal cell contamination during prenatal diagnosis (PND).
Glycogen storage diseases (GSDs) are the heterogeneous group of disorders caused by mutations in ... more 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 ...
Background Glycogen storage disease (GSD) is a rare inborn error of the synthesis or degradation ... more 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 mark...
Background: Pre-implantation Genetic Diagnosis (PGD) has recently been introduced as a reproducti... more Background: Pre-implantation Genetic Diagnosis (PGD) has recently been introduced as a reproductive choice for individuals who carry a disease-causing BRCA1/2 mutation. Since this technology has not yet been launched for patients at the Cancer Institute of Imam Khomeini Hospital harboring gene mutations that predispose patients to breast cancer, this study aimed to introduce a PGD-based model using a single cell lymphocyte instead of an embryonic blastomere. Methods: Two affected and unrelated women with a known mutation in BRCA1/2 were enrolled in this study. Each patient (together with her siblings) was considered as an embryo derived from a hypothetical couple. Blood samples were collected from these individuals as well as their parents. Linkage analysis was performed. Following this process, a mutation-free individual and a mutation carrier was selected from the first and second family, respectively. A single lymphocyte was then extracted from their freshly taken peripheral bloo...
Iranian Journal of Reproductive Medicine, Jan 9, 2023
Background: Citrullinemia type 1 is an autosomal recessive disease resulting in ammonia accumulat... more Background: Citrullinemia type 1 is an autosomal recessive disease resulting in ammonia accumulation in the blood, and if uncontrolled may progress to coma or death in the early months after birth. Cases presentation: 7 families from Southwest Iran having one or more children in their families or relatives, who died in the early months after birth due to citrullinemia type 1 visited for genetic counseling and prenatal diagnosis. Whole-exome sequencing was performed on peripheral blood specimens and chorionic villus samples. Sanger sequencing confirmed the genetic results. Both parents were identified as carriers for the exon 15 c.1168G>A mutation in each family. The fetus in 6 out of 7 families was homozygote for A substitution on the argininosuccinate synthetase 1 gene. Conclusion: The presence of a common mutation in the argininosuccinate synthetase 1 gene in all affected families of Southwest Iran shows a possible population cluster in this area. Key words: Argininosuccinate synthetase, Chorionic villus sampling, Point mutation.
International Journal of Reproductive BioMedicine (IJRM)
Background: Citrullinemia type 1 is an autosomal recessive disease resulting in ammonia accumulat... more Background: Citrullinemia type 1 is an autosomal recessive disease resulting in ammonia accumulation in the blood, and if uncontrolled may progress to coma or death in the early months after birth. Cases presentation: 7 families from Southwest Iran having one or more children in their families or relatives, who died in the early months after birth due to citrullinemia type 1 visited for genetic counseling and prenatal diagnosis. Whole-exome sequencing was performed on peripheral blood specimens and chorionic villus samples. Sanger sequencing confirmed the genetic results. Both parents were identified as carriers for the exon 15 c.1168G>A mutation in each family. The fetus in 6 out of 7 families was homozygote for A substitution on the argininosuccinate synthetase 1 gene. Conclusion: The presence of a common mutation in the argininosuccinate synthetase 1 gene in all affected families of Southwest Iran shows a possible population cluster in this area. Key words: Argininosuccinate s...
We define a class of first-order formulas $\mathsf{P}^{\ast }$ which exactly contains formulas $\... more We define a class of first-order formulas $\mathsf{P}^{\ast }$ which exactly contains formulas $\varphi$ such that satisfaction of $\varphi$ in any classical structure attached to a node of a Kripke model of intuitionistic predicate logic deciding atomic formulas implies its forcing in that node. We also define a class of $\mathsf{E}$-formulas with the property that their forcing coincides with their classical satisfiability in Kripke models which decide atomic formulas. We also prove that any formula with this property is an $\mathsf{E}$-formula. Kripke models of intuitionistic arithmetical theories usually have this property. As a consequence, we prove a new conservativity result for Peano arithmetic over Heyting arithmetic.
Quarterly of the Horizon of Medical Sciences, 2020
Aims Morquio syndrome is a mucopolysaccharidosis (type 4) that has autosomal recessive inheritanc... more Aims Morquio syndrome is a mucopolysaccharidosis (type 4) that has autosomal recessive inheritance. Moreover, it is caused by defects in the two genes; GALNS (Murcio A) and GLB1 (Murcio B). The prevalence rate of this condition is estimated to be about 1 per 200000 live births globally. Besides, Middle Eastern cases shape the greatest ratio, due to higher rates of consanguineous marriages. The most frequent clinical manifestations of the disease include skeletal abnormalities, hearing and vision problems, decreased physical growth, and cardiac malformations. Methods & Materials This study investigated the pathogenic mutations in two Iranian individuals. Both cases were the result of consanguineous marriages with mucopolysaccharidosis type 4 (A or B types, each). Following of genomic DNA extraction, Whole Exome Sequencing was conducted for the study patients. Then, for the validation of observed pathogenic mutations, sanger sequencing was performed for the patients. Findings Two expl...
Objective: 45, X is a very rare condition that usually results from Y/autosomal translocations or... more Objective: 45, X is a very rare condition that usually results from Y/autosomal translocations or insertions. Here we present an infertile azoospermic man who had 45, X t(Yp;15) karyotype and deletion of AZF (azoospermia factor) gene region. Case report: A 35-year-old infertile azoospermic man with a typical male appearance came for infertility genetic counseling. He was infertile for more than ten years and had short height. High-resolution of metaphase chromosomes of 50 peripheral white blood cells were analyzed for karyotyping. Fluorescence in situ hybridization (FISH) analysis and Polymerase chain reaction (PCR) were done for SRY and AZF gene localization. Karyotyping and FISH analysis revealed 45, X t(Yp;15) karyotype and no mosaicism. More investigation on the Y chromosome revealed no deletion in the SRY region, but AZF a/b/c were deleted. It was revealed that Yp's subtelomeric region but not Yq was translocated to chromosome 15. Conclusion: This study shows that despite t...
Although it has been about 30 years since the discovery of circular RNAs (circRNAs) in mammalian ... more Although it has been about 30 years since the discovery of circular RNAs (circRNAs) in mammalian cells, these subtypes of RNAs’ capabilities have come into focus in recent years. The unique structure and various functional roles of circRNAs in many cellular processes have aroused researchers’ interest and raised many questions about whether circRNAs can facilitate the diagnosis and treatment of diseases. To answer these questions, we will illustrate the main known functions and regulatory roles of circRNAs in the cell after presenting a brief history of the discovery of circRNAs and the main proposed theories of the biogenesis of circRNAs. Afterward, the practical application of circRNAs as biomarkers of different pathophysiological conditions will be discussed, mentioning some examples and challenges in this area. We also consider one of the main questions that human beings have always been faced, “the origin of life,” and its possible connection to circRNAs. Finally, focusing on t...
Spinal muscular atrophies (SMAs) are a heterogeneous group of neuromuscular diseases characterize... more Spinal muscular atrophies (SMAs) are a heterogeneous group of neuromuscular diseases characterized by loss of motor neurons, muscle weakness, hypotonia and muscle atrophy, with different modes of inheritance; however, the survival motor neuron 1 (SMN1) gene is predominantly involved. The aims of the current study were to clarify the genetic basis of SMA and determine the mutation spectrum of SMN1 and other associated genes, in order to provide molecular information for more accurate diagnosis and future prospects for treatment. We performed a comprehensive analysis of 5q SMA in 1765 individuals including 528 patients from 432 unrelated families with at least one child with suspected clinical presentation of SMA. Copy number variations of the SMN1 and SMN2 genes and linkage analysis were performed using multiplex ligation-dependent probe amplification (MLPA) and short tandem repeat (STR) markers linked to the SMN1 gene. Cases without mutation in the SMA locus on 5q were analyzed for the DNAJB2, IGHMBP2, SIGMAR1 and PLEKHG5 genes using linked STR markers. Sanger sequencing of whole genes was performed for cases with homozygous haplotypes. Whole-genome sequencing (WGS) and whole-exome analysis was conducted for some of the remaining cases. Mutations in the SMN1 gene were identified in 287 (66.43%) families including 269 patients (62.26%) with homozygous deletion of the entire SMN1 gene. Only one of the patients had a homozygous point mutation in the SMN1 gene. Among the remaining families, three families showed mutations in either the DNAJB2, SIGMAR1 or PLEKHG5 genes, which were linked using STR analysis and Sanger sequencing. From 10 families who underwent WGS, we found six homozygous point mutations in six families for either the TNNT1, TPM3, TTN, SACS or COL6A2 genes. Two mutations in the PLA2G6 gene were also found in another patient as compound heterozygous. This rather large cohort allowed us to identify genotype patterns in Iranian 5q SMA patients. The process of identifying 11 mutations (9 novel) in 9 different genes among non-5q SMA patients shows the diversity of genes involved in non-5q SMA in Iranians. Genotyping of patients with SMA is essential for prenatal and preimplantation genetic diagnosis (PGD), and may be very helpful for guiding treatment, with the advent of new, more effective, albeit very expensive, therapies. Also, combining linkage analysis was shown to be beneficial in many ways, including sample authenticity and segregation analysis, and for ruling out maternal cell contamination during prenatal diagnosis (PND).
Glycogen storage diseases (GSDs) are the heterogeneous group of disorders caused by mutations in ... more 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 ...
Background Glycogen storage disease (GSD) is a rare inborn error of the synthesis or degradation ... more 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 mark...
Background: Pre-implantation Genetic Diagnosis (PGD) has recently been introduced as a reproducti... more Background: Pre-implantation Genetic Diagnosis (PGD) has recently been introduced as a reproductive choice for individuals who carry a disease-causing BRCA1/2 mutation. Since this technology has not yet been launched for patients at the Cancer Institute of Imam Khomeini Hospital harboring gene mutations that predispose patients to breast cancer, this study aimed to introduce a PGD-based model using a single cell lymphocyte instead of an embryonic blastomere. Methods: Two affected and unrelated women with a known mutation in BRCA1/2 were enrolled in this study. Each patient (together with her siblings) was considered as an embryo derived from a hypothetical couple. Blood samples were collected from these individuals as well as their parents. Linkage analysis was performed. Following this process, a mutation-free individual and a mutation carrier was selected from the first and second family, respectively. A single lymphocyte was then extracted from their freshly taken peripheral bloo...
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