Additive Diagnostic Yield of Homozygosity Regions Identified During Chromosomal microarray Testing in Children with Developmental Delay, Dysmorphic Features or Congenital Anomalies

2019 ◽  
Vol 58 (1) ◽  
pp. 74-101
Author(s):  
Mohamed A. M. Ali ◽  
Abdelrahman M. Hassan ◽  
Mosaab A. Saafan ◽  
Adel A. Abdelmagid
Keyword(s):  
Developmental Delay ◽  
Congenital Anomalies ◽  
Diagnostic Yield ◽  
Chromosomal Microarray ◽  
Dysmorphic Features

scholarly journals Relationship between Clinical Parameters and Chromosomal Microarray Data in Infants with Developmental Delay

Healthcare ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 305
Author(s):  
Zeeihn Lee ◽  
Byung Joo Lee ◽  
Sungwon Park ◽  
Donghwi Park
Keyword(s):  
Developmental Delay ◽  
Diagnostic Yield ◽  
Copy Number Variations ◽  
Gene Copy ◽  
Chromosomal Microarray ◽  
Clinical Parameters ◽  
Brain Anomalies ◽  
Pathogenic Cnvs ◽  
Clinical Records ◽  
The Relationship

Chromosomal microarray (CMA) is considered a first-tier test for genetic analysis as it can be used to examine gene copy number variations (CNVs) throughout the entire genome, with enhanced sensitivity for detecting submicroscopic deletions and duplications. However, its cost can represent a heavy burden. Moreover, the diagnostic yield of CMA in infants with developmental delay (DD) was reported to be less than 10%. Therefore, we aimed to investigate the relationship between CMA results and clinical features and risk factors of DD. The study included 59 infants with DD who were recruited between August 2019 and February 2020 during a visit to the outpatient clinic of a rehabilitation department. We reviewed the clinical records of the infants regarding gender, age, body weight at birth, delivery method, brain imaging data, perinatal history, and parent-related clinical parameters, such as mother and father age at birth. The infants were categorized according to CMA results, and differences in clinical parameters were evaluated. Except for brain anomalies, there was no statistically significant differences between infants who had pathogenic and variants of unknown significance (VOUS)-likely pathogenic CNVs groups compared with those within the VOUS-likely no sub-classification, VOUS-likely benign, benign, and normal CNVs groups. The incidence of brain anomalies was significantly higher within infants with pathogenic and VOUS-likely pathogenic CNVs groups (p < 0.05). Our study suggests that infants with DD who present dysmorphism or brain anomaly may benefit from early CMA analysis, for adequate diagnosis and timely treatment. Further studies are warranted to confirm the relationship between DD clinical parameters and CMA results.

scholarly journals Genome sequencing demonstrates high diagnostic yield in children with undiagnosed global developmental delay/intellectual disability: a prospective study

2021 ◽  
Author(s):  
Yu Sun ◽  
Jing Peng ◽  
Desheng Liang ◽  
Xiantao Ye ◽  
Na Xu ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Developmental Delay ◽  
Genome Sequencing ◽  
Clinical Utility ◽  
Diagnostic Yield ◽  
Chromosomal Microarray ◽  
Global Developmental Delay ◽  
Chromosomal Microarray Analysis ◽  
High Diagnostic Yield ◽  
Wide Range

Genome sequencing(GS) has been applied in the diagnosis of global developmental delay(GDD)/intellectual disability(ID). However, the performance in those with inconclusive results from chromosomal microarray analysis(CMA) and exome sequencing(ES) is unknown. We recruited 100 pediatric GDD/ID patients from multiple sites in China from February 2018 to August 2020 for GS. Patients have received at least one genomic diagnostic test prior to enrollment. Reanalysis of CMA/ES data was performed. The yield of GS was calculated and explanations for missed diagnoses by CMA/ES were investigated. Clinical utility was assessed by interviewing the parents by phone. The overall diagnostic yield of GS was 23%. Seven families could have been solved with reanalysis of ES data. 13 families were missed by previous CMA/ES due to improper method. Three remained unsolved after ES reanalysis due to allele dropout, complex variants missed by ES, and a CNV in untranslated regions. Follow-up of the diagnosed families revealed that nine families experienced changes in clinical management, including identification of targeted treatments, cessation of unnecessary treatment, and considerations for family planning. GS demonstrated high diagnostic yield and clinical utility in this cohort of undiagnosed GDD/ID patients, detecting a wide range of variant types of different sizes in a single workflow.

Diagnostic yield of chromosomal microarray and trio whole exome sequencing in cryptogenic cerebral palsy

2021 ◽  
pp. jmedgenet-2021-107884
Author(s):  
Michal Yechieli ◽  
Suleyman Gulsuner ◽  
Hilla Ben-Pazi ◽  
Aviva Fattal ◽  
Adi Aran ◽  
...  
Keyword(s):  
Cerebral Palsy ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Congenital Anomalies ◽  
Point Mutations ◽  
High Yield ◽  
Chromosomal Microarray ◽  
Dysmorphic Features ◽  
Whole Exome ◽  
Clinically Significant

ObjectiveTo determine the yield of genetic diagnoses using chromosomal microarray (CMA) and trio whole exome sequencing (WES), separately and combined, among patients with cryptogenic cerebral palsy (CP).MethodsTrio WES of patients with prior CMA analysis for cryptogenic CP, defined as disabling, non-progressive motor symptoms beginning before the age of 3 years without known cause.ResultsGiven both CMA analysis and trio WES, clinically significant genetic findings were identified for 58% of patients (26 of 45). Diagnoses were eight large CNVs detected by CMA and 18 point mutations detected by trio WES. None had more than one severe mutation. Approximately half of events (14 of 26) were de novo. Yield was significantly higher in patients with CP with comorbidities (69%, 22 of 32) than in those with pure motor CP (31%, 4 of 13; p=0.02). Among patients with genetic diagnoses, CNVs were more frequent than point mutations among patients with congenital anomalies (OR 7.8, 95% CI 1.2 to 52.4) or major dysmorphic features (OR 10.5, 95% CI 1.4 to 73.7). Clinically significant mutations were identified in 18 different genes: 14 with known involvement in CP-related disorders and 4 responsible for other neurodevelopmental conditions. Three possible new candidate genes for CP were ARGEF10, RTF1 and TAOK3.ConclusionsCryptogenic CP is genetically highly heterogeneous. Genomic analysis has a high yield and is warranted in all these patients. Trio WES has higher yield than CMA, except in patients with congenital anomalies or major dysmorphic features, but these methods are complementary. Patients with negative results with one approach should also be tested by the other.

scholarly journals Chromosomal microarray analysis of 410 Han Chinese patients with autism spectrum disorder or unexplained intellectual disability and developmental delay

2022 ◽  
Vol 7 (1) ◽  
Author(s):  
Yi Liu ◽  
Yuqiang Lv ◽  
Mehdi Zarrei ◽  
Rui Dong ◽  
Xiaomeng Yang ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Developmental Delay ◽  
Microarray Analysis ◽  
Diagnostic Yield ◽  
Autism Spectrum ◽  
Han Chinese ◽  
Chinese Patients ◽  
European Ancestry ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis

AbstractCopy number variants (CNVs) are recognized as a crucial genetic cause of neurodevelopmental disorders (NDDs). Chromosomal microarray analysis (CMA), the first-tier diagnostic test for individuals with NDDs, has been utilized to detect CNVs in clinical practice, but most reports are still from populations of European ancestry. To contribute more worldwide clinical genomics data, we investigated the genetic etiology of 410 Han Chinese patients with NDDs (151 with autism and 259 with unexplained intellectual disability (ID) and developmental delay (DD)) using CMA (Affymetrix) after G-banding karyotyping. Among all the NDD patients, 109 (26.6%) carried clinically relevant CNVs or uniparental disomies (UPDs), and 8 (2.0%) had aneuploidies (6 with trisomy 21 syndrome, 1 with 47,XXY, 1 with 47,XYY). In total, we found 129 clinically relevant CNVs and UPDs, including 32 CNVs in 30 ASD patients, and 92 CNVs and 5 UPDs in 79 ID/DD cases. When excluding the eight patients with aneuploidies, the diagnostic yield of pathogenic and likely pathogenic CNVs and UPDs was 20.9% for all NDDs (84/402), 3.3% in ASD (5/151), and 31.5% in ID/DD (79/251). When aneuploidies were included, the diagnostic yield increased to 22.4% for all NDDs (92/410), and 33.6% for ID/DD (87/259). We identified a de novo CNV in 14.9% (60/402) of subjects with NDDs. Interestingly, a higher diagnostic yield was observed in females (31.3%, 40/128) compared to males (16.1%, 44/274) for all NDDs (P = 4.8 × 10−4), suggesting that a female protective mechanism exists for deleterious CNVs and UPDs.

A 46,XY Female with a 9p24.3p24.1 Deletion and a 8q24.11q24.3 Duplication: A Case Report and Review of the Literature

2019 ◽  
Vol 158 (2) ◽  
pp. 74-82 ◽  
Author(s):  
Valentina Bruni ◽  
Katia Roppa ◽  
Francesca Scionti ◽  
Rosalbina Apa ◽  
Simona Sestito ◽  
...  
Keyword(s):  
Developmental Delay ◽  
Chromosomal Aberration ◽  
Clinical History ◽  
Ambiguous Genitalia ◽  
Chromosome 8 ◽  
Chromosome 9 ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis ◽  
Balanced Translocation ◽  
Dysmorphic Features

Deletion of distal 9p is associated with a rare clinical condition characterized by dysmorphic features, developmental delay, and ambiguous genitalia. The phenotype shows variable expressivity and is related to the size of the deletion. 8q24 duplication has been reported in only few cases to date, all showing dysmorphic features and mild psychomotor developmental delay. A case of chromosomal aberration involving a 9p terminal deletion with an 8q duplication has never been reported. Here, we describe a child with a female phenotype, male karyotype, dysmorphic features, ambiguous genitalia, and developmental delay. In order to assess the cause of the patient's phenotype, conventional karyotyping, FISH, and a chromosomal microarray analysis were performed on the patient and her parents. The cytogenetic and molecular analysis revealed an unbalanced chromosomal aberration with a duplication in the long arm of chromosome 8 at 8q24.11q24.3 associated with a distal deletion in the short arm of chromosome 9 at 9p24.3p24.1, derived from a maternal balanced translocation. We compared the clinical picture of our patient with other similar cases reported in the literature and found that some clinical findings, such as strabismus, symphalangism of the first finger, and cubitus valgus, have never been previously associated with 9p deletion or 8q duplication expanding the phenotypic range of this condition. This study is aimed to better define the clinical history and prognosis of patients with this rare chromosomal aberration.

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