scholarly journals Application of Chromosome Microarray Analysis in the Investigation of Developmental Disabilities and Congenital Anomalies: Single Center Experience and Review of NRXN3 and NEDD4L Deletions

2020 ◽  
Vol 11 (4) ◽  
pp. 197-206
Author(s):  
Alper Han Çebi ◽  
Şule Altıner
Keyword(s):  
Developmental Disabilities ◽  
Microarray Analysis ◽  
Congenital Anomalies ◽  
Copy Number Variations ◽  
Step Test ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis ◽  
Multiple Congenital Anomalies ◽  
Single Center Experience ◽  
Genome Wide

Chromosomal microarray analysis (CMA) is a first step test used for the diagnosis of patients with developmental delay, intellectual disability, autistic spectrum disorder, and multiple congenital anomalies. Its widespread usage has allowed genome-wide identification of copy number variations (CNVs). In our study, we performed a retrospective study on clinical and microarray data of 237 patients with developmental disabilities and/or multiple congenital anomalies and investigated the clinical utility of CMA. Phenotype-associated CNVs were detected in 15.18% of patients. Besides, we detected submicroscopic losses on 14q24.3q31.1 in a patient with speech delay and on 18q21.31q21.32 in twin patients with seizures. Deletions of <i>NRXN3</i> and <i>NEDD4L</i> were responsible for the phenotypes, respectively. This study showed that CMA is a powerful diagnostic tool in this patient group and expands the genotype-phenotype correlations on developmental disabilities.

Rapid Diagnosis of Imprinting Disorders Involving Copy Number Variation and Uniparental Disomy Using Genome-Wide SNP Microarrays

2015 ◽  
Vol 146 (1) ◽  
pp. 9-18 ◽  
Author(s):  
Weiqiang Liu ◽  
Rui Zhang ◽  
Jun Wei ◽  
Huimin Zhang ◽  
Guojiu Yu ◽  
...  
Keyword(s):  
Copy Number ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Copy Number Variations ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis ◽  
Imprinting Disorders ◽  
Genome Wide ◽  
Number Variation ◽  
Efficient Alternative

Imprinting disorders, such as Beckwith-Wiedemann syndrome (BWS), Prader-Willi syndrome (PWS) and Angelman syndrome (AS), can be detected via methylation analysis, methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), or other methods. In this study, we applied single nucleotide polymorphism (SNP)-based chromosomal microarray analysis to detect copy number variations (CNVs) and uniparental disomy (UPD) events in patients with suspected imprinting disorders. Of 4 patients, 2 had a 5.25-Mb microdeletion in the 15q11.2q13.2 region, 1 had a 38.4-Mb mosaic UPD in the 11p15.4 region, and 1 had a 60-Mb detectable UPD between regions 14q13.2 and 14q32.13. Although the 14q32.2 region was classified as normal by SNP array for the 14q13 UPD patient, it turned out to be a heterodisomic UPD by short tandem repeat marker analysis. MS-MLPA analysis was performed to validate the variations. In conclusion, SNP-based microarray is an efficient alternative method for quickly and precisely diagnosing PWS, AS, BWS, and other imprinted gene-associated disorders when considering aberrations due to CNVs and most types of UPD.

scholarly journals Performance of Chromosomal Microarray Analysis for Detection of Copy Number Variations in Fetal Echogenic Bowel

2021 ◽  
Vol Volume 14 ◽  
pp. 1431-1438
Author(s):  
Xiangqun Fan ◽  
Hailong Huang ◽  
Xiyao Lin ◽  
Huili Xue ◽  
Meiying Cai ◽  
...  
Keyword(s):  
Microarray Analysis ◽  
Copy Number ◽  
Copy Number Variations ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis

scholarly journals A single center experience with publicly funded clinical exome sequencing for neurodevelopmental disorders or multiple congenital anomalies

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ben Pode-Shakked ◽  
Ortal Barel ◽  
Amihood Singer ◽  
Miriam Regev ◽  
Hana Poran ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Neurodevelopmental Disorders ◽  
Congenital Anomalies ◽  
Brain Magnetic Resonance Imaging ◽  
Autism Spectrum ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis ◽  
Publicly Funded ◽  
Multiple Congenital Anomalies ◽  
Tertiary Center

AbstractExome sequencing (ES) is an important diagnostic tool for individuals with neurodevelopmental disorders (NDD) and/or multiple congenital anomalies (MCA). However, the cost of ES limits the test's accessibility for many patients. We evaluated the yield of publicly funded clinical ES, performed at a tertiary center in Israel, over a 3-year period (2018–2020). Probands presented with (1) moderate-to-profound global developmental delay (GDD)/intellectual disability (ID); or (2) mild GDD/ID with epilepsy or congenital anomaly; and/or (3) MCA. Subjects with normal chromosomal microarray analysis who met inclusion criteria were included, totaling 280 consecutive cases. Trio ES (proband and parents) was the default option. In 252 cases (90.0%), indication of NDD was noted. Most probands were males (62.9%), and their mean age at ES submission was 9.3 years (range 1 month to 51 years). Molecular diagnosis was reached in 109 probands (38.9%), mainly due to de novo variants (91/109, 83.5%). Disease-causing variants were identified in 92 genes, 15 of which were implicated in more than a single case. Male sex, families with multiple-affected members and premature birth were significantly associated with lower ES yield (p < 0.05). Other factors, including MCA and coexistence of epilepsy, autism spectrum disorder, microcephaly or abnormal brain magnetic resonance imaging findings, were not associated with the yield. To conclude, our findings support the utility of clinical ES in a real-world setting, as part of a publicly funded genetic workup for individuals with GDD/ID and/or MCA.

scholarly journals Application of chromosome microarray analysis in prenatal diagnosis

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Mingjing Xia ◽  
Xinhong Yang ◽  
Jing Fu ◽  
Zhenjuan Teng ◽  
Yan Lv ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Microarray Analysis ◽  
Detection Rate ◽  
Karyotype Analysis ◽  
Copy Number Variations ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis ◽  
Genetic Abnormalities ◽  
Significant Difference ◽  
Chromosomal Karyotype

Abstract Background To explore the application value of chromosomal microarray analysis (CMA) in prenatal diagnosis. Methods The results of chromosome karyotype analysis and CMA of 477 cases undergoing amniocentesis were analyzed. The results of the no ultrasound abnormality group and the ultrasound abnormality group were compared separately. Within the ultrasound abnormality group, the results of the ultrasound structural malformation group, the ultrasound soft index abnormality group, and other ultrasound abnormality (including abnormal amniotic fluid volume and fetal growth restriction) groups were compared. Results Abnormal chromosome and CMA results were found in a total of 71 cases (15.88%, 71/447), which can be broken down into a total of 23 karyotype abnormalities (5.15%, 23/447), consisting of 18 cases of aneuploidy (4.03%, 18/447), 2 cases of unbalanced chromosome rearrangements (0.44%, 2/447), and 3 cases of chimerism (0.67%, 3/447); 17 cases with detection of pathogenic copy number variations (pCNVs) (3.80%, 17/447); and 31 cases of detection of clinical variants of unknown significance (VOUS) (6.93%, 31/447). CMA detected 3.8% more genetic abnormalities than karyotype analysis (in addition to the abnormalities detected simultaneously by karyotype analysis). Between the no ultrasound abnormality group and the ultrasound abnormality group, there was an extremely significant difference in the detection rate of an abnormal chromosomal karyotype (P < 0.01) and of VOUS (P < 0.01), but there was no significant difference in the detection rate of pCNV (P > 0.05). Comparing the ultrasound structural malformation group, the ultrasound soft index abnormality group, and the other ultrasound abnormality group, there were no significant differences in the detection rate of abnormal chromosomal karyotypes (P > 0.05), pCNV (P > 0.05) or VOUS (P > 0.05). Conclusions The detection rate of chromosomal karyotype abnormalities in prenatal diagnosis in cases with no ultrasound abnormalities was higher. For cases with fetal ultrasound structural abnormalities, when compared with traditional karyotype analysis, CMA can improve the detection rate of fetal genetic abnormalities. However, the no ultrasound abnormality group also had a high VOUS abnormality detection rate, so it is necessary to strictly define the CMA indications.

scholarly journals Levy-Shanske syndrome: mosaic tetrasomy 15q25.3→qter and review of the literature

2019 ◽  
pp. 40-47
Author(s):  
М.Е. Миньженкова ◽  
Ж.Г. Маркова ◽  
Н.А. Демина ◽  
А.А. Тарлычева ◽  
И.В. Канивец ◽  
...  
Keyword(s):  
Congenital Anomalies ◽  
Marker Chromosome ◽  
Distal Portion ◽  
Chromosomal Microarray ◽  
Chromosomal Microarray Analysis ◽  
Chromosome 15 ◽  
Review Of The Literature ◽  
Multiple Congenital Anomalies ◽  
Molecular Cytogenetic ◽  
Inverted Duplication

Введение. Тетрасомия дистального района длинного плеча хромосомы 15 является довольно редким событием. В электронной базе данных по сверхчисленным маркерным хромосомам имеются сведения о 24 зарегистрированных случаях с инвертированной дупликацией дистального района длинного плеча хромосомы 15. Частичная тетрасомия 15q может наблюдаться вследствие появления сверхчисленной анальфоидной маркерной хромосомы, состоящей из инвертированной дупликации дистальной части длинного плеча хромосомы 15. Представлен случай мозаичной тетрасомии 15q25.3-qter, у пациента со множественными признаками дизэмбриогенеза. Цель. Молекулярно-цитогенетическая диагностика мозаичного случая инвертированной дупликации 15q25.3→qter у пациента с множественными врожденными аномалиями развития и обзор аналогичных случаев. Методы. Для идентификации малой сверхчисленной маркерной хромосомы и определения уровня мозаицизма использовали комплексную молекулярно-цитогенетическую диагностику, включающую хромосомный микроматричный анализ и FISH-исследование. Результаты. При стандартном цитогенетическом исследовании обнаружена сверхчисленная маркерная хромосома в мозаичном состоянии: 47,ХХ,+mar[8]/46,XX[23]. Для идентификации геномного дисбаланса использовали хромосомный микроматричный анализ, выявивший дупликацию участка длинного плеча хромосомы 15 размером 16,4 млн п.н. FISH-исследование позволило установить, что сверхчисленная маркерная хромосома представлена инвертированной дупликацией района q25.3→qter хромосомы 15 с неоцентромерой, и помогло уточнить уровень мозаицизма, который составил 35%. Заключение. Идентификация структуры и происхождения сверхчисленных маркерных хромосом у пациентов с множественными врожденными аномалиями развития является важной задачей цитогенетической лаборатории. Современные молекулярно-цитогенетические методы диагностики хромосомных аномалий позволяют выявить и охарактеризовать любой случай неоцентромерной формации. Introduction: Tetrasomy for the distal chromosome 15q is rare. Only 24 cases have been described in the literature to date. Tetrasomy for the distal portion of chromosome 15q can be due to a supernumerary analphoid marker chromosome consisting of an inverted duplication of the distal long arm of chromosome 15. We report on a molecular cytogenetic diagnosis of mosaic tetrasomy 15q25.3-qter in a patient with multiple congenital anomalies. Aim: Molecular cytogenetic diagnosis of mosaic case with inverted duplication for the distal portion of 15q25.3→qter in a patient with multiple congenital anomalies and review of the literature. Methods: The case of mosaic supernumerary marker chromosome was characterized by GTG-banding, chromosomal microarray analysis and FISH diagnosis. Results: The chromosome analysis of a child revealed a supernumerary marker chromosome in mosaicism: 47,ХХ,+mar[8]/46,XX[23]. Chromosomal microarray analysis detected a copy gain of 16.4 Mb from the distal long arm of chromosome 15. Further FISH analysis showed an inverted duplication of distal long arm of chromosome 15 with neocentromere. Conclusion: Identification of structure and origin supernumerical marker chromosomes at patients with multiple congenital anomalies is an important problem of cytogenetic diagnostics. Modern molecular -cytogenetic diagnostic methods of chromosomal anomalies allow identifying and characterizing any case of neocentromeres.

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