Submicroscopic Chromosomal Imbalances Research Articles

Comparison of Chromosomal Microarray Analysis and Noninvasive Prenatal Testing in Pregnant Women with Fetal Ultrasonic Soft Markers.

This study aimed to assess the utility of chromosomal microarray analysis (CMA) and noninvasive prenatal testing (NIPT) in detecting clinically significant chromosomal abnormalities among fetuses presenting ultrasonic soft markers (USMs). A retrospective observational study, spanning from January 1, 2019, to September 30, 2022, enrolled 539 singleton pregnant women with fetal USMs at our center. Of these, 418 cases (77.6%) underwent NIPT, while 121 cases (22.4%) opted for invasive prenatal diagnosis post-appropriate genetic counseling. Cases with high-risk NIPT results proceeded to invasive prenatal diagnosis, where conventional karyotyping and CMA were concurrently performed. Further stratification was done based on the number of USMs, classifying cases into single-USM and multiple-USM groups. Of the 24 cases (4.5%) exhibiting abnormal findings, 17 presented numerical chromosomal abnormalities, 2 featured clinically significant copy number variations (CNVs), 3 showed variants of unknown significance (VOUS), 1 displayed LOH, and 1 exhibited chromosome nine inversion. Notably, 18 cases (75%) theoretically detectable by karyotyping (eg, sizes above 10Mb) and 16 cases (66.7%) detectable by NIPT for five common aneuploidies were identified. Six submicroscopic findings (25%) were exclusively detectable by CMA. The predominant clinically relevant aberrations were observed in the thickened nuchal-translucency (TNT) group (9/35, 25.7%), followed by the multiple soft markers group (3/32, 9.3%). In the NIPT group, the false positive rate was 1.22%, and the false negative rate was 0%. The prevalence of chromosome aneuploidy exceeded that of submicroscopic chromosomal imbalance in pregnant women with fetal USMs. NIPT demonstrated efficacy, particularly for soft markers like echogenic intracardiac focus. However, for those with TNT and multiple soft markers, invasive prenatal diagnosis, including CMA testing, is recommended as the primary investigative approach.

Submicroscopic chromosomal imbalances contribute to early abortion

BackgroundChromosomal abnormalities are one of the genetic mechanisms associated with abortion. However, the roles of submicroscopic chromosomal imbalances in early abortion are still unclear. This study aims to find out whether submicroscopic chromosomal imbalances contribute to early abortion.MethodsA total of 78 chorionic villus specimens from early spontaneous abortion patients with no obvious abnormality are collected after miccroassay analysis (the case group). At the same time, 60 chorionic villus specimens from induced abortion patients with no obvious abnormality are selected as the control group. The submicroscopic structures of chromosomes from two groups are analyzed using an array-based comparative genomic hybridization (aCGH).ResultsIn the case group, 15 specimens show submicroscopic chromosomal abnormalities including 14 micro-deletion/micro-duplication in chromosomes 2, 4, 5, 6, 7, 8, 9, 12, 15, 16, 18, and 22, and 1 uniparental disomy (UPD) in chromosome 19. Moreover, no pathogenic copy number variations are found in the control group. The results between these two groups exhibit significantly statistical difference.ConclusionSubmicroscopic chromosomal imbalances may be one of the main reasons for early abortion.

Comprehensive Genetic Analysis of Pregnancy Loss by Chromosomal Microarrays: Outcomes, Benefits, and Challenges

(Abstracted from Genet Med 2017;19(1):83–89) High-resolution chromosomal microarray analysis (CMA) with single-nucleotide polymorphism (SNP)–based arrays is increasingly used for pediatric and prenatal diagnoses as they can simultaneously detect aneuploidies, submicroscopic chromosomal imbalances, triploidy, and regions of allelic homozygosity. Overall, 15% to 20% of clinically recognized pregnancies end in miscarriage, and approximately 1% of couples experience recurrent (at least 2) pregnancy losses.

Associations between the clinical findings of cases having submicroscopic chromosomal imbalances at chromosomal breakpoints of apparently balanced structural rearrangements

Although the carriers with apparently balanced structural rearrangements have usually normal phenotype, phenotypical abnormalities can be seen in approximately 6% de novo cases. A number of different mechanisms are involved in the appearance of these phenotypic abnormalities, one of which is submicroscopic chromosomal imbalances at chromosomal breakpoints. Our goal was to unravel the possible submicroscopic chromosomal imbalances at chromosomal breakpoints by using array-CGH analysis in patients with apparently balanced structural rearrangements and to link these to the clinical findings. A total of nine patients with reciprocal translocation carriers (2 familial, 7 de novo) and six patients with inversion carriers (2 familial, 4 de novo) were included in this study. In order to evaluate the possible microdeletions and microduplications at the chromosomal breakpoints, DNA samples were isolated from the peripheral blood of the patients (and their parents) and investigated using array-CGH analysis. Array-CGH analysis revealed submicroscopic chromosomal imbalances at breakpoints in 3 of the 7 (43%) de novo reciprocal translocation carriers. Additionally, 1 out of 4 (25%) de novo inversion carriers were found to have a submicroscopic chromosomal imbalance in unrelated chromosome seen in cytogenetic analysis. Furthermore, no submicroscopic chromosomal imbalances were detected in either of the two familially transmitted reciprocal translocation carriers. Based on the results of both array-CGH analysis and conventional cytogenetic analysis, the karyotypes of the patients were designated as follows:46,XY,t(13;16)(q14;q12.1)dn.arr[hg19]13q14.2-q21.1(50,131,521–57,306,322)x1dn; 46,XY,t(6;9)(q13;p12)dn.arr[hg19]6q14.1(78,016,882–83,293,127),9p23p22.3(12,249,507–15,939,627)x1dn;46,XX,t(X;16)(p11.21;p11.2)dn.arr[hg19]Xp11.22(50,367,783–50,441,087)x3dn; 46,XX,inv.(18)(p11.23q11.2)dn.arr[hg19]22q11.21(18,706,001–21,505,417)x1mat.Our results demonstrate the necessity of using array-CGH to evaluate patients with apparently balanced structural rearrangements in order to determine the submicroscopic chromosomal imbalances at chromosomal breakpoints that are related to the observed clinical abnormalities.

Use of Affymetrix Arrays in the Diagnosis of Gene Copy‐Number Variation

Diagnosing constitutional pathogenic copy number variants (CNVs) requires detecting submicroscopic segmental chromosomal imbalances. The Affymetrix GeneChip mapping array was one of the initial microarray platforms used to measure duplication and deletion of genetic material in DNA samples. Unlike oligonucleotide microarrays from NimbleGen and Agilent, developed around the same time to infer copy number status for the DNA sequence covered by the probe, the Affymetrix GeneChip system used 25-mer oligonucleotide probes designed to interrogate SNPs. Thus, it was possible to use the Affymetrix 'SNP chips' to both identify SNPs and to identify copy number status. Affymetrix now offers the CytoScan microarray platforms, which are optimized for copy-number analyses, and provides accompanying software. They also offer several other microarray platforms suitable for copy-number analyses. Here we discuss the application of the CytoScan high-density (HD) platform for the detection of genomic imbalance. We provide an overview of the sequence of computational analyses involved in identifying pathogenic CNVs and highlight important parameters for consideration in assessing the pathogenicity of a detected CNV.

Copy-number variation associated with congenital anomalies of the kidney and urinary tract.

The most common cause of end-stage renal disease in children can be attributed to congenital anomalies of the kidney and urinary tract (CAKUT). Despite this high incidence of disease, the genetic mutations responsible for the majority of CAKUT cases remain unknown. To identify novel genomic regions associated with CAKUT, we screened 178 children presenting with the entire spectrum of structural anomalies associated with CAKUT for submicroscopic chromosomal imbalances (deletions or duplications) using single-nucleotide polymorphism (SNP) microarrays. Copy-number variation (CNV) was detected in 10.1% (18/178) of the patients; in 6.2% of the total cohort, novel duplications or deletions of unknown significance were identified, and the remaining 3.9% harboured CNV of known pathogenicity. CNVs were inherited in 90% (9/10) of the families tested. In this cohort, patients diagnosed with multicystic dysplastic kidney (30%) and posterior urethral valves (24%) had a higher incidence of CNV. The genes contained in the altered genomic regions represent novel candidates for CAKUT. This study has demonstrated that a significant proportion of patients with CAKUT harbour submicroscopic chromosomal imbalances, warranting screening in clinics for CNV.

Genome-wide screening of copy number variants in children born small for gestational age reveals several candidate genes involved in growth pathways.

The etiology of prenatal-onset short stature with postnatal persistence is heterogeneous. Submicroscopic chromosomal imbalances, known as copy number variants (CNVs), may play a role in growth disorders. To analyze the CNVs present in a group of patients born small for gestational age (SGA) without a known cause. A total of 51 patients with prenatal and postnatal growth retardation associated with dysmorphic features and/or developmental delay, but without criteria for the diagnosis of known syndromes, were selected. Array-based comparative genomic hybridization was performed using DNA obtained from all patients. The pathogenicity of CNVs was assessed by considering the following criteria: inheritance; gene content; overlap with genomic coordinates for a known genomic imbalance syndrome; and overlap with CNVs previously identified in other patients with prenatal-onset short stature. In 17 of the 51 patients, 18 CNVs were identified. None of these imbalances has been reported in healthy individuals. Nine CNVs, found in eight patients (16%), were categorized as pathogenic or probably pathogenic. Deletions found in three patients overlapped with known microdeletion syndromes (4q, 10q26, and 22q11.2). These imbalances are de novo, gene rich and affect several candidate genes or genomic regions that may be involved in the mechanisms of growth regulation. Pathogenic CNVs in the selected patients born SGA were common (at least 16%), showing that rare CNVs are probably among the genetic causes of short stature in SGA patients and revealing genomic regions possibly implicated in this condition.

Performance of chromosomal microarray for patients with intellectual disabilities/developmental delay, autism, and multiple congenital anomalies in a Chinese cohort.

BackgroundChromosomal microarray (CMA) is currently the first-tier genetic test for patients with idiopathic neuropsychiatric diseases in many countries. Its improved diagnostic yield over karyotyping and other molecular testing facilitates the identification of the underlying causes of neuropsychiatric diseases. In this study, we applied oligonucleotide array comparative genomic hybridization as the molecular genetic test in a Chinese cohort of children with DD/ID, autism or MCA.ResultsCMA identified 7 clinically significant microduplications and 17 microdeletions in 19.0% (20/105) patients, with size of aberrant regions ranging from 11 kb to 10.7 Mb. Fourteen of the pathogenic copy number variant (CNV) detected corresponded to well known microdeletion or microduplication syndromes. Four overlapped with critical regions of recently identified genomic syndromes. We also identified a rare de novo 2.3 Mb deletion at 8p21.3-21.2 as a pathogenic submicroscopic CNV. We also identified two novel CNVs, one at Xq28 and the other at 12q21.31-q21.33, in two patients (1.9%) with unclear clinical significance. Overall, the detection rate of CMA is comparable to figures previously reported for accurately detect submicroscopic chromosomal imbalances and pathogenic CNVs except mosaicism, balanced translocation and inversion.ConclusionsThis study provided further evidence of an increased diagnostic yield of CMA and supported its use as a first line diagnostic tool for Chinese individuals with DD/ID, ASD, and MCA.

Molecular Characterization of De Novo Unbalanced 5;21 Translocation Associated With Multiple Congenital Abnormalities and Developmental Delay by Array-Based Comparative Genomic Hybridization

Chromosomal imbalances are a significant cause of congenital disorders. Microarray-based comparative genomic hybridization, also known as chromosomal microarray (CMA), is a relatively new technology that can identify microscopic and submicroscopic chromosomal imbalances. We report the case of a 12-year-old boy with multiple congenital abnormalities referred for cytogenetic and CMA evaluation. The patient had developmental delay, microcephaly, bilateral iris colobomas, ventricular septal defect, …

Molecular Karyotyping as a Relevant Diagnostic Tool in Children with Growth Retardation with Silver-Russell Features

To determine the contribution of submicroscopic chromosomal imbalances to the etiology of Silver-Russell syndrome (SRS) and SRS-like phenotypes. We performed molecular karyotyping in 41 patients with SRS or SRS-like features without known chromosome 7 and 11 defects using the Affymetrix SNP Array 6.0 system (Affymetrix, High Wycombe, United Kingdom). In 8 patients, pathogenic copy number variations with sizes ranging from 672 kb to 9.158 Mb were identified. The deletions in 1q21, 15q26, 17p13, and 22q11 were associated with known microdeletion syndromes with overlapping features with SRS. The duplications in 22q13 and Xq25q27 represent unique novel copy number variations but have an obvious influence on the phenotype. In 5 additional patients, the pathogenetic relevance of the detected variants remained unclear. Pathogenic submicroscopic imbalances were detectable in a significant proportion of patients with short stature and features reminiscent of SRS. Therefore, molecular karyotyping should be implemented in routine diagnostics for growth-retarded patients with even slight dysmorphisms suggestive for SRS.

Analysis of de novo copy number variations in a family affected with autism spectrum disorders using high-resolution array-based comparative genomic hybridization

To analyze de novo copy number variations (CNVs) in a Chinese family affected with autism spectrum disorders (ASD). Affymetrix Cytogenetics Whole Genome 2.7M Array assay was performed to identify potential CNVs in four members from the family. A total of 89 de novo CNV regions were identified in the autistic siblings. The CNV regions in total have exceeded 1/1000 of the lengths of chromosomes 5, 11 and 14. In addition, de novo CNV regions were also identified at 3p26.1, 4q22.2, and 5p15.2, which encompassed 10 genes associated with nerve development including GRM7, GRID2 and CTNND2. A number of nerve development associated genes were at the de novo CNV sites, which may provide new clues for genetic research of ASD. High-resolution array-comparative genomic hybridization is an effective method for detecting submicroscopic chromosomal imbalances.

Detection of Genomic Imbalances by Array-Based Comparative Genomic Hybridization in Bulgarian Patients with Autism Spectrum Disorders

ABSTRACTAutism spectrum disorders (ASDs) constitute a group of behaviorally-defined conditions whose main features are qualitative changes in social interactions, defect in communication abilities, and repetitive and stereotyped interests and activities. ASDs are disorders which can be either isolated, or syndromic. The exact etiology of autism remains unknown, although it is likely to result from a complex combination of genetic and nongenetic factors. One genetic mechanism known to be associated with ASDs is submicroscopic chromosomal imbalances that are undetectable at the level of traditional cytogenetic analysis. Array-based comparative genomic hybridization (array CGH) is a powerful and high-resolution approach for detection of DNA copy number variants (CNVs). Forty-seven autistic patients were investigated using a whole-genome oligo-based array CGH, covering the genome at an average distance of 35 kb. Four clinically significant rearrangements, ranging from 494 kb to 3.47 Mb in size, were identified in 3 patients. Confirmation studies were performed on array CGH results using FISH. These data strongly support the idea that only a whole-genome high-resolution analysis such as array CGH is able to provide an accurate diagnosis for chromosomal imbalance in patients with ASDs.

Could Submicroscopical Chromosomal Imbalances Cause Cono-Truncal Malformations in Twins?

The course of normal heart formation in the embryo has been known for decades, but little is known about the genes that control its development. To further improve our understanding of the molecular and genetic mechanisms involved in congenital heart disease, we screened for submicroscopic chromosomal aberrations using bacterial artificial chromosome-based array comparative genomic hybridization analysis in two Danish twin pairs, one pair of monozygotic twins with tetralogy of Fallot, and one twin pair of unknown zygosity with pulmonary valve stenosis. We did not find any major chromosome defects, although a number of submicroscopic copy number variations were present. The question of whether these submicroscopic chromosomal imbalances alone or in conjunction with unknown intrauterine factors causes the observed cono-truncal malformations remains unanswered.

Clinical Applications of Chromosomal Microarray Analysis

Chromosomal microarray analysis (CMA) enables the genome-wide detection of submicroscopic chromosomal imbalances with greater precision and accuracy. In most other countries, CMA is now a commonly used clinical diagnostic test, replacing conventional cytogenetics or targeted detection such as FISH or PCR-based methods. Recently, some consensus statements have proposed utilization of CMA as a first-line test in patients with multiple congenital anomalies not specific to a well- delineated genetic syndrome, developmental delay/intellectual disability, or autism spectrum disorders. CMA can be used as an adjunct to conventional cytogenetics to identify chromosomal abnormalities observed in G-banding analysis in constitutional or acquired cases, leading to a more accurate and comprehensive assessment of chromosomal aberrations. Although CMA has distinct advantages, there are several limitations, including its inability to detect balanced chromosomal rearrangements and low-level mosaicism, its interpretation of copy number variants of uncertain clinical significance, and significantly higher costs. For these reasons, CMA is not currently a replacement for conventional cytogenetics in prenatal diagnosis. In clinical applications of CMA, knowledge and experience based on genetics and cytogenetics are required for data analysis and interpretation, and appropriate follow-up with genetic counseling is recommended.

A novel mutation of GATA4 in a familial atrial septal defect

Previous studies have identified that mutations in a few genes, including T-BOX5, NKX2-5, EVC and GATA4, are associated with atrial septal defect (ASD). A family of three generations with 4 members who were affected with ASD was investigated. To exclude the presence of any sub-microscopic chromosomal imbalance, high-resolution 1M array-based comparative genomic hybridization (aCGH) was performed. SNaPShot was used to certify the specificity of the finding mutation in the other family members. The coding region of GATA4 and NKX2-5 genes was screened by sequencing in another 30 cases including 10 cases of ventricular septal defect (VSD), 10 cases of atrial septal defect (ASD), 8 cases of VSD combined with ASD and 2 cases of atrioventricular septal defects (AVSD). No pathogenic copy number variant was detected by aCGH in the four affected family members with ASD. A novel non-synonymous variant, c.839C>T (T280M) in GATA4, was identified and segregated with all the ASD patients within this Chinese family. Such mutation was absent in other family members or present among sporadic CHD patients. In addition, we identified a non-synonymous variant in the NKX2-5 gene (P257A) associated with one congenital heart disease patient with VSD. Both mutations were not identified among healthy controls. T280M mutation of GATA4 is suggested to be associated with ASD in this Chinese family.

A retrospective study by oligonucleotide array‐CGH analysis in 50 fetuses with multiple malformations

To retrospectively define the frequency and the nature of submicroscopic chromosomal imbalances among fetuses with multiple congenital anomalies (MCA). We used oligonucleotide arrays to perform comparative genomic hybridization after termination of pregnancy in 50 polymalformated fetuses with a normal karyotype. These fetuses presented with at least three significant malformations (42 cases) or a severe brain anomaly (eight cases). We identified a deleterious copy number variation (CNV) in five fetuses (10%). De novo genomic imbalances identified in this study consisted of a 6qter deletion in a fetus with brain and renal malformations, a mosaicism for a 8p tetrasomy in a fetus with agenesis of corpus callosum, growth retardation, mild facial dysmorphic features, and vertebral anomalies, a 17p13.3 deletion in a fetus with a complex brain malformation, and a partial 11p trisomy in a fetus with severe growth retardation and oligoamnios. In one case, we identified a partial 17q trisomy resulting from malsegregation of a cryptic-balanced translocation. This study shows that array comparative genomic hybridization (aCGH) is particularly effective for identifying the molecular basis of the disease phenotype in fetuses with multiple anomalies. Our study should help to define clinical relevant regions that would need to be included in targeted arrays designed for prenatal testing.

DECIPHER: Databas e of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources

Many patients suffering from developmental disorders harbor submicroscopic deletions or duplications that, by affecting the copy number of dosage-sensitive genes or disrupting normal gene expression, lead to disease. However, many aberrations are novel or extremely rare, making clinical interpretation problematic and genotype-phenotype correlations uncertain. Identification of patients sharing a genomic rearrangement and having phenotypic features in common leads to greater certainty in the pathogenic nature of the rearrangement and enables new syndromes to be defined. To facilitate the analysis of these rare events, we have developed an interactive web-based database called DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources) which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance, inversions, and translocations. DECIPHER catalogs common copy-number changes in normal populations and thus, by exclusion, enables changes that are novel and potentially pathogenic to be identified. DECIPHER enhances genetic counseling by retrieving relevant information from a variety of bioinformatics resources. Known and predicted genes within an aberration are listed in the DECIPHER patient report, and genes of recognized clinical importance are highlighted and prioritized. DECIPHER enables clinical scientists worldwide to maintain records of phenotype and chromosome rearrangement for their patients and, with informed consent, share this information with the wider clinical research community through display in the genome browser Ensembl. By sharing cases worldwide, clusters of rare cases having phenotype and structural rearrangement in common can be identified, leading to the delineation of new syndromes and furthering understanding of gene function.

Use of Affymetrix Mapping Arrays in the Diagnosis of Gene Copy Number Variation

Diagnosing constitutional pathogenic copy number variants requires measuring the submicroscopic segmental chromosomal imbalance. The Affymetrix GeneChip mapping array has been used to measure duplication and deletion of genetic material in DNA samples. This protocol describes the measurement and analysis processes, specifically the computational analyses that are involved in identifying pathogenic copy number variants.

Identification of chromosome abnormalities in subtelomeric regions by microarray analysis: A study of 5,380 cases

Subtelomeric imbalances are a significant cause of congenital disorders. Screening for these abnormalities has traditionally utilized GTG-banding analysis, fluorescence in situ hybridization (FISH) assays, and multiplex ligation-dependent probe amplification. Microarray-based comparative genomic hybridization (array-CGH) is a relatively new technology that can identify microscopic and submicroscopic chromosomal imbalances. It has been proposed that an array with extended coverage at subtelomeric regions could characterize subtelomeric aberrations more efficiently in a single experiment. The targeted arrays for chromosome microarray analysis (CMA), developed by Baylor College of Medicine, have on average 12 BAC/PAC clones covering 10 Mb of each of the 41 subtelomeric regions. We screened 5,380 consecutive clinical patients using CMA. The most common reasons for referral included developmental delay (DD), and/or mental retardation (MR), dysmorphic features (DF), multiple congenital anomalies (MCA), seizure disorders (SD), and autistic, or other behavioral abnormalities. We found pathogenic rearrangements at subtelomeric regions in 236 patients (4.4%). Among these patients, 103 had a deletion, 58 had a duplication, 44 had an unbalanced translocation, and 31 had a complex rearrangement. The detection rates varied among patients with a normal karyotype analysis (2.98%), with an abnormal karyotype analysis (43.4%), and with an unavailable or no karyotype analysis (3.16%). Six patients out of 278 with a prior normal subtelomere-FISH analysis showed an abnormality including an interstitial deletion, two terminal deletions, two interstitial duplications, and a terminal duplication. In conclusion, genomic imbalances at subtelomeric regions contribute significantly to congenital disorders. Targeted array-CGH with extended coverage (up to 10 Mb) of subtelomeric regions will enhance the detection of subtelomeric imbalances, especially for submicroscopic imbalances.

High frequency of submicroscopic chromosomal imbalances in patients with syndromic craniosynostosis detected by a combined approach of microsatellite segregation analysis, multiplex ligation-dependent probe amplification and array-based comparative genome hybridisation

We present the first comprehensive study, to our knowledge, on genomic chromosomal analysis in syndromic craniosynostosis. In total, 45 patients with craniosynostotic disorders were screened with a variety of methods...