Submicroscopic Chromosomal Deletions Research Articles

Copy number variants suggest different molecular pathways for the pathogenesis of bladder exstrophy.

Bladder exstrophy is a rare congenital malformation leaving the urinary bladder open in the midline of the abdomen at birth. There is a clear genetic background with chromosome aberrations, but so far, no consistent findings apart from 22q11-duplications detected in about 2%-3% of all patients. Some genes are implicated like the LZTR1, ISL1, CELSR3, and the WNT3 genes, but most are not explained molecularly. We have performed chromosomal microarray analysis on a cohort of 140 persons born with bladder exstrophy to look for submicroscopic chromosomal deletions and duplications. Pathogenic or possibly pathogenic microdeletions or duplications were found in 16 patients (11.4%) and further 9 with unknown significance. Two findings were in regions linked to known syndromes, two findings involved the same gene (MCC), and all other findings were unique. A closer analysis suggests a few gene networks that are involved in the pathogenesis of bladder exstrophy; the WNT-signaling pathway, the chromosome 22q11 region, the RIT2 and POU families, and involvement of the Golgi apparatus. Bladder exstrophy is a rare malformation and is reported to be associated with several chromosome aberrations. Our data suggest involvement of some specific molecular pathways.

Cytogenetics and holoprosencephaly: A chromosomal microarray study of 222 individuals with holoprosencephaly.

Holoprosencephaly (HPE), a common developmental forebrain malformation, is characterized by failure of the cerebrum to completely divide into left and right hemispheres. The etiology of HPE is heterogeneous and a number of environmental and genetic factors have been identified. Cytogenetically visible alterations occur in 25% to 45% of HPE patients and cytogenetic techniques have long been used to study copy number variants (CNVs) in this disorder. The karyotype approach initially demonstrated several recurrent chromosomal anomalies, which led to the identification of HPE-specific loci and, eventually, several major HPE genes. More recently, higher-resolution cytogenetic techniques such as subtelomeric multiplex ligation-dependent probe amplification and chromosomal microarray have been used to analyze chromosomal anomalies. By using chromosomal microarray, we sought to identify submicroscopic chromosomal deletions and duplications in patients with HPE. In an analysis of 222 individuals with HPE, a deletion or duplication was detected in 107 individuals. Of these 107 individuals, 23 (21%) had variants that were classified as pathogenic or likely pathogenic by board-certified medical geneticists. We identified multiple patients with deletions in established HPE loci as well as three patients with deletions encompassed by 6q12-q14.3, a CNV previously reported by Bendavid et al. In addition, we identified a new locus, 16p13.2 that warrants further investigation for HPE association. Incidentally, we also found a case of Potocki-Lupski syndrome, a case of Phelan-McDermid syndrome, and multiple cases of 22q11.2 deletion syndrome within our cohort. These data confirm the genetically heterogeneous nature of HPE, and also demonstrate clinical utility of chromosomal microarray in diagnosing patients affected by HPE.

Williams-Beuren Syndrome: Manifestation with Attention Deficit Hyper Activity Disorder and Voiding Dysfunction with Kidney Anomalies; Good Response to Ritalin

Williams-Beuren syndrome is a rare neurodevelopmental disease, in which mental retardation is common with this submicroscopic chromosomal deletion genetically disease. We reported a boy with Williams-Beuren syndrome and highlighted the clinical characteristics and response to treatment with Ritaline of such an individual with ADHD and voiding dysfunction. The patient was a six year-old boy with typical presentation of WBS and some psychiatric problems referred because of hyperactivity symptom and attention deficit. Children with mental retardation and WBS have a comorbidity of psychiatric disorders and kidney anomalies. Williams-Beuren syndrome can present with hyperactivity and Ritalin can improve some symptoms and voiding dysfunction. Keywords: Williams-Beuren Syndrome; Attention Deficit Disorder with Hyperactivity; Ritalin ; Methylphenidate.

Copy Number Variation in Congenital Heart Defects

Congenital heart defects (CHDs) are the most common birth defect and a major contributor to mortality, morbidity, and healthcare costs throughout the world. Although improvements in surgical advances and cardiac care have increased the lifespan of individuals with CHDs, the underlying etiologies of disease remain elusive and there have been no interventions that decrease disease incidence. Genetic, epigenetic, and environmental factors all influence the development of CHDs, and an improved understanding of causation is a prerequisite for prevention. Genetic causes of CHDs include both structural chromo- some abnormalities and single gene disorders. Copy num- ber variation (CNV), or submicroscopic chromosomal deletions or duplications, has emerged as an important contributor to congenital genetic disorders, including CHDs, and has identified critical dosage sensitive genes important for cardiac development. Common CNVs asso- ciated with highly penetrant CHDs were first identified in genomic disorders such as 22q11.2 deletion syndrome and Williams-Beuren syndrome. More recently, research investigations and clinical diagnostic testing support a role for CNVs in CHDs with extracardiac abnormalities (ECAs) as well as isolated CHD. It is estimated that CNVs con- tribute to 3-25 % of CHDs with ECAs and 3-10 % of isolated CHDs. While somewhat less clear, new evidence suggests that there is an increase in rare, large, genic CNVs in patients with CHDs, indicating that the overall CNV burden may also be an important factor in disease. As genetic testing for CHDs moves forward, CNVs will play an important role in diagnosis and gene discovery.

Insights into Common Microdeletion Syndromes

Microdeletion syndromes are due to submicroscopic chromosomal deletions and display a complex clinical and behavioral phenotype. This occurs because of an imbalance of normal dosage of genes that are present in that segment of chromosome. Many clinical characteristics of the well-known microdeletion syndromes are very specific and have been well defined. It is not always possible to detect these microdeletions by using the conventional or high resolution karyotyping. This necessitates the application of molecular cytogenetic techniques and the recent widespread usage and an in-depth knowledge of methods such as G-band karyotyping, multiples ligation-dependent probe amplification (MLPA), quantitative fluorescent PCR (QFPCR), sequencing and microarray-based comparative genomic hybridization (array CGH) had further led to identification of new microdeletions and sound description of identification of new microdeletion syndromes. This review appraises the common microdeletion syndromes focusing on the incidence rate, clinical manifestations and the mechanism involved therein.

Molecular cytogenetic evaluation of chromosomal microdeletions: the experience of a public hospital in Southern Brazil

Introduction: During the past few decades, the number of diseases identified to be caused by chromosomal microdeletions has increased quickly, bringing a new and crucial role for cytogenetics on the diagnosis of these conditions. The purpose of this study was to identify and characterize chromosomal microdeletions associated with malformation syndromes and intellectual disability. Methods: We retrospectively evaluated a consecutive series of samples from a cohort of 598 subjects with clinical symptoms of a microdeletion syndrome, including the deletion of chromosomes 4p16.3, 5p15.2, 5q35, 7q11.23, 8q24.12, 15q11.2, 16p13.3, 17p13.3, 17p11.2,2, and 22q11.2, as investigated by fluorescence in situ hybridization (FISH). Array-based comparative genomic hybridization (array-CGH) was performed on 25 samples with microdeletions. Results: A total of 598 samples were evaluated from patients whose clinical phenotypes were most indicative of 22q11.2 deletion syndrome (29.10%), Prader-Willi syndrome (23.41%), Angelman syndrome (16.89%), and Williams-Beuren syndrome (14.72%). In 142 of the samples (23.75%), a chromosomal imbalance associated with phenotypic abnormalities was found. The deletion of 7q11.23 was the most frequent (8.03%), followed by del22q11.2 (5.68%) and del15q11.2 (5%). Conclusion: Our study reinforces the idea that the effort to improve the capacity to perform molecular cytogenetic investigations associated with a qualified clinical evaluation is crucial for the detection and precise characterization of submicroscopic chromosome deletions, bringing benefits to patients, relatives, and genetic counselors. It also contributes to the continuing education of cytogeneticists and to the knowledge of chromosomal rearrangements associated with genomic disorders.

A highly specific coding system for structural chromosomal alterations

The Spanish Collaborative Study of Congenital Malformations (ECEMC, from the name in Spanish) has developed a very simple and highly specific coding system for structural chromosomal alterations. Such a coding system would be of value at present due to the dramatic increase in the diagnosis of submicroscopic chromosomal deletions and duplications through molecular techniques. In summary, our new coding system allows the characterization of: (a) the type of structural anomaly; (b) the chromosome affected; (c) if the alteration affects the short or/and the long arm, and (d) if it is a non-pure dicentric, a non-pure isochromosome, or if it affects several chromosomes. We show the distribution of 276 newborn patients with these types of chromosomal alterations using their corresponding codes according to our system. We consider that our approach may be useful not only for other registries, but also for laboratories performing these studies to store their results on case series. Therefore, the aim of this article is to describe this coding system and to offer the opportunity for this coding to be applied by others. Moreover, as this is a SYSTEM, rather than a fixed code, it can be implemented with the necessary modifications to include the specific objectives of each program.

5q12.1 deletion: Delineation of a phenotype including mental retardation and ocular defects

Array-CGH enables the detection of submicroscopic chromosomal deletions and duplications and leads to an accurate delineation of the imbalances, raising the possibility of genotype to phenotype and mapping minimal critical regions associated with particular patterns of clinical features. We report here on four patients sharing common clinical features (psychomotor retardation, coarse facies and ocular anomalies), with proximal 5q deletions identified by oligo array-CGH. The deletions range from 5.75 to 17.26-Mb in size and occurred de novo. A common 2.63-Mb region between the deletions described here can be defined in 5q12.1 (59,390,122-62,021,754 bp from 5pter, hg18) and includes 12 genes. Among them, KIF2A, which encodes a kinesin superfamily protein, is a particularly interesting candidate for the phenotype, as it suppresses the growth of axonal collateral branches and is involved in normal brain development. Ocular defects, albeit unspecific, seem to be common in the 5q12.1 deletion. Identification of additional cases of deletions involving the 5q12.1 region will allow more accurate genotype-phenotype correlations.

High Frequency Of Submicroscopic Chromosomal Deletions in Patients with Idiopathic Congenital Eye Malformations

The purpose of this study was to evaluate the clinical usefulness of the array comparative genomic hybridization technique for the genetic analysis of patients with congenital ocular malformations. Laboratory investigation. This was a multicenter study. Samples were collected from 37 patients with negative results for the routine diagnostic work-up, including normal karyotype and mutation analysis of appropriate genes. Samples from both parents also were tested. High-resolution genome-wide Agilent 244K oligoarray (Agilent Technologies) was applied. Confirmation of the results was obtained with independent techniques. Causal deletions were identified in 5 (13%) patients, affecting OTX2, FOXC1 and VPS13B (COH1), the downstream regulatory region of PAX6, and a 1,5 Megabases de novo deletion on chromosome 16. This high frequency of causal submicroscopic chromosomal aberrations in patients with congenital ocular malformation warrants implementation of array comparative genomic hybridization in the diagnostic work-up of these patients. Moreover, this screening technique broadens the phenotypic and mutational spectrum associated with genes known to cause congenital ocular malformation.

14q32/miRNA Clusters loss of heterozygosity in acute lymphoblastic leukemia is associated with up‐regulation of BCL11a

This study evaluated the loss and expression level of miRNAs 14q32 clusters in acute lymphoblastic leukemia (ALL) patients with cryptic deletions at 14q32 chromosomal band to investigate their involvement in this disease. We demonstrate that a subset of ALL cases bearing 14q32 LOH showed a down-regulation of miRNA 14q32 clusters, which is directly linked to the submicroscopic chromosomal deletion. As a consequence of miRNAs deregulation we reported an inverse correlation with the expression of their target BCL11a, a transcription factor involved in lymphoid differentiation. These results suggest that 14q32/miRNA clusters LOH may be another mechanism involved in lymphoid B cell transformation and differentiation and therefore, could be used as a diagnostic marker and therapeutic target in subsets of ALL.

Array-CGH in unclear syndromic nephropathies identifies a microdeletion in Xq22.3-q23

To investigate whether submicroscopic chromosomal deletions or duplications can be causative of unclear syndromic nephropathies, we analyzed ten patients with congenital abnormalities of the kidney and urinary tract or glomerulopathies combined with important extrarenal anomalies by whole-genome array-based comparative genomic hybridization. In a 14-year-old girl presenting with hematuria, proteinuria, mental retardation (MR), sensorineural hearing loss, dysmorphisms, and epilepsy, we detected a microdeletion in chromosome Xq22.3-q23. This deletion was verified and characterized by fluorescence in situ hybridization and multiplex ligation-dependent probe amplification analyses, found to be de novo, uniallelic and 3.3 Mb in size. Electron microscopy of a kidney biopsy showed glomerular basement membrane thinning and segmental splitting of the lamina densa compatible with Alport syndrome. Cranial magnetic resonance and diffusion tensor imaging detected a severe neuronal migration disorder with double cortex formation and pronounced reduction of the fronto-occipital tract system. Thus, in one of ten patients with unclear syndromic nephropathies we identified a previously undescribed contiguous gene syndrome at Xq22.3-q23. The microdeletion contains the X-linked Alport syndrome gene COL4A5, the MR genes FACL4 and PAK3, and parts of the X-chromosomal lissencephaly gene DCX associated with double cortex formation in girls, MR, and epilepsy. The phenotype in our patient combines features of the Alport-MR contiguous gene syndrome with lissencephaly.

Neurexin 1 (NRXN1) Deletions in Schizophrenia

Over the last 2 years, several reports have suggested that submicroscopic chromosomal deletions that disrupt the gene neurexin 1 (NRXN1) increase the risk of developing schizophrenia. In this article, we will review the evidence for this association. NRXN1 encodes NRXN1, a synaptic neuronal adhesion molecule. NRXNs are found presynaptically and are believed to interact with postsynaptic neuroligins (NLGNs) in excitatory and inhibitory synapses in the brain. The structure and possible function of NRXNs and NLGNs have recently been comprehensively reviewed.1 Vertebrate NRXNs and NLGNs are the only adhesion molecules for which a specifically synaptic function has been demonstrated.1 Current evidence suggests that NRXNs and NLGNs act transsynaptically to mediate essential signaling between presynaptic and postsynaptic specializations. Evidence from cell culture experiments and the study of mouse knockouts suggest that these molecules are required for synapse function but not for synapse formation, that they influence transsynaptic activation of synaptic transmission; and that their dysfunction impairs the properties of synapses and disrupts neural networks without completely abolishing synaptic transmission. NRXNs and NLGNs probably function by binding to each other and by interacting with intracellular proteins (most notably those with PDZ domain), but the precise mechanisms involved remain unknown.1 Whatever the mechanism and their relationship to synaptic function, it is clear that mice lacking NRXNs or NLGNs show marked deficits in synaptic transmission.1 There are 5 NLGN genes and 3 NRXN genes in humans (NRXN1 [2p16.3], NRXN2 [11q13], NRXN3 [14q31]). The 3 NRXN genes each encode an α protein and a β protein from independent promoters. NRXNs have a striking molecular diversity: the messenger RNA can be processed by alternative splicing, giving potentially thousands of distinct protein isoforms.2

The European Cytogenetic Initiative (ECI): Molecular karyotyping of 120 patients with unexplained mental retardation by Mapping 500K SNP arrays

The underlying genetic defect remains difficult to diagnose in the majority of patients suffering from mental retardation. Recent developments in genomic microarray technology now allow for the genomewide detection of submicroscopic chromosomal alterations, deletions and duplications, smaller than 100 Kb. These Copy Number Variations (de novo CNV) can be detected in approximately 15% of patients with mental retardation or syndromic diseases. Thus, their frequency is higher than chromosomal aberrations detectable by conventional karyotyping methods. Molecular karytyping technology (i.e. array-CGH, SNP-arrays) has rapidly matured and now appears ready for widespread introduction in a routine clinical setting.

Characterization of de novo microdeletions involving 17q11.2q12 identified through chromosomal comparative genomic hybridization

High-resolution array-comparative genome hybridization (CGH) is a powerful tool for detection of submicroscopic chromosome deletions and duplications. We describe two patients with mild mental retardation (MR) and de novo microdeletions of 17q11.2q12. Although the deletions did not involve the neurofibromatosis type 1 (NF1) gene, they overlap with long-range deletions of the NF1 region which have been encountered in a small group of NF1 patients with more severe MR. Given the overlap of the deletions in our two patients with the large-sized NF1 microdeletions but not with the more frequent and smaller NF1 deletions, we hypothesize that more than one gene in the 17q11.2q12 region may be involved in MR. We discuss candidate genes for MR within this interval that was precisely defined through array-CGH analysis.

Chromosomal microarray analysis (CMA) detects a large X chromosome deletion including FMR1, FMR2, and IDS in a female patient with mental retardation

Chromosomal microarray analysis (CMA) by array-based comparative genomic hybridization (CGH) is a new clinical test for the detection of well-characterized genomic disorders caused by chromosomal deletions and duplications that result in gene copy number variation (CNV). This powerful assay detects an abnormality in approximately 7-9% of patients with various clinical phenotypes, including mental retardation. We report here on the results found in a 6-year-old girl with mildly dysmorphic facies, obesity, and marked developmental delay. CMA was requested and showed a heterozygous loss in copy number with clones derived from the genomic region cytogenetically defined as Xq27.3-Xq28. This loss was not cytogenetically visible but was seen on FISH analysis with clones from the region. Further studies confirmed a loss of one copy each of the FMR1, FMR2, and IDS genes (which are mutated in Fragile X syndrome, FRAXE syndrome, and Hunter syndrome, respectively). Skewed X-inactivation has been previously reported in girls with deletions in this region and can lead to a combined Fragile X/Hunter syndrome phenotype in affected females. X-inactivation and iduronate 2-sulfatase (IDS) enzyme activity were therefore examined. X-inactivation was found to be random in the child's peripheral leukocytes, and IDS enzyme activity was approximately half of the normal value. This case demonstrates the utility of CMA both for detecting a submicroscopic chromosomal deletion and for suggesting further testing that could possibly lead to therapeutic options for patients with developmental delay.

Syndrome de Fryns. Présentation de 3 nouvelles observations

Background Fryns syndrome is a lethal autosomal recessive syndrome which includes congenital diaphragmatic hernia (CDH), pulmonary hypoplasia, cranio-facial manifestations including a coarse face, a cleft palate / lip and cloudy corneae, distal limb hypoplasia and internal malformations including central nervous system, cardiovascular, gastrointestinal, urogenital and skeletal anomalies. Cases report We report on 3 patients with Fryns syndrome in the french Indian Ocean islands (La Réunion and Mayotte islands). Pregnancies were complicated by polyhydramnios. All patients had coarse face, cloudy corneae, cleft lip / palate or high-arched palate, hypoplastic nails and brachytelephalangy. They died in the neonatal period. Two had CDH and 1 did not have a diaphragmatic involvement but a severe respiratory distress syndrome with refractory hypoxemia. Cytogenetic studies of blood lymphocytes and skin fibroblasts were normal. Conclusions Fryns syndrome is the most common multiple congenital anomaly associated with CDH. The diagnosis is strongly suggested when CHD and brachytelephalangy are associated. Phenotypes with CDH similar to Fryns syndrome have been described with cytogenetic aberrations with G-banded chromosome analysis and submicroscopic chromosome deletions detected by high resolution karyotyping or array comparative genomic hybridization (CGH). Exclusion of chromosome aberrations (including isochromosome 12p in skin fibroblasts) is needed prior to making the diagnosis of Fryns syndrome. In sporadic cases, high resolution karyotyping or array CGH should be performed for correct diagnosis and genetic counselling.

Characterization of a 5.3 Mb deletion in 15q14 by comparative genomic hybridization using a whole genome “tiling path” BAC array in a girl with heart defect, cleft palate, and developmental delay

High-resolution array CGH utilizing sets of overlapping BAC and PAC clones ("tiling path") covering the whole genome is a powerful novel tool for fast detection of submicroscopic chromosome deletions or duplications. We describe the successful application of a submegabase resolution whole genome "tiling path" BAC array to confirm and characterize a de novo interstitial deletion of chromosome 15. The deletion has a size of 5.3 Mb and is located within chromosome band 15q14, distal to the Prader-Willi/Angelman region. The affected girl had a heart defect, cleft palate, recurrent infections, and developmental delay. In contrast to GTG banding, array CGH determined the exact number of deleted genes and thus allowed the identification of candidate genes for cleft palate (GREM1, CX36, MEIS2), congenital heart defect (ACTC, GREM1, CX36, MEIS2), and mental retardation (ARHGAP11A, CHRNA7, CHRM5).

Analysis of Loss of Heterozygosity in Adult Patients with De Novo Acute Myeloid Leukemia and Normal Karyotype.

A large proportion of acute myeloid leukemia (AML) exhibits a normal karyotype in which the underlying pathomechanisms still have to be determined. Novel techniques like arrayCGH or single nucleotide polymorphism (SNP) chip analysis allow the identification and characterization of molecular rearrangements at the sub-megabase level. Recently, the application of genome-wide SNP array technology revealed frequent uniparental disomy (UPD) in approximately 20% of AML suggesting that UPD represents a nonrandom event in leukemogenesis. Uniparental disomy is acquired by somatic recombination and therefore not accessible by conventional cytogenetic methods or arrayCGH. In this study we analyzed DNA from AML patients with normal karyotype for the presence of LOH. SNP analysis was performed on the Mapping 100k GeneChip (Affymetrix, Santa Clara, CA). DNA was extracted from paired samples of 56 de novo AML patients with normal karyotype at diagnosis and in complete remission, respectively. Signal intensity data were analyzed by the GCOS GeneChip analysis software and statistical analysis of SNP call data was performed by the dChipSNP software. In addition, standard mutation screening of the genes encoding NPM1, FLT3, CEBPA, MLL and NRAS was performed in all cases. Using the 100k SNP array, a mean SNP call rate of 98.2% was reached, resulting in > 110,000 SNP genotype calls per sample. Signal intensity data analysis revealed submicroscopic chromosomal deletions resulting in hemizygosity in three patients. Patient 1 had a single 2 Mb deletion in chromosomal band 3p14.1, patient 2 had two small deletions affecting chromosome 12q23 and 12p13, the latter encompassing the ETV6 locus, and patient 3 had two small deletions within the long arm of chromosome 8. Besides these small chromosomal regions of copy number alterations, we found 4 large stretches of somatically acquired homozygosity without numeric alterations, affecting chromosome 6 (6p21 to 6 pter and 6q26 to 6 qter), chromosome 11 (11p12 to 11pter) and chromosome 13 (13q11 to 13qter). Noteworthy, in the case with uniparental disomy of chromosome 13, we could detect a homozygous FLT3-ITD mutation, supporting the findings that acquired isodisomy for chromosome 13 is common in AML, and associated with FLT3-ITD mutations (Griffiths et al., Leukemia, 2005). In summary, high resolution SNP assay technology in AML patients with normal karyotype allowed the identification of distinct chromosomal regions affected by UPD, supporting the postulated nonrandom mechanism of acquired mitotic recombination events in AML. Besides known chromosomal regions known to be affected by genomic aberrations in AML, we found additional submicroscopic chromosomal aberrations in cases with normal karyotype. Analysis of larger patient series will allow the identification of novel regions of interest harboring genes that might be involved in the pathogenesis of AML.

Targeted Array CGH

Targeted Array CGH

Development and evaluation of real competitive PCR for high-throughput quantitative applications

Real competitive PCR (rcPCR) has been shown to have high sensitivity, reproducibility, and high-throughput potential. We describe further development and evaluation of this methodology as a tool for measuring nucleic acid abundance within a cell. Modifications to the original protocol allow analysis of gene expression levels using standard conditions regardless of mRNA abundance and assay type, thereby increasing throughput and ease of reaction setup while decreasing optimization time. In addition, we have developed a software package, TITAN, to automatically analyze the results. The details are relevant to researchers performing competitive PCR using any detection technique. The effectiveness of the described developments is demonstrated using 12 genes known to have differential expression in cell lines grown under normal and hypoxic conditions. Quantitative and qualitative comparisons to real-time PCR are presented. It is also demonstrated that the technique is capable of detecting submicroscopic chromosomal DNA deletions.