Identifying of 22q11.2 variations in Chinese patients with development delay

SNV/Indel and CNV Analysis in Trio-WES for Intellectual and Developmental Disabilities: Diagnostic Yield & Cost-Effectiveness

Intellectual and developmental disabilities (IDD) are clinically and genetically heterogeneous disorders of global concern. While whole exome sequencing (WES) is used to identify single nucleotide variants (SNVs) and small insertions/deletions (Indels) in IDD patients, its detection rate is limited. This study evaluated the value of integrating copy number variation (CNV) analysis into traditional SNV/Indel analysis based on trio-WES. One hundred eighty seven patients with IDD in 140 families from southwest China were incorporated into the study cohort. The overall diagnostic rate was 40.11% (75/187), with 33.16% (62/187) from SNV/Indel analysis and 6.95% (13/187) from CNV analysis. SNV/Indel analysis identified 52 variants in 42 genes, including 30 novel and 22 reported variants; CNV analysis identified 11 CNVs, comprising 1 repeat and 10 deletions, with sizes ranging from 1313 to 55 184 kb. 39.29% (55/140) families benefited from this study for their clinical diagnosis, treatment, and reproduction. Furthermore, our strategy, with an incremental cost-effectiveness ratio (ICER) of $2546.22/diagnosis, had demonstrated significant advantages in terms of cost-effectiveness and detection speed compared to previous methods. In general, by incorporating SNV/Indel and CNV analysis based on trio-WES, a robust, cost-effective, and time-saving approach for diagnosing IDD has been developed.

Development of Speech and Communication in Polish Children with 22q11.2 Deletion Syndrome: A Cross-Sectional Study

BACKGROUND/OBJECTIVES

22q11.2 microdeletion syndrome (22q11DS) is a genetic disease caused by aberration of chromosome 22 that results in some phenotypic features and developmental disorders. This paper presents a cross-sectional study on speech and communication of Polish children with 22q11DS.

METHODS

Individuals affected with 22q11DS may show difficulties in functioning, including speech and hearing. Therefore, we prepared a speech development questionnaire and employed it to obtain data from parents (or legal guardians) of 54 children with 22q11DS. The questionnaire covered the following speech and communication development stages: babbling, using first words, first sentences, verbal and non-verbal communication, speech disfluencies, hearing loss, speech intelligibility, difficulties in interpersonal contact, and participation in speech therapy. The obtained answers underwent statistical analysis to verify relationships between the stages of personal development and selected dysfunctions and disorders.

RESULTS

In the study group we observed delays in achieving subsequent speech developmental stages and that hearing loss was associated with delays in producing first words. Hearing loss was reported in about a quarter of cases, but a significant proportion of children (55.56%) reported speech disfluencies, which had not been emphasized in previous works, where hearing loss is considered a common co-occurring disorder.

CONCLUSIONS

Our findings suggest that this may represent a phenomenon associated with 22q11DS that warrants further investigation using standardized tests for assessing disfluencies. Additionally, we observed that speech therapists and caregivers were perceived as not fully aware of the speech development impairments caused by 22q11DS. These preliminary observations point to the need for future studies and increased awareness efforts in this area.

Quantifying attention in children with intellectual and developmental disabilities through multicenter electrooculogram signal analysis

In a multicenter case-control investigation, we assessed the efficacy of the Electrooculogram Signal Analysis (EOG-SA) method, which integrates attention-related visual evocation, electrooculography, and nonlinear analysis, for distinguishing between intellectual and developmental disabilities (IDD) and typical development (TD) in children. Analyzing 127 participants (63 IDD, 64 TD), we applied nonlinear dynamics for feature extraction. Results indicated EOG-SA's capability to distinguish IDD, with higher template thresholds and Correlation Dimension values correlating with clinical severity. The template threshold proved a robust indicator, with higher values denoting severe IDD. Discriminative metrics showed areas under the curve of 0.91 (template threshold) and 0.85/0.91 (D2), with sensitivities and specificities of 77.6%/95.9% and 93.5%/71.0%, respectively. EOG-SA emerges as a promising tool, offering interpretable neural biomarkers for early and nuanced diagnosis of IDD.

A Systematic Investigation of Complement and Coagulation-Related Protein in Autism Spectrum Disorder Using Multiple Reaction Monitoring Technology

Autism spectrum disorder (ASD) is one of the common neurodevelopmental disorders in children. Its etiology and pathogenesis are poorly understood. Previous studies have suggested potential changes in the complement and coagulation pathways in individuals with ASD. In this study, using multiple reactions monitoring proteomic technology, 16 of the 33 proteins involved in this pathway were identified as differentially-expressed proteins in plasma between children with ASD and controls. Among them, CFHR3, C4BPB, C4BPA, CFH, C9, SERPIND1, C8A, F9, and F11 were found to be altered in the plasma of children with ASD for the first time. SERPIND1 expression was positively correlated with the CARS score. Using the machine learning method, we obtained a panel composed of 12 differentially-expressed proteins with diagnostic potential for ASD. We also reviewed the proteins changed in this pathway in the brain and blood of patients with ASD. The complement and coagulation pathways may be activated in the peripheral blood of children with ASD and play a key role in the pathogenesis of ASD.

Chromosome classification via deep learning and its application to patients with structural abnormalities of chromosomes

BACKGROUND AND OBJECTIVE

Karyotyping is an important technique in cytogenetic practice for the early diagnosis of genetic diseases. Clinical karyotyping is tedious, time-consuming, and error-prone. The objective of our study was to develop a single-stage deep convolutional neural networks (DCNN)-based model to automatically classify normal and abnormal chromosomes in an end-to-end manner.

METHODS

We analyzed 2,424 normal chromosomes and 544 abnormal chromosomes. A preliminary support vector machine (SVM) model was developed to evaluate the basic recognition performance on the dataset. A DCNN-based model was then proposed to process the same dataset.

RESULTS

By utilizing the SVM model, the classification accuracy of 24 normal chromosomes was 86.01 %. The 32 types of normal and abnormal chromosomes got an accuracy of 85.37 %. The accuracy of the DCNN-based model performing the 24 normal chromosomal classification was 91.75 %. The accuracy of the 32 type classification was 87.76 %. To differentiate eight common structural abnormalities, we obtained accuracies that ranged from 90.84 % to 100 %, and the values of the AUC ranged from 91.81 % to 100 %.

CONCLUSIONS

Our proposed DCNN-based model effectively performed the karyotype classification in an end-to-end manner. It had the competence to be used as a prediction tool for abnormal karyotype detection and screening in genetic diagnosis without initial feature extraction. We believe our work is meaningful for genetic triage management to lower the cost in clinical practice.

Language Profiles of School-Aged Children with 22q11.2 Copy Number Variants

Although it is known that copy number variants (CNVs) on chromosome 22, such as 22q11.2 deletion (22q11.2DS) and 22q11.2 duplication (22q11.2Dup) syndromes, are associated with higher risk for neurodevelopmental issues, few studies have examined the language skills across 22q11.2Dup nor compared them with the 22q11.2DS. The current study aims to characterize language abilities in school-aged children with 22q11.2Dup (n = 29), compared to age-matched children with 22q11.2DS (n = 29). Standardized language tests were administered, assessing receptive and expressive language skills across different language domains. Results indicate that children with 22q11.2Dup demonstrate significantly more language problems compared to the general population. Mean language skills were not significantly different among children with 22q11.2 CNVs in this cohort. While children with 22q11.2DS demonstrated language difficulties starting at the word level, the most common language problems in children with 22q11.2Dup started at the sentence level. Importantly, both expressive and receptive language as well as lexico-semantic and morphosyntactic domains were impaired in children with 22q11.2 CNVs. Early identification, therapeutic intervention, and follow-up of language impairments in children with 22q11.2Dup are recommended to support language development and to reduce longitudinal impact of language and communicative deficits.

22q11 Copy Number Variations in a Brazilian Cohort of Children with Congenital Heart Disorders

Introduction

Congenital heart disease (CHD) is the most common type of congenital defect reported to be one of the leading causes of mortality in the first year of life. Microdeletion and microduplication syndromes (MMS) are associated with cardiac malformations. Understanding which genetic factors are involved in these conditions directly impacts treatment decisions. We aimed to identify the occurrence of genetic alterations and their association with MMS in CHD pediatric patients evaluated in a reference service of Southern Brazil.

Methods

Participants were recruited during 2010 in the intensive care unit of a pediatric hospital. MMs and regions of chromosome 22 were screened by SALSA MLPA Probemix P245 Microdeletion Syndromes-1A kit for detection of copy number variations (CNVs).

Results

MMS were detected in 11 from 207 patients (5.3%). Heterozygous deletion in the 22q11.2 chromosome region was the most prevalent CNV (5 from 11 patients). Also, atypical RTDR1 deletion and 22q11.2 duplication were detected. MLPA was able to reveal microdeletions in SNRPN and NF1 genes in patients with a normal karyotype and FISH.

Conclusion

Our study reports the prevalence and variability of genomic alterations associated with MMS in CHD pediatric patients. The results by MLPA are of great help in planning and specialized care.

Hypoparathyroidism and late-onset hypogonadism in an adult male with familial 22q11.2 deletion syndrome: a case report with 3-year follow-up and review of the literature

BACKGROUND

22q11.2 deletion syndrome (DiGeorge syndrome) is associated with multiple organ dysfunctions such as cardiac defects, immunodeficiency, and hypoplasia of parathyroid glands. Moreover, the phenotype of 22q11.2 DS has clinical variability and heterogeneity.

CASE PRESENTATION

In this report, we present the case of a 35-year-old patient with a past medical history that included recurrent infections, mild learning difficulties in childhood, pediatric obesity, and cataract. He was admitted to the endocrinology department for the management of hypogonadism and hypocalcemia. During the 3-year follow-up, the patient gradually developed primary hypoparathyroidism, hypogonadism, chronic renal failure, and heart failure, and his medical condition deteriorated. Meanwhile, in order to improve clinicians' awareness of the endocrine manifestations of adult 22q11.2 DS and reduce missed diagnoses, we reviewed 28 case reports of adult 22q11.2 DS to analyze the clinical characteristics.

DISCUSSION

Here, we report the case of a young man diagnosed with 22q11.2 DS presented a rare combination of multiple endocrine disorders. This is the first time that a patient with 22q11.2DS had late-onset hypogonadism caused by primary testicular failure combined with decreased pituitary gonadotropin reserve in a patient with 22q11.2DS.

Prenatal phenotype of 22q11 micro-duplications: A systematic review and report on 12 new cases

The 22q11 region is prone to generating recurring Copy Number Variations (CNVs) as a result of the large numbers of Low Copy Repeats (LCRs). Typical duplications encompass the LCR-A-to-D region but atypical duplications of various sizes have also been reported. These duplications are responsible for highly variable phenotypes with incomplete penetrance and expressivity, which is challenging for adequate genetic counselling, especially in the prenatal period. To better delineate prenatal phenotypes associated with these CNVs, we report here a clinical and molecular description of twelve cases (9 foetuses and 3 deceased new-borns babies) carrying recurrent 22q11 duplications (diagnosed via aCGH), along with a review of the existing literature. 22q11 duplications were inherited from an apparently healthy parent in almost 60% of the cases. Other CNVs were diagnosed for 8% of the cases. Increased nuchal translucency and cardiac anomalies (CHD) were the most prominent phenotypes observed, along with mild renal and skeletal anomalies. Duplications encompassing the LCR-C-to-D region (and the CRKL gene) seemed more likely to generate CHDs and renal malformations. Cleft lip/palate were observed in foetuses with duplications encompassing the LCR-A-to-B region or the SPECC1L gene, as previously suggested. However, genotype-phenotype correlations remain difficult to ascertain. Second-hit point variants, epigenetic or environmental variations could play a role in the phenotypic variability of 22q11 duplications, but remain a challenge for assessment in the short period of pregnancy.

Cross-sectional and longitudinal findings in patients with proximal 22q11.2 duplication: A retrospective chart study

Duplications on Chromosome 22q11.2 (22q11.2 dup) are associated with a wide spectrum of physical and neurodevelopmental features. In this chart review, physical, developmental, and behavioral features of 28 patients with 22q11.2 dup (median age = 17.11 years) are reported, and phenotypes of de novo and inherited duplications are compared. Common medical anomalies include nutritional problems (57%), failure to thrive (33%), transient hearing impairment (52%), and congenital heart defects (33%). Developmental, speech-language, and motor delay are common in infancy, while attention (64%), learning (60%), and motor problems (52%) are typically reported at primary school age. Attention-deficit/hyperactivity disorders are diagnosed in 44%. Median full-scale intelligence quotient is in the borderline range (IQ 76), with one-fifth of patients having mild intellectual disability. Longitudinal data in 11 patients, with the first assessment at a median age of 5.2 years and the second assessment at a median age of 8.8 years, indicate that almost two-third of patients have a relative stable cognitive trajectory, whereas one-third show a growing into deficit profile. In patients with de novo duplications, there is a trend of more failure to thrive, while more patients with inherited duplications follow special education.

Molecular and phenotypic characteristics of 15q24 microdeletion in pediatric patients with developmental disorders

Chromosome 15q24 microdeletion is a rare genetic disorder characterized by development delay, facial dysmorphism, congenital malformations, and occasional autism spectrum disorder (ASD). In this study, we identified five cases of 15q24 microdeletion using multiplex ligation-dependent probe amplification (MLPA) technology in a cohort of patients with developmental delay and/or intellectual disability. Two of these five cases had deletions that overlapped with the previously defined 1.1 Mb region observed in most reported cases. Two cases had smaller deletions (< 0.57 Mb) in the 15q24.1 low copy repeat (LCR) B-C region. They presented significant neurobehavioral features, suggesting that this smaller interval is critical for core phenotypes of 15q24 microdeletion syndrome. One case had minimal homozygous deletion of less than 0.11 Mb in the 15q24.1 LCR B-C region, which contained CYP1A1 (cytochrome P450 family 1 subfamily A member 1) and EDC3 (enhancer of mRNA decapping 3) genes, resulting in poor immunity, severe laryngeal stridor, and lower limbs swelling. This study provides additional evidence of 15q24 microdeletion syndrome with genetic and clinical findings. The results will be of significance to pediatricians in their daily practice.

Copy number variations of chromosome 17p11.2 region in children with development delay and in fetuses with abnormal imaging findings

BACKGROUND

Deletion and duplication of the 3.7 Mb region in 17p11.2 result in two syndromes, Smith-Magenis syndrome and Potocki-Lupski syndrome, which are well-known development disorders. The purpose of this study was to determine the prevalence, genetic characteristics and clinical phenotypes of 17p11.2 deletion/duplication in Chinese children with development delay and in fetuses with potential congenital defects.

METHODS

7077 children with development delay and/or intellectual disability were screened by multiplex ligation-dependent probe amplification P245 assay. 7319 fetuses with potential congenital defects were tested using next generation sequencing technique.

RESULTS

417 of 7077 pediatric patients were determined to carry chromosome imbalance. 28 (28/7077, 0.4%) cases had imbalance at chromosome 17p11.2. Among them, 12 cases (42.9%) had heterozygous deletions and 16 cases (57.1%) had heterozygous duplications. The clinical phenotypes were variable, including neurobehavioral disorders, craniofacial/skeletal anomalies, immunologic defects, ocular problems and organ malformations. 263 of 7319 fetuses were recognized to have genomic copy number variations. Only 2 of them were found to harbor 17p11.2 imbalance. The fetus with deletion presented with ventricular septal defect and the fetus with duplication had cerebral ventricle dilation.

CONCLUSION

Our study highlights the phenotypic variability associated with 17p11.2 variations in China. The results further expand the phenotypic spectrum of SMS/PTLS and increase awareness of these disruptive mutations among clinicians.