Contiguous Gene Deletion Research Articles

Quantitative analysis of copy number variants based on real-time LightCycler PCR.

Quantitative real-time PCR is PCR visualized in real time by the use of fluorescent or intercalating dyes, which are employed to measure gene expression or gene quantification including contiguous gene deletions or duplications. A simple method is described here to quantify DNA copy number from human samples.

LETM1 haploinsufficiency causes mitochondrial defects in Wolf-Hirschhorn syndrome patient cells: implications for dissecting underlying pathomechanisms in this condition

Wolf-Hirschhorn syndrome (WHS) represents an archetypical example of a contiguous gene deletion disorder – a condition comprising a complex set of developmental phenotypes with a multigenic origin. Epileptic seizures, intellectual disability, growth restriction, motor delay and hypotonia are major co-morbidities in WHS. Haploinsufficiency of LETM1, which encodes a mitochondrial inner-membrane protein functioning in ion transport, has been proposed as an underlying pathomechanism, principally for seizures but also for other core features of WHS, including growth and motor delay. Growing evidence derived from several model organisms suggests that reduced LETM1 expression is associated with some element of mitochondrial dysfunction. Surprisingly, LETM1-dependent mitochondrial functional deficits have not previously been described in cells from individuals with WHS. Here, using a unique panel of WHS-patient-derived cell lines with deletions of differing sizes, incorporating LETM1 or not, we show, for the first time, that LETM1 expression is reduced in mitochondria isolated from WHS-patient cells. Furthermore, we show that this is associated with distinct mitochondrial phenotypes, including altered intracellular [Ca2+] levels, dysfunctional mitochondrial transition-pore opening, hyperpolarization and superoxide leakage from resting mitochondria. Interestingly, we find that these phenotypes segregate with seizures in our WHS cohort. Our findings identify novel cellular phenotypes in WHS attributable to a 50% reduction in LETM1 expression level; these phenotypes could underlie and/or contribute to some of the core clinical features of this condition.

Elastin Insufficiency Predisposes Mice to Impaired Glucose Metabolism.

Williams-Beuren syndrome is the consequence of a large contiguous-gene deletion on the seventh human chromosome that includes the elastin gene. Elastin is an extracellular matrix protein responsible for the cardiovascular abnormalities associated with Williams’s syndrome, including hypertension and aortic stenosis. A high percentage of individuals with Williams’s syndrome also have impaired glucose tolerance, independent of traditional risk factors for diabetes. Here, we show that murine adipose tissue does assemble elastic fibers; however, isolated elastin insufficiency (Eln+/−) in mice does not independently influence glucose metabolism or tissue lipid accumulation. Similarly, isolated ApoE deficiency (ApoE−/−), a model of hyperlipidemia and atherosclerosis, does not impair insulin sensitivity. However, Eln+/−; ApoE−/− double mutant mice exhibit notable hyperglycemia, adipocyte hypertrophy, inflammation of adipose tissue, and ectopic lipid accumulation in liver tissue. Further, Eln+/−; ApoE−/− mutants have significant impairment of insulin sensitivity by insulin tolerance testing, independent of body weight or diet, suggesting that elastin insufficiency predisposes to metabolic disease in susceptible individuals.

Narrowing of the responsible region for severe developmental delay and autistic behaviors in WAGR syndrome down to 1.6 Mb including PAX6, WT1, and PRRG4

Interstitial deletions of the 11p13 region are known to cause WAGR (Wilms tumor, aniridia, genitourinary malformation, and "mental retardation") syndrome, a contiguous gene deletion syndrome due to haploinsufficiencies of the genes in this region, including WT1 and PAX6. Developmental delay and autistic features are major complications of this syndrome. Previously, some genes located in this region have been suggested as responsible for autistic features. In this study, we identified two patients who showed the chromosomal deletions involving 11p13. Patient 1, having an 8.6 Mb deletion of chr11p14.1p12:29,676,434-38,237,948, exhibited a phenotype typical of WAGR syndrome and had severe developmental delay and autistic behaviors. On the other hand, Patient 2 had a larger aberration region in 11p14.1-p12 which was split into two regions, that is, a 2.2-Mb region of chr11p14.1: 29,195,161-31,349,732 and a 10.5-Mb region of chr11p13p12: 32,990,627-43,492,580. As a consequence, 1.6 Mb region of the WAGR syndrome critical region was intact between the two deletions. This patient showed no symptom of WAGR syndrome and no autistic behaviors. Therefore, the region responsible for severe developmental delay and autistic features on WAGR syndrome can be narrowed down to the region remaining intact in Patient 2. Thus, the unique genotype identified in this study suggested that haploinsufficiencies of PAX6 or PRRG4 included in this region are candidate genes for severe developmental delay and autistic features characteristic of WAGR syndrome.

Microarray and FISH‐based genotype–phenotype analysis of 22 Japanese patients with Wolf–Hirschhorn syndrome

Wolf-Hirschhorn syndrome (WHS) is a contiguous gene deletion syndrome of the distal 4p chromosome, characterized by craniofacial features, growth impairment, intellectual disability, and seizures. Although genotype-phenotype correlation studies have previously been published, several important issues remain to be elucidated including seizure severity. We present detailed clinical and molecular-cytogenetic findings from a microarray and fluorescence in situ hybridization (FISH)-based genotype-phenotype analysis of 22 Japanese WHS patients, the first large non-Western series. 4p deletions were terminal in 20 patients and interstitial in two, with deletion sizes ranging from 2.06 to 29.42 Mb. The new Wolf-Hirschhorn syndrome critical region (WHSCR2) was deleted in all cases, and duplication of other chromosomal regions occurred in four. Complex mosaicism was identified in two cases: two different 4p terminal deletions; a simple 4p terminal deletion and an unbalanced translocation with the same 4p breakpoint. Seizures began in infancy in 33% (2/6) of cases with small (<6 Mb) deletions and in 86% (12/14) of cases with larger deletions (>6 Mb). Status epilepticus occurred in 17% (1/6) with small deletions and in 87% (13/15) with larger deletions. Renal hypoplasia or dysplasia and structural ocular anomalies were more prevalent in those with larger deletions. A new susceptible region for seizure occurrence is suggested between 0.76 and 1.3 Mb from 4 pter, encompassing CTBP1 and CPLX1, and distal to the previously-supposed candidate gene LETM1. The usefulness of bromide therapy for seizures and additional clinical features including hypercholesterolemia are also described.

Periventricular nodular heterotopia and transverse limb reduction defect in a woman with interstitial 11q24 deletion in the Jacobsen syndrome region

Jacobsen syndrome (JS) is a disorder of developmental delay, growth retardation, thrombocytopenia, dysmorphic features, and cardiac abnormalities, among other congenital anomalies. JS is caused by contiguous gene deletion in distal chromosome 11q, generally varying in size from 7 to 20 Mb. Periventricular nodular heterotopia (PVNH) is a neuronal migration disorder in which neurons are abnormally located in nodules along the edges of the lateral ventricles. PVNH can also be seen with other congenital anomalies, including a recurrent association with distal limb defects. Transverse limb defects have previously been reported in two patients with JS. We report on a patient with a 3.162 Mb interstitial deletion at chromosome region 11q24 overlapping the region commonly affected in JS. The patient had PVNH and a transverse limb reduction defect, with minimal typical findings of JS. This is the first report of PVNH associated with a microdeletion at chromosome 11q and may represent an expansion of the phenotypic spectrum associated with JS. This is the third report of transverse limb reduction defects in association with JS, supporting a widening of the skeletal phenotypic spectrum in JS to include more severe limb anomalies. ETS1 is proposed as a candidate gene for involvement in limb anomalies in JS.

Phenotypic and molecular characterization of 19q12q13.1 deletions: A report of five patients

A syndrome associated with 19q13.11 microdeletions has been proposed based on seven previous cases that displayed developmental delay, intellectual disability, speech disturbances, pre- and post-natal growth retardation, microcephaly, ectodermal dysplasia, and genital malformations in males. A 324-kb critical region was previously identified as the smallest region of overlap (SRO) for this syndrome. To further characterize this microdeletion syndrome, we present five patients with deletions within 19q12q13.12 identified using a whole-genome oligonucleotide microarray. Patients 1 and 2 possess deletions overlapping the SRO, and Patients 3-5 have deletions proximal to the SRO. Patients 1 and 2 share significant phenotypic overlap with previously reported cases, providing further definition of the 19q13.11 microdeletion syndrome phenotype, including the first presentation of ectrodactyly in the syndrome. Patients 3-5, whose features include developmental delay, growth retardation, and feeding problems, support the presence of dosage-sensitive genes outside the SRO that may contribute to the abnormal phenotypes observed in this syndrome. Multiple genotype-phenotype correlations outside the SRO are explored, including further validation of the deletion of WTIP as a candidate for male hypospadias observed in this syndrome. We postulate that unique patient-specific deletions within 19q12q13.1 may explain the phenotypic variability observed in this emerging contiguous gene deletion syndrome.

An unusual cause of pseudoachalasia

Alport syndrome (AS) is a hereditary disease characterized by glomerular nephropathy progressing to end-stage renal disease, frequently associated with sensorineural deafness and ocular abnormalities. Rarely, AS coexists with diffuse leiomyomatosis, a benign proliferation of smooth muscle in the gastrointestinal tract, mostly of the oesophagus, but also of the tracheobronchial tree and the female genital tract. Patients with this association have been shown to have contiguous gene deletion involving both COL4A5 and COL4A6 genes. The authors report the case of a 25-year-old man with AS and long-standing dysphagia. The patient received a renal transplant at the age of 23 because of end-stage renal disease. Clinical assessment as well as endoscopic, manometric and radiologic studies suggested the diagnosis of achalasia, which was treated by Heller's myotomy with Dor fundoplication. Postprocedure dysphagia led to an endoscopic ultrasound that showed diffuse thickening of the second layer, resulting in the hypothesis of oesophageal leiomyomatosis. The diagnosis was confirmed through histological study of endoscopic biopsies and genetic analysis.

Congenital adrenal hypoplasia, glycerol kinase deficiency and myopathy: condition requiring prompt identification. Clinical and biochemical findings in two cases

Coincident expression of otherwise unrelated inborn errors of metabolism may occur as a result of large deletions of multiple gene, referred to as the contiguous gene deletion syndrome. We describe two male infants who presented with failure to thrive and raised urinary glycerol levels, leading diagnosis of glycerol kinase deficiency, congenital adrenal hypoplasia and myopathy.These clinical diagnoses, suggest Xp21 contiguous gene deletion syndrome. The two male infants currently 48 months and 3 months old, presented with failure to thrive at 10 months and 1 month of age respectively. On evaluation for metabolic causes of poor weight gain, urine organic acids showed high levels of glycerol. Further results revealed pseudo-hypertriglyceridemia which raised the suspicion of glycerol kinase deficiency. Both infants were persistently hyponatremic and hyperkalemic, and the synacthen test showed a suboptimal cortisol peaks. Plasma renin was high with low aldosterone indicating mineralocorticoid defiency.The older male infant who presented at 10 months of age also had significant developmental delay with muscular weakness and markedly raised creatinine kinase.He was confirmed to have Duchene Muscular Dystrophy. Both the infants were started on steroid and salt replacement and monogen feeds containing medium chain triglycerides. Their weight improved with normalization of sodium & potassium levels. The above spectrum of clinical & biochemical features is consistent with a diagnosis of Xp21 contiguous gene deletion syndrome. Although rare, raised urinary glycerol and serum triglycerides leads to suspicion and allows early recognition of this condition, where prompt treatment can prevent life-threatening adrenal crises.

Lissencephaly and facial dysmorphism: is it Miller–Dieker syndrome?

An 8-month-old girl presented with developmental delay and flexor jerks for the past 2 months. Examination showed unusual facial characteristics, such as bitemporal hollowing, prominent upper lip, high arched palate and retrognathia (Fig. 1a), microcephaly, spasticity, brisk muscle stretch reflexes and flexor-infantile spasms. She had no neck-control, visual following or social smile. Magnetic resonance imaging showed lissencephaly (Fig. 1b). Genetic analysis confirmed deletion of the 17p13.3 chromosome. Electroencephalograph showed hypsarrhythmia. Adrenocoticotropic hormone or Corticotropin therapy, rehabilitation and antenatal diagnosis for future pregnancies was offered to the parents. Lissencephaly can occur either as a result of a contiguous gene deletion disorder known as Miller–Dieker syndrome or as an isolated form known as isolated lissencephaly sequence (i.e. without facial dysmorphism or other abnormalities, such as abnormal genitalia or cerebellar hypoplasia) as a result of a single gene mutation in the LIS1 or DCX gene. Miller–Dieker syndrome, as a result of chromosome-band 17p13.3 deletions, is a multiple malformation syndrome characterized by severe lissencephaly (Dobyns’ grade 2; diffuse agyria with a few shallow sulci); characteristic facial features such as high, prominent forehead, bitemporal hollowing, short nose with upturned nares, protuberant upper lip and small jaw; and severe psychomotor impairment. Early-infantile seizures, especially infantile spasms with evolution into Lennox–Gastaut syndrome occur in the majority of patients. Genetic confirmation is crucial for prognosis and prenatal diagnosis.

Deletions involving genes WHSC1 and LETM1 may be necessary, but are not sufficient to cause Wolf–Hirschhorn Syndrome

Wolf-Hirschhorn syndrome (WHS) is a complex genetic disorder caused by the loss of genomic material from the short arm of chromosome 4. Genotype-phenotype correlation studies indicated that the loss of genes within 4p16.3 is necessary for expression of the core features of the phenotype. Within this region, haploinsufficiency of the genes WHSC1 and LETM1 is thought to be a major contributor to the pathogenesis of WHS. We present clinical findings for three patients with relatively small (<400 kb) de novo interstitial deletions that overlap WHSC1 and LETM1. 3D facial analysis was performed for two of these patients. Based on our findings, we propose that hemizygosity of WHSC1 and LETM1 is associated with a clinical phenotype characterized by growth deficiency, feeding difficulties, and motor and speech delays. The deletion of additional genes nearby WHSC1 and LETM1 does not result in a marked increase in the severity of clinical features, arguing against their haploinsufficiency. The absence of seizures and typical WHS craniofacial findings in our cohort suggest that deletion of distinct or additional 4p16.3 genes is necessary for expression of these features. Altogether, these results show that although loss-of-function for WHSC1 and/or LETM1 contributes to some of the features of WHS, deletion of additional genes is required for the full expression of the phenotype, providing further support that WHS is a contiguous gene deletion disorder.

Deletion of the 5′exons of COL4A6 is not needed for the development of diffuse leiomyomatosis in patients with Alport syndrome

BackgroundAlport syndrome (AS), a hereditary type IV collagen nephropathy, is a major cause of end-stage renal disease in young people. About 85% of the cases are X-linked (ATS), due to...

Microdeletions of 3p21.31 characterized by developmental delay, distinctive features, elevated serum creatine kinase levels, and white matter involvement

Interstitial deletions of chromosome 3 are rare, and only one patient with a microdeletion of 3p21.31 has been reported to date. We identified two additional cases of patients with microdeletions of 3p21.31. The characteristic clinical features of developmental delay and distinctive facial features (including arched eyebrows, hypertelorism, epicanthus, and micrognathia) were seen both in the previously reported patient and in the two newly identified patients. In these two new cases, additional features, including elevated serum creatine kinase levels and characteristic neuroradiological features with white matter involvement, were seen. These features had not been described in the previous case in which the patient was examined during infancy, suggesting an age-dependent mechanism. The shortest region of overlap among the three deletions narrowed down the candidate genes that may be responsible for the common neurological features to the bassoon (presynaptic cytomatrix protein) gene (BSN), which has an important function in neuronal synapses. In this study, we confirmed common phenotypic features in the patients with microdeletions of 3p21.31 and identified additional features that have not been reported previously. Because the constellation of such characteristic features is quite unique, clinical manifestations of the patients with microdeletions of 3p21.31 would be clinically recognizable as a contiguous gene deletion syndrome.

Assessment of Intellectual and Visuo-Spatial Abilities in Children and Adults with Williams Syndrome

The Williams-Beuren syndrome (SWB), also known as Williams syndrome, is a contiguous gene deletion of the region 7q.11.23. The main clinical characteristics are typical faces, supravalvular aortic stenosis, failure to thrive, short stature, transient neonatal hypercalcemia, delayed language, friendly personality, hyperacusis and intellectual disability. The diagnosis of SWB is confirmed by the detection of micro deletion by different techniques of molecular cytogenetics, FISH, MLPA or polymorphic markers. This study assessed the verbal intelligence quotient (IQ) and performance and visuospatial skills in children and adults with WBS. The composed group was of 31 WBS patients (19 M and 12 F), whose ages ranged from 9 to 26 years (M 14.45 y). All patients had the diagnosis confirmed molecularly. The tests used were the WISC-III, WAIS-III and Rey-Osterrieth Complex Figure Test. The results indicated a total IQ ranged from 51 to 86 (M 63): 22 with mild intellectual disability, 4 with moderate intellectual disability, 4 borderlines and 1 below the normal media. All patients had marked visual-spatial deficits. The results suggest nonverbal reasoning, visuo-spatial perception, spatial representation, working memory, motor planning and executive functions are very affected in this group.

Williams–Beuren syndrome with brain malformation and hypertrophic cardiomyopathy

Williams–Beuren syndrome (WBS) is a multisystemic genetic disorder caused by a contiguous gene deletion at 7q11.23. We report a severely affected WBS patient with cerebral and cerebellar dysplasia as well as hypertrophic cardiomyopathy. Microarray comparative genomic hybridization (aCGH) detected a deletion on 7q11.23 expanding from RP11-614D7 to RP11-137E8, which is a typical deletion in WBS. To the best of our knowledge, this is the first case report of a WBS patient with severe congenital central nervous system anomaly and progressive hypertrophic cardiomyopathy. The relationship between the genes deleted in WBS and a CNS anomaly plus hypertrophic cardiomyopathy requires further analysis.

Cryptic Genomic Rearrangements in Three Patients with 46,XY Disorders of Sex Development

Background46,XY disorders of sex development (46,XY DSD) are genetically heterogeneous conditions. Recently, a few submicroscopic genomic rearrangements have been reported as novel genetic causes of 46,XY DSD.Methodology/Principal FindingsTo clarify the role of cryptic rearrangements in the development of 46,XY DSD, we performed array-based comparative genomic hybridization analysis for 24 genetic males with genital abnormalities. Heterozygous submicroscopic deletions were identified in three cases (cases 1–3). A ∼8.5 Mb terminal deletion at 9p24.1–24.3 was detected in case 1 that presented with complete female-type external genitalia and mental retardation; a ∼2.0 Mb interstitial deletion at 20p13 was identified in case 2 with ambiguous external genitalia and short stature; and a ∼18.0 Mb interstitial deletion at 2q31.1–32 was found in case 3 with ambiguous external genitalia, mental retardation and multiple anomalies. The genital abnormalities of case 1 could be ascribed to gonadal dysgenesis caused by haploinsufficiency of DMRT1, while those of case 3 were possibly associated with perturbed organogenesis due to a deletion of the HOXD cluster. The deletion in case 2 affected 36 genes, none of which have been previously implicated in sex development.Conclusions/SignificanceThe results indicate that cryptic genomic rearrangements constitute an important part of the molecular bases of 46,XY DSD and that submicroscopic deletions can lead to various types of 46,XY DSD that occur as components of contiguous gene deletion syndromes. Most importantly, our data provide a novel candidate locus for 46,XY DSD at 20p13.

Microdeletions of 5.5 Mb (4q13.2–q13.3) and 4.1 Mb (7p15.3–p21.1) associated with a saethre–chotzen‐like phenotype, severe intellectual disability, and autism

We observed a patient with a Saethre-Chotzen-like phenotype with severe neurological features. Saethre-Chotzen syndrome (acrocephalosyndactyly type III; SCS; OMIM #101400) is an autosomal dominant craniosynostosis syndrome characterized by craniofacial and mild limb abnormalities. The phenotypic features of chromosomal microdeletions involving the 7p21.1, where the twist homolog 1 gene (TWIST1) responsible for SCS is located, are recognized as a contiguous gene deletion syndrome with SCS and other phenotypic manifestations. In this study, we identified microdeletions in 4q13.2 and 7p21.1 in a patient with SCS and severe neurological features including developmental delay and autistic behavior. In comparison to other SCS patients with intragenic mutations or small deletions in 7p21.1, neurological features seen in this patient were extremely severe, likely modified by a concurrent deletion of 4q13.2. Both microdeletions were de novo and paternal in origin. Further information on such concurrent chromosomal deletions should be accumulated for better understanding of the mechanism.

Further delineation of genotype–phenotype correlation in homozygous 2p21 deletion syndromes: First description of patients without cystinuria

Homozygous contiguous gene deletion syndromes are rare. On 2p21, however, several overlapping homozygous gene deletion syndromes have been described, all presenting with cystinuria but otherwise distinct phenotypes. Hypotonia-cystinuria syndrome (HCS, OMIM606407) is characterized by infantile hypotonia, poor feeding, and growth hormone deficiency. Affected individuals carry homozygous deletions including the cystinuria gene SLC3A1 and the adjacent PREPL gene. Larger homozygous deletions in this region encompassing the PPM1B, SLC3A1, PREPL, and C2orf34 (CAMKMT) genes result in a more severe phenotype, the 2p21 deletion syndrome. A phenotype intermediate to HCS and the 2p21 deletion syndrome is termed atypical HCS and is caused by deletion of SLC3A1, PREPL, and C2orf34 (CAMKMT). Using high resolution SNP array molecular karyotyping we identified two siblings with a homozygous deletion of 83 kb partially encompassing the genes PREPL and C2orf34 (CAMKMT), but not the SLC3A1 gene. The affected siblings display a recognizable phenotype which is similar to atypical HCS with regard to growth failure and neuro-muscular features, but is characterized by lack of cystinuria. The patients also exhibit features which have not been reported to date such as cleft palate and genital abnormalities. In conclusion, we report the first patients with a homozygous 2p21 deletion syndrome without cystinuria and further delineate the complex genotype-phenotype correlations of homozygous microdeletion syndromes of this region.

Xp22.3 interstitial deletion: A recognizable chromosomal abnormality encompassing VCX3A and STS genes in a patient with X-linked ichthyosis and mental retardation

X-linked ichthyosis is a genetic disorder affecting the skin and caused by a deficit in the steroid sulfatase enzyme (STS), often associated with a recurrent microdeletion at Xp22.31. Most of the STS deleted patients have X-linked ichthyosis as the only clinical feature and it is believed that patients with more complex disorders including mental retardation could be present as a result of contiguous gene deletion. In fact, VCX3A gene, a member of the VCX (variable charge, X chromosome) gene family, was previously proposed as the candidate gene for X-linked non-specific mental retardation in patients with X-linked ichthyosis.We report on a boy with familial ichthyosis, dysmorphic features and moderate mental retardation with approximately 2Mb interstitial deletion on Xp22.3 involving VCX3A and STS genes.

Mutations in CERS3 Cause Autosomal Recessive Congenital Ichthyosis in Humans

Autosomal recessive congenital ichthyosis (ARCI) is a rare genetic disorder of the skin characterized by abnormal desquamation over the whole body. In this study we report four patients from three consanguineous Tunisian families with skin, eye, heart, and skeletal anomalies, who harbor a homozygous contiguous gene deletion syndrome on chromosome 15q26.3. Genome-wide SNP-genotyping revealed a homozygous region in all affected individuals, including the same microdeletion that partially affects two coding genes (ADAMTS17, CERS3) and abolishes a sequence for a long non-coding RNA (FLJ42289). Whereas mutations in ADAMTS17 have recently been identified in autosomal recessive Weill-Marchesani-like syndrome in humans and dogs presenting with ophthalmologic, cardiac, and skeletal abnormalities, no disease associations have been described for CERS3 (ceramide synthase 3) and FLJ42289 so far. However, analysis of additional patients with non-syndromic ARCI revealed a splice site mutation in CERS3 indicating that a defect in ceramide synthesis is causative for the present skin phenotype of our patients. Functional analysis of patient skin and in vitro differentiated keratinocytes demonstrated that mutations in CERS3 lead to a disturbed sphingolipid profile with reduced levels of epidermis-specific very long-chain ceramides that interferes with epidermal differentiation. Taken together, these data present a novel pathway involved in ARCI development and, moreover, provide the first evidence that CERS3 plays an essential role in human sphingolipid metabolism for the maintenance of epidermal lipid homeostasis.