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Background Genetic factors are major contributors to autism spectrum disorders (ASD), with copy number variations (CNVs) playing a significant role. Our objective was to identify and assess CNVs and their associated gene-level impacts in Egyptian ASD patients. Methods Our cohort comprised 40 non-syndromic ASD children, ranging in age from one year and nine months to 12 years. We conducted karyotyping, multiple ligation-dependent probe amplification (MLPA), Methylation-Specific MLPA (MS-MLPA), and chromosomal microarray (CMA) analyses for all patients. Additionally, quantitative real-time PCR (qPCR) analyses were performed on selected patients and their parents. Results We identified pathogenic or likely pathogenic CNVs in seven patients (17.5%), variants of uncertain significance (VUS) in 10 patients (25%), and classified other variants as benign. Pathogenic or likely pathogenic CNVs affected chromosomes 16p11.2 (two patients), 15q11q13 (three patients), 22q11.2 (one patient), and 7q11.23 (one patient). Many of the affected genes are associated with neuronal functions. Patients with CNVs exhibited increases in three parameters on the Children’s Autism Rating Scale (CARS): restrictive and repetitive behavior, adaptation to changes, and responses to taste, smell, and touch. According to the Autism Diagnostic Interview-Revised (ADI-R), patients with pathogenic or likely pathogenic CNVs had an increased third parameter for restricted, repetitive, and stereotyped patterns of behavior. Patients with pathogenic or likely pathogenic CNVs demonstrated some clinical manifestations involving microcephaly (two patients), macrocephaly (one patient), and abnormal electroencephalogram (EEG) with generalized epileptic focus (two patients). qRT-PCR was performed for some parents, and the CNVs were found to be de novo. Conclusions CNV detection via CMA proved invaluable and is considered a primary tool in ASD diagnosis. Distinguishing between inherited and de novo CNVs is crucial for accurate genetic counseling. Most genes involved in the detection of pathological or likely pathogenic CNVs are linked to neuronal functions, and these CNVs impact specific parameters in CARS and ADI-R assessments. Future efforts should prioritize a more comprehensive understanding of the genetic underpinnings of ASD, enabling the adoption of personalized treatment strategies.

The prenatal diagnosis of syndromes caused by chromosomal abnormality is a long-established part of obstetric care. Several DNA-based molecular approaches have provided rapid prenatal diagnosis of of cytogenomic abnormalities. MLPA has become available for rapid aneuploidy detection of the most common chromosome abnormalities. The aim of this study is to introduce the MLPA technique as a method for the prenatal detection of aneuploidy in Egypt by its validation compared to the FISH technique. Fifty AF samples were collected for this study and were subjected to MLPA and FISH assays to detect the most common prenatal chromosomal abnormality. Our study confirmed previous reports that MLPA is analogous to FISH for detecting common aneuploidies and could be a quick and dependable tool for prenatal diagnosis. Therefore, initial prompt testing of AF samples for the copy number of the most common occurring aneuploidies is recommended.

Autism spectrum disorder is a condition related to brain development that affects a person's perception and socialization, resulting in problems in social interaction and communication. It has no single known cause, yet several different genes appear to be involved in autism. As a genetically complex disease, dysregulation of miRNA expression and miRNA-mRNA interactions might be a feature of autism spectrum disorder. The aim of the current study was to investigate the expression profile of circulating miRNA-128, miRNA-7 and SHANK gene family in ASD patients and to assess the possible influence of miRNA-128 and miRNA-7 on SHANK genes, which might provide an insight into the pathogenic mechanisms of ASD and introduce noninvasive molecular biomarkers for the disease diagnosis and prognosis. Quantitative real-time PCR technique was employed to determine expression levels of miRNA-128, miRNA-7 and SHANK gene family in blood samples of 40 autistic cases along with 30 age- and sex-matched normal volunteer subjects. Our study revealed a statistical significant upregulation of miRNA-128 expression levels in ASD cases compared to controls (p value < 0.001). A statistical significant difference in SHANK-3 expression was encountered on comparing cases to controls (p value < 0.001). However, miRNA-7 expression showed no significant difference between the studied groups. MiRNA-128 and SHANK-3 gene are emerging players in the field of ASD. They are promising candidates as noninvasive biomarkers in autism. Future studies are needed to emphasize their pivotal role.

Chronic lymphocytic leukemia (CLL) is the most common form of adult leukemia. This disease is genetically heterogeneous, and approximately 85% of patients with CLL harbor chromosomal aberrations that are considered effective prognostic biomarkers. The most frequent aberrations include deletions in 13q14, followed by trisomy 12, and deletions in 11q22.3 and 17p13 (TP53). Currently, fluorescence in situ hybridization (FISH) is the most widely used molecular cytogenetic technique to detect these aberrations. However, FISH is laborious, time-consuming, expensive, and has a low throughput. In contrast, multiplex ligation-dependent probe amplification (MLPA) is a reliable, cost-effective, and relatively rapid technique that can be used as a first-line screening tool and complement with FISH analysis. This study aimed to evaluate the contributions of MLPA as a routine standalone screening platform for recurrent chromosomal aberrations in CLL in comparison to other procedures. Thirty patients with CLL were screened for the most common genomic aberrations using MLPA with SALSA MLPA probemix P038-B1 CLL and FISH. In 24 of the 30 cases (80%), the MLPA and FISH results were concordant. Discordant results were attributed to a low percentage of mosaicism. Moreover, the MLPA probemix contains probes that target other genomic areas known to be linked to CLL in addition to those targeting common recurrent CLL aberrations. The usage of MLPA as the first screening platform followed by FISH technique for only the negative cases is the most appropriate approach for CLL diagnosis and prognosis.

The presence of comorbid Irlen syndrome (IS) in children with developmental dyslexia (DD) may have an impact on their reading and cognitive abilities. Furthermore, the brain‐derived neurotrophic factor (BDNF) was reported to be expressed in brain areas involved in cognitive and visual processing. The aim of this study was to evaluate some cognitive abilities of a group of dyslexic children with IS and to measure and compare the plasma BDNF level to dyslexic children without IS and neurotypical (NT) children. The participants were 60 children with DD (30 in the DD + IS group; 30 in the DD group) and 30 NT children. The Irlen reading perceptual scale, the Stanford Binet intelligence scale, 4th ed, the dyslexia assessment test, and the Illinois test of psycholinguistic abilities were used. The BDNF level was measured using the enzyme‐linked immunosorbent assay. One‐minute writing and visual closure deficits were more prevalent, while phonemic segmentation deficits were less prevalent in the DD + IS group compared to the DD group. The BDNF level in the DD groups was lower than that in NT children (p < 0.001). Some reading and non‐reading tasks were influenced by the presence of a coexisting IS. The reduced BDNF level could play a role in the deficits noticed in the abilities of children with DD. The aim of this study was to evaluate some cognitive abilities of a group of children manifesting developmental dyslexia with Irlen syndrome (IS) and to measure and compare the plasma brain‐derived neurotrophic factor (BDNF) level to dyslexic children without IS and neurotypicals. The participants were 30 children with dyslexia and IS, 30 children showing dyslexia without IS, and 30 neurotypical children. Various tests and scales were used for assessment of reading, writing, and other cognitive abilities. ELISA was used for measuring the BDNF level. Despite the low prevalence of phonological awareness deficits, the visual burden caused by IS influenced the writing performance in children with dyslexia. The plasma level of BDNF in the children showing dyslexia with and without IS was lower than that in neurotypical children (p < 0.001), which could have influenced their learning performance.

Background Autism spectrum disorder (ASD) is one of the most common neurodevelopmental disorders. In DSM-IV, the diagnostic criteria of autism consisted of three domains: impairment in social interaction, communication deficits, and stereotypic behavior, while in DSM-5 they were condensed into two domains: social communication deficits and restricted patterns of behavior to which sensory processing deficits (SPD) were added, manifested by hypo- or hyper-reactivity to sensory stimuli or uncommon interests in sensory aspects of the surrounding environment. The purpose of this study is to determine the relation between SPD and the symptom triad in ASD namely social interaction, communication deficits, and stereotypic behavior. To our knowledge, this issue was not studied before in Egyptian literature. Results There was a significant negative correlation between SPD (assessed by short sensory profile: SSP) and symptom triad in ASD. As regards social interaction, the ADI-R (A), there was significant negative correlation with the SSP total scores and all subscales except for low energy/weak and visual/auditory sensitivity, whereas under-responsive/seeks sensation held the highest negative correlation ( p ˂ 0.008). As regards communication deficits, the ADI-R (B), there was significant negative correlation with the SSP total scores and the auditory filtering held the highest negative correlation ( p ˂ 0.008), and as regards stereotypic behavior, the ADI-R (C), there was significant negative correlation with the SSP total scores and all subscales except for low energy/weak and visual/auditory sensitivity whereas taste/smell sensitivity and auditory filtering held the highest negative correlation ( p ˂ 0.001). There was a high significant negative correlation between the severity of autistic symptoms (assessed by CARS) and the SSP total scores, and for all subscales ( p ˂ 0.001) except for low energy/weak, the correlation was significant (not highly significant) ( p ˂ 0.05). Finally, there was high percentage of parental consanguinity among the participants (80%). Conclusions SPD negatively affected the ASD symptom triad which highlights the importance of sensory integration therapy (SIT) as a major core of ASD treatment alongside the other treatment modalities. Early ASD screening is mandatory in families with parental consanguinity.

Background This study aimed to delineate the clinical phenotype of patients with 9p deletions, pinpoint the chromosomal breakpoints, and identify the critical region for trigonocephaly, which is a frequent finding in 9p terminal deletion. Methods We investigated a cohort of nine patients with chromosome 9p terminal deletions who all displayed developmental delay, intellectual disability, hypotonia, and dysmorphic features. Of them, eight had trigonocephaly, seven had brain anomalies, seven had autistic manifestations, seven had fair hair, and six had a congenital heart defect (CHD). Results Karyotyping revealed 9p terminal deletion in all patients, and patients 8 and 9 had additional duplication of other chromosomal segments. We used six bacterial artificial chromosome (BAC) clones that could identify the breakpoints at 17–20 Mb from the 9p terminus. Array CGH identified the precise extent of the deletion in six patients; the deleted regions ranged from 16 to 18.8 Mb in four patients, patient 8 had an 11.58 Mb deletion and patient 9 had a 2.3 Mb deletion. Conclusion The gene deletion in the 9p24 region was insufficient to cause ambiguous genitalia because six of the nine patients had normal genitalia. We suggest that the critical region for trigonocephaly lies between 11,575 and 11,587 Mb from the chromosome 9p terminus. To the best of our knowledge, this is the minimal critical region reported for trigonocephaly in 9p deletion syndrome, and it warrants further delineation. Nine patients with chromosome 9p terminal deletion presented with developmental delay, intellectual disability, and dysmorphic features. We concluded that the deletion of the genes in the 9p24 region are not sufficient to cause ambiguous genitalia as six out of our nine patients had normal genitalia. Based on our study we suggested that the critical region for trigonocephaly may lies within 11.8 kb in 9p23 cytoband.

Insulin-like growth factor-1 (IGF-1) is required for normal intrauterine and postnatal growth, and this action is mediated through IGF1 receptor (IGF1R). IGF1R copy number variants (CNVs) can cause pre- and postnatal growth restriction, affecting an individual's height. In this study, we used multiplex ligation-dependent probe amplification (MLPA) to detect CNVs in IGF1R, IGFALS, and IGFBP3 genes in the diagnostic workup of short stature for 40 Egyptian children with short stature. We detected a heterozygous deletion of IGF1R (exons 4 through 21) in 1 out of the 40 studied children (2.5%). Meanwhile, we did not detect any CNVs in either IGFALS or IGFBP3. The diagnostic workup of short stature using MLPA for CNVs of IGF1R and other recognized height-related genes, such as SHOX and GH, in non-syndromic short stature children can be a fast and inexpensive diagnostic tool to recognize a subcategory of patients in which growth hormone treatment can be considered.

Short stature is defined as a body height below the third percentile, based on chronological age, or 2 standard deviations (SD) below the national height standard. The prevalence of short stature is around 2% of children worldwide. Several gene deficiencies have been associated with the etiology of short stature. The SHOX is an important candidate gene for short stature, as its haploinsufficiency underlies syndromic and non-syndromic short stature. Partial and complete duplications of SHOX have been reported in patients with short stature. Proper genetic diagnosis of these children allows for appropriate therapeutic approaches to be administered. Since copy number variation (CNV) is a possible mechanism of interhuman variability and pathogenic disease, the multiplex ligation-dependent probe amplification technique (MLPA) can be used as an initial screening technique. Cartilage tissue expresses specific microRNAs (miRNAs), which play an essential role in the regulation of chondrocyte proliferation and differentiation during growth plate development. We aimed to assess the SHOX/PAR1 region using CNV profiling for non-syndromic short stature in Egyptian children with and without growth hormone deficiency using the MLPA technique and expression profiling of miR-1, miR-15a, and miR-140 using quantitative real-time polymerase chain reaction (qRT-PCR) in a group of Egyptian children with non-syndromic short stature. Of the fifty cases included in this study, different CNVs were detected in ten children (20%), in/outside the SHOX region. Moreover, in children with short stature, the expression level of miRNA-140 was significantly different from that of healthy controls. This is one of the first studies that have assessed CNVs in the SHOX/PAR1 region in a group of Egyptian children with short stature. MLPA analysis of SHOX/PAR1 identified different CNVs in children with non-syndromic short stature, suggesting that the MLPA should be used as an initial screening technique in short children, as proper genetic diagnosis of these children leads to implementation of the appropriate therapeutic approach. Alterations in the levels of miRNA-140 in children with short stature suggest that changes in the expression levels of this miRNA are associated with the pathogenesis of short stature.

Background Wolf–Hirschhorn syndrome (WHS) (OMIM 194190) is a multiple congenital anomalies/intellectual disability syndrome. It is caused by partial loss of genetic material from the distal portion of the short arm of chromosome. Methods We studied the phenotype–genotype correlation. Results We present the clinical manifestations and cytogenetic results of 10 unrelated Egyptian patients with 4p deletions. Karyotyping, FISH and MLPA was performed for screening for microdeletion syndromes. Array CGH was done for two patients. All patients exhibited the cardinal clinical manifestation of WHS. FISH proved deletion of the specific WHS locus in all patients. MLPA detected microdeletion of the specific locus in two patients with normal karyotypes, while array CGH, performed for two patients, has delineated the extent of the deleted segments and the involved genes. LETM1, the main candidate gene for the seizure phenotype, was found deleted in the two patients tested by array CGH; nevertheless, one of them did not manifest seizures. The study emphasized the previous. Conclusion WHS is a contiguous gene syndrome resulting from hemizygosity of the terminal 2 Mb of 4p16.3 region. The Branchial fistula, detected in one of our patients is a new finding that, to our knowledge, was not reported. clinical, neurological, and molecular cytogenetic analysis of 10 Egyptian patients diagnosed with Wolf–Hirschhorn syndrome (WHS). Diagnosis was confirmed by genetic analysis through karyotype, FISH, MLPA, and array CGH with a new clinical finding which that, to our knowledge, was not reported before in WHS, extending the phenotypic spectrum of the disorder.