whole exome sequencing

To identify the potential genetic factors responsible for retinal capillary hemangioblastoma (RCH) and Type II granular corneal dystrophy (GCDII), with autosomal dominant inheritance. We used whole-exome sequencing (WES) in an Iranian family to identify the possible genetic etiology of RCH and GCDII with other manifestations of von Hippel–Lindau (VHL) disease.

This study included one Iranian family for WES in index patients and Sanger sequencing in all available individuals.

Clinical presentations of these patients included RCH, GCD, central nervous system hemangioblastoma as well as pancreatic cyst. WES disclosed a heterozygous known pathogenic variant c.371G>A (p.R124H) in exon 4 of gene TGFBI.

For the first time, our research identified the potential involvement of TGFBI: c.371G>A (p.R124H) in an Iranian family with RCH, GCDII, and other symptoms of VHL disease. In the future, TGFBI could offer a new understanding and a promising therapeutic approach for both GCDII and VHL diseases simultaneously. Before using the variant in genetic counseling, it is recommended to conduct functional analysis using appropriate animal models to understand its pathogenesis mechanism.

WHIM syndrome (Warts, Hypogammaglobulinemia, Immunodeficiency, and Myelokathexis syndrome), a type of severe congenital neutropenia (SCN), involves Warts, Hypogammaglobulinemia, Infections, and Myelokathexis as its main components of clinical presentation, which results from mutations in the C-X-C chemokine receptor type 4 (CXCR4) gene.
Here, we present an Iranian 4-year-old girl with severe congenital neutropenia without warts and normal bone marrow examination, lacking evidence of myelokathexis. Whole Exome Sequencing (WES) was performed for the patient. Subsequently, Sanger segregation/validation was done of the patient and her parents. Whole exam sequencing identified a heterozygous stop variant mutation in CXCR4 (NM_001008540.2:c.1012C>T; p.Arg338Ter) in the patient. Two of the main clinical criteria in WHIM syndrome, including warts and myelokathexis, were not observed in our patient. So, the absence of warts is not deceptive in ruling out the disease. This case report also represents the high importance of genetic analysis as a primary tool for the accurate differential diagnosis of patients with neutropenia.

Mitochondrial DNA (mtDNA) is a valuable marker for population studies and forensic investigations. Recent advancements in massively parallel sequencing technologies enable whole mitochondrial genome sequencing. This study collected blood samples from unrelated Iranian participants from four ethnic groups: Persian, Kurd, Lur, and Azeri. We mapped mtDNA haplogroups according to genetic ancestry and investigated the ethnic similarities within the Iranian population.

Complete mtDNA sequences were generated with targeted mtDNA sequencing method and haplogroups were determined on the base of mitogenome polymorphisms. Additionally, we used data from the whole exome sequencing (WES) of the current samples to compare the variants identified by two different mitochondrial testing methods. Principal component analysis (PCA) calculations were performed using the R software to determine diversity between unrelated individuals of various ethnicities.

A total of 129 sub-haplogroups were identified in 15 main haplogroups. The findings revealed high frequencies of haplogroups U and H (22.4% and 20.3%, respectively) in the Iranian population. The PCA scatter plots revealed overlapping diversity, with no distinct trends separating the groups in these four groups within the Iranian population. In the present samples, the WES method identified only 57.8% of the variants detected by the targeted mtDNA sequencing method.

Variant studies do not show much difference, which indicate a small genetic difference between the central ethnic groups of Iran. Furthermore, comparing the targeted whole mitochondrial genome to mitochondrial data from WES in our study samples highlights the notion that targeted entire mitochondrial genome is a gold standard method for variant detection.

Ataxia Telangiectasia (A-T) is a rare autosomal recessive neurodegenerative disease caused by mutations in the ataxia telengiectasia mutated (ATM) gene. The gene is on chromosome 11q22-23 and codes for the protein kinase ATM, which plays an essential role in DNA damage repair. In this study, we review the clinical characteristics of 13 A-T patients, 2 of whom displayed novel mutations. Thirteen patients with ataxia-telangiectasia from 10 unrelated families were referred to  Immunology, Asthma and Allergy Research Institute, Tehran, Iran. After clinical confirmation, blood samples were collected from the patients and their parents. Genetic analysis for 8 patients was conducted using whole-exome sequencing; in the other 3 patients, polymerase chain reaction was used, followed by sequencing. We identified 11 different mutations in the ATM gene. Two patients had mutations as compound heterozygous, while 9 other patients were homozygous for the mutations. Among these, 2 likely pathogenic mutations (ie, c.2639-1G>A and c.7940_7970del​TTCCAGCAGA​CCAGCCAATT​ACTAAACTTAA) have not been reported. Our study highlights the significance of next-generation sequencing techniques in identifying novel ATM mutations in A-T patients. Although all reported A-T mutations reside in 1 gene, the absence of a mutation hotspot for this gene necessitates the use of next-generation sequencing techniques. Specifically, we identified 2 mutations that have not been reported previously, emphasizing the importance of continued research in this area. This study provides new insights into the genetic underpinnings of A-T and underscores the potential clinical implications of identifying novel mutations.

Next-Generation Sequencing (NGS) methods specifically Whole-Exome Sequencing (WES) have demonstrated promising findings with a high accuracy of 91%-99% in Pharmacogenomics (PGx). A PGx-based panel can be utilized to minimize adverse drug reactions (ADRs) and maximize the treatment efficacy. Remarkably, Cancer Pain Management (CPM) is a cutting-edge concept in modern medicine. Thus, this study aimed to investigate the WES results by a PGx-based panel containing genes involved in Pain, Anti-inflammatory, and Immunomodulating agents (PAIma) signaling pathways.  A total of 200 unrelated Iranians (100 western and 100 northern) were included. 100 WES results were analyzed through the PAIma panel. After DNA extraction, 100 samples were genotyped by Multiplex-Amplification-Refractory Mutation System (ARMS) PCR. A primary in silico investigation performed on 128 candidate genes through Protein-Protein Interactions (PPIs) and Gene-miRNA Interactions (GMIs) via the STRING database, and miRTargetLink2, respectively. Additionally, Enrichment Analysis (EA) was applied to find the unknown interplays among these three major pathways by Enrichr.  55,590 annotations through 21 curated pathways were filtered, 900 variants were found, and 128 genes were refined. Finally, 54 candidate variants (48 non-synonymous single nucleotide variants (nsSNVs), 2 stop-gained, 1 frameshift, and 3 splicing) remained.  Conclusively, six potentially actionable variants including rs1695 (GSTP1), rs628031 (SLC22A1), rs17863778 (UGT1A7), rs16947 (CYP2D6), rs2257401 (CYP3A7), and rs2515641 (CYP2E1) had the most deviations among Iranians, compared with the reference genome, which should be genotyped for drug prescribing. Remarkably, PPIs, GMIs, and EA revealed potential risks of carcinogenesis and cancer phenotypes resulting from PAIma pathways genes.

Mitochondrial complex V deficiency refers to a shortage (deficiency) of a protein complex called complex V or a loss of its function. The TMEM70 gene provides the blueprint for mitochondrial ATP synthase, a protein essential for cellular energy production through oxidative phosphorylation. The diagnostic method based on whole-exome sequencing (WES) provides more appropriate genetic counseling by saving time and money.

This study investigated three patients presenting with similar clinical symptoms using WES. After DNA extraction, WES was performed, and a novel mutation (c.311T > G: p.V104G) in the TMEM70 gene was identified. Sanger sequencing was used to confirm the variant in the parents.

The novel TMEM70 mutation (c.311T > G: p.V104G) was identified as a potential cause of the disease in these patients.

This study highlights the utility of WES in the rapid and cost-effective identification of pathogenic variants associated with mitochondrial disorders. The identification of a novel TMEM70 mutation underscores the importance of this gene in mitochondrial function and further emphasizes the need for comprehensive genetic screening in individuals presenting with clinical symptoms consistent with mitochondrial ATP synthase deficiency. Further research is needed to elucidate the specific functional consequences of this mutation and to investigate the prevalence of TMEM70 mutations in various populations.

Here, we report a case with concomitant variants: a novel homozygous HERC1 gene variant and a novel heterozygous PMP22 duplication. The 2-year-old male presented with seizures, developmental delay, macrocephaly, hypotonia, unilateral hypertrophy, thoracic scoliosis, normal brain MRI, and elevated homocysteine level which normalized after treatment. Whole exome sequencing (WES) revealed a co-occurrence of a homozygous novel likely pathogenic variant in the HERC1 gene (NM_003922.3:c.1280dup (p.ILe469Aspfs*33) and a novel heterozygous large duplication of exon 1-5 in the PMP22 gene, which has not been reported previously. The case underscores the challenges in understanding genotype-phenotype correlations and suggests a potential interplay between these genetic variants in shaping the current and future clinical phenotype of the patient. In the case of genetic diseases, this event may have important implications on family members’ counseling, and concomitant variants in Charcot–Marie–Tooth (CMT) families should be considered when significant intra-familial clinical heterogeneity is observed.

Dystroglycanopathies represent heterogeneous clinical and genetic disorders typically characterized by weakness of the limb muscle. Pathogenic mutations in the GMPPB gene (OMIM # 615320) have been identified in various syndromes, including CMD, LGMD, and CMS. In this present study, our aim is to elucidate the presence of pathogenic mutation in two consanguineous Iranian families affected by LGMD2T.

 Two families with affected children diagnosed with LGMD2T were recruited in the study. Comprehensive clinical examinations were performed by an expert neurologist on the proband and their respective families. Whole-exome sequencing (WES) was performed on genomic DNA extracted from peripheral blood mononuclear cells. Subsequently, candidate variants were identified using a bioinformatics pipeline, and familial co-segregation was confirmed through sanger sequencing.

The present study is focused on two families whose identified variants are confirmed. Our findings revealed a heterozygous missense mutation in the GMPPB gene (NM_021971.4, c.308C>T (p. Pro103Leu) that entirely segregated from the observed phenotypes within his family. This variant was not identified in either the Exome Aggregation Consortium or the 1000 Genomes Project.
 

The present findings contribute to the expansion of genetic data for Iranian individuals affected by LGMD2T. This data can be instrumental in enhancing screening, diagnosis, and interpretation within families with a history of this disease.

Veno-occlusive disease with immunodeficiency (VODI) syndrome is a rare genetic disorder characterized by immunesystem irregularities and a significant mortality rate, despite its infrequency. SP110, situated on chromosome 2q37.1,plays a pivotal role in VODI syndrome, and its association with tuberculosis has been extensively studied. Theidentification of SP110 mutations holds promise for accelerating the diagnosis and treatment of VODI syndrome, byproviding a comprehensive panel for diagnosis and potentially leading to targeted therapies. In this case study, weexamined a three-year-old girl born to a consanguineous union who was suspected of having an immunodeficiencydisorder. Whole-exome sequencing (WES) and clinical assessments were conducted to screen for and confirmpotentially pathogenic mutations. The detected mutation was further analyzed using bioinformatics tools to forecastits impact on protein structure. WES analysis revealed a novel deletion-insertion mutation, c.1181-1182delAGinsT,within SP110. Protein analysis indicated substantial structural modifications in the SP110 protein. This study identifieda novel deletion-insertion mutation as a potential contributor to VODI syndrome by affecting the functionality of theSP110 protein. By including various mutations associated with the SP110 gene, this study aimed to expedite diagnosisby creating a comprehensive panel for VODI syndrome.

This case report presents a 10-year-old patient diagnosed with pheochromocytoma/paraganglioma syndrome type 1 (PPGL1), underlined by a novel heterozygous pathogenic variant (c.154_161del, p.ser52Profster14) in the SDHD gene. Initially, the patient manifested symptoms unusual for pheochromocytoma, including polyuria and polydipsia; however, further diagnostic investigations revealed a pheochromocytoma (PCC) tumor in the adrenal gland. Subsequently, whole exome sequencing (WES) test identified a pathogenic frameshift variant in the SDHD gene, strongly suggestive of PPGL1. This study highlights the importance of considering atypical symptoms in diagnosing rare pediatric pheochromocytoma/paraganglioma tumors and underscores the value of genetic testing in identifying underlying genetic causes, thereby facilitating personalized management of the condition.

We report a 4.5-year-old girl with recurrent episodes of bilateral lower limb weakness following periods of upper respiratory tract infection since the age of 1.5 years. Nerve conduction velocity and electromyography studies suggested distal motor neuropathy. The whole exome sequencing analysis revealed a homozygous variant, c.955G>A (p.Gly319Ser), of the mitochondrial trifunctional protein α-subunit (HADHA) gene. This variant has already been reported as pathogenic in an Iranian consanguineous family with a probable diagnosis of Charcot-Marie-Tooth disease. In addition, this variant, in compound heterozygosity with another likely pathogenic variant, has been known to be linked with mitochondrial trifunctional protein deficiency.

To look for causative genetic mutations in a series of Iranian families with strabismus. In addition, we systematically reviewed all the published articles regarding the role of genetic variations in primary and nonsyndromic comitant strabismus.

Four families with a history of multiple cases of primary and nonsyndromic comitant strabismus were enrolled in this study. Polymerase chain reaction and Sanger sequencing of exons 23, 11, and 3 of the Abelson helper integration site 1 (AHI1), nebulin (NEB), and paired box 3 (PAX3) genes were performed, respectively. One offspring of a consanguineous marriage underwent whole‑exome sequencing (WES) to look for possible causative variants. To conduct a systematic review, we thoroughly searched PubMed, Scopus, and ISI Web of Knowledge extracting relevant publications, released by April 2021.

We examined four Iranian strabismus pedigrees with multiple affected offspring in different generations. Among these 17 participants, 10 family members had strabismus and 7 were healthy. Sanger sequencing did not reveal a causative mutation. Therefore, to further investigate, one affected offspring was chosen for WES. The WES study demonstrated two possible variants in MYO5B and DHODH genes. These genetic variants showed high allele frequency in our population and are thought to be polymorphisms in our series of Iranian families.

We demonstrated that mutations in AHI1, NEB, and PAX3 genes were not common in a series of Iranian patients with familial strabismus. Moreover, by performing WES, we revealed that two variants of uncertain significance as possible causative variants for strabismus are not related to this disease in our population.

Hereditary sensory autonomic neuropathy type VIII (HSAN-VIII) is a rare genetic disease that occurs due to mutations in the PRDM12 gene. Here, we describe a novel homozygous mutation c.826_840dupTGCAACCGCCGCTTC (p.Cys276_Phe280dup) on exon 5 in the PRDM12 gene identified by WES and confirmed using Sanger sequencing method.

Encephalopathy is a syndrome of overall brain dysfunction with unknown causes despite its well-recognized etiology. This study reports clinical laboratory, radiological, and magnetic resonance imaging (MRI) findings as well as whole-exome sequencing (WES) of a female patient aged 19 months and 7 days with encephalopathy. To this end, the documented files of the hospitalized encephalopathy patients in Ayat Allah Mosavi hospital (Zanjan, Iran), referred from Khodabandeh city, Zanjan, Iran, were investigated. The initial symptoms, laboratory tests, computerized tomography (CT) scans, MRI, WES, and the course of disease were reported. The laboratory examination revealed mild anemia, and the normal range of the CSF, ESR, and CRP. Brain CT indicated brain edema while the MRI analysis of the brain revealed hypersignality. The c. 352G>A heterozygote variant was diagnosed in the PPP2RIA gene in exon four of chromosome 19. According to the observations, the frequency of this disorder was higher in this region of Zanjan province than other areas. The limitation of this study such as lack of access to the patients or biological samples of other similar patients hindered further evaluation. Hence, comprehensive research must be conducted to reveal the underlying etiology.

Intellectual disability (ID) represents a significant health challenge due to its diverse and intricate nature. A multitude of genes play a role in brain development and function, with defects in these genes potentially leading to ID. Considering that many of these genes have yet to be identified, and those identified have only been found in a small number of patients, no complete description of the phenotype created by these genes is available. CC2D1A is one of the genes whose loss-of-function mutation leads to a rare form of non-syndromic ID- 3(OMIM*610055), and four pathogenic variants have been reported in this gene so far.

In the current study, two affected females were included with an initial diagnosis of ID who were from an Iranian family with consanguineous marriage. Whole-exome sequencing was used to identify the probable genetic defects. The Genotypic and phenotypic characteristics of the patients were compared with a mutation in the CC2D1A gene, and then the structure of the gene and its reported variants were investigated.

The patients carried a novel homozygous splicing variant (NM_017721, c.1641+1G>A) in intron 14, which is pathogenic according to the ACMG guideline. Loss-of-function mutations in CC2D1A have severe phenotypic consequences such as ID, autism spectrum disorder (ASD),  and seizures. However, missense mutations lead to ASD with or without ID, and in some patients, they cause ciliopathy.

This study reports the fifth novel, probably pathogenic variant in the CC2D1A gene. Comparing the clinical and molecular genetic features of the patients with loss-of-function mutation helped to describe the phenotype caused by this gene more precisely. Investigating the CC2D1A gene's mutations and structure revealed that it performs multiple functions. The DM14 domain appears more pivotal in triggering severe clinical symptoms, including ID, than the C2 domain.

Hearing loss is the second most common disease after mental retardation in Iran.Autosomal recessive non-syndromic hearing loss (ARNSHL) is an extreme and highly heterogeneous disease, for which more than 70 genes have been identified. Considering the frequency of family marriage as well as the im-portance of ARNSHLin Iran, we evaluated the genetic factors involved in this type of deafness.

We performed the whole exome sequencing (WES) of eight Iranian subjects with severe non-syndromic hearing loss selected from 110 well-characterized subjects with non-syndromic hearing loss from 2017-2019.The patients with mutated GJB2and GJB6genes were excluded from the study.

The use of the whole exome sequencing method revealed 10 different mutations in 7 genes, including SLC26A4 (c.1234G>T), FGF3(c.45DelC, c.466T>C), ADGRV1(c.12528-2A>C, c.16226-16227insAGTC), OTOG(c.7454delG), OTOF(c.3570+2T>C), ESPN(c.992G>A), OTOA(c.2359G>T, c.2353A>C). Seven new variants were observed in seven families including SLC26A4 (c.1234G>T), FGF3(c.45DelC), ADGRV1(c.12528-2A>C), OTOG(c.7454delG), ADGRV1(c.16226-16227insAGTC), OTOF(c.3570+2T>C).

The causal mutation of ARNSHLwas found in all patients using the WES. Meta-analysis studies can help to identify common mutations causing deafness in any population to facilitate identification of carriers and subjects with deafness.

 Genetic factors play an important role in the occurrence of many diseases, including skeletal diseases. Skeletal diseases are sometimes caused by a mutation in a gene that passes on to children according to the Mendelian inheritance pattern, and sometimes several genes are involved in this path and cause heterogeneous disease. The whole-exome sequencing (WES) technique can be a powerful tool in diagnosing this disease.

 Peripheral blood samples (5 mL) were collected from the individuals in EDTA tubes. After sequencing the patient's genome using the WES technique, the candidate genes were checked using the polymerase chain reaction (PCR) technique and Chromas software to confirm the variant in the family.

 After studying the genome using the WES method and analyzing the results, mutation NM_001005373.4:c.1985C>T was identified by creating a nonsense change in the LRSAM1 gene.

 The data obtained by the WES technique can help diagnose the disease faster. In addition, these data can be used as background information in the development of a special panel to diagnose this disorder.