Unexplained Mental Retardation Research Articles

Diagnostic Genome Profiling in Mental Retardation

Mental retardation (MR) occurs in 2%-3% of the general population. Conventional karyotyping has a resolution of 5-10 million bases and detects chromosomal alterations in approximately 5% of individuals with unexplained MR. The frequency of smaller submicroscopic chromosomal alterations in these patients is unknown. Novel molecular karyotyping methods, such as array-based comparative genomic hybridization (array CGH), can detect submicroscopic chromosome alterations at a resolution of 100 kb. In this study, 100 patients with unexplained MR were analyzed using array CGH for DNA copy-number changes by use of a novel tiling-resolution genomewide microarray containing 32,447 bacterial artificial clones. Alterations were validated by fluorescence in situ hybridization and/or multiplex ligation-dependent probe amplification, and parents were tested to determine de novo occurrence. Reproducible DNA copy-number changes were present in 97% of patients. The majority of these alterations were inherited from phenotypically normal parents, which reflects normal large-scale copy-number variation. In 10% of the patients, de novo alterations considered to be clinically relevant were found: seven deletions and three duplications. These alterations varied in size from 540 kb to 12 Mb and were scattered throughout the genome. Our results indicate that the diagnostic yield of this approach in the general population of patients with MR is at least twice as high as that of standard GTG-banded karyotyping.

Subtelomeric chromosome aberrations: still a lot to learn

Subtelomeric chromosome aberrations: still a lot to learn.Cryptic subtelomeric chromosome aberrations are a significant cause of mental retardation (MR). More than 4000 patients have been investigated, and the mean overall prevalence of subtelomeric rearrangements has been found to be 5.2%. In order to contribute to knowledge on the clinical presentation of subtelomeric rearrangements, we retrospectively studied patients with unexplained MR who had been evaluated for subtelomeric abnormalities by different fluorescence in situ hybridization (FISH) techniques. Hundred and two patients had an unexplained combination of MR with dysmorphism, congenital anomalies, and/or a positive family history and were investigated by total subtelomeric (TS) FISH (89/102), or by total painting (TP) in an obligate carrier in the case of familial MR (13/102). In 59 additional patients, a sequence-specific FISH was performed on clinical indication. In the 102 patients studied by TS or TP, six pathogenic aberrations (5.9%) were found in addition to one polymorphism. In total, eight clinically significant subtelomeric aberrations were found in the 161 index patients; four of these eight aberrations were familial. We report on the clinical presentation of all patients with an aberration and review the relevant literature. Factors complicating the interpretation of subtelomeric rearrangements are discussed, such as the occurrence of variants, clinical variability, and limited knowledge of the phenotype.

Identification of an unbalanced X-autosome translocation by array CGH in a boy with a syndromic form of chondrodysplasia punctata brachytelephalangic type

Screening of a large series of patients with unexplained mental retardation with a 1 Mb BAC array resulted in the detection of several cryptic chromosomal imbalances. In this paper we present the findings of array CGH screening in a 14-year-old boy with the brachytelephalangic type of chondrodysplasia punctata, mental retardation and obesity. On several occasions, cytogenetic analysis of this boy revealed a normal karyotype. Subsequent screening with array CGH resulted in the detection of a distal 9p trisomy and distal Xp nullisomy caused by an unbalanced X;9 translocation: 46,Y,der(X)t(X;9)(p22.32;p23). The identification of this de novo chromosomal rearrangement not only made accurate genetic counselling possible but also explained most of the phenotypic abnormalities observed in this patient. This study confirms the power of array CGH in the detection of subtle or submicroscopic chromosomal changes.

Detection and calibration of microdeletions and microduplications by array-based comparative genomic hybridization and its applicability to clinical genetic testing

AbstractPurpose: Genome-wide telomere screening by fluorescence in situ hybridization (FISH) has revealed that ≈ 6% of unexplained mental retardation is due to submicroscopic telomere imbalances. However, the use of FISH for telomere screening is labor intensive and time consuming, given that 41 telomeres are interrogated. We have evaluated the use of array-based Comparative Genomic Hybridization (aCGH) as a more efficient tool for identifying telomere rearrangements. MethodsIn this study, 102 individuals with unexplained mental retardation, with either normal or abnormal FISH results, were selected for a blinded retrospective study using aCGH. Results between the two methodologies were compared to ascertain the ability of aCGH to be used in a clinical diagnostics setting. ResultsWe detected 100% of all imbalances previously identified by FISH (n = 17) and identified two additional abnormalities, a 10q telomere duplication and an interstitial duplication of 22q11. Interphase FISH analysis verified all abnormal array results. We also demonstrated that aCGH can accurately calibrate the size of telomere imbalances by using an array with “molecular rulers” for the telomeric regions of 1p, 16p, 17p, and 22q. ConclusionThis study demonstrates that aCGH is an equivalent methodology to telomere FISH for detecting submicroscopic deletions. In addition, small duplications that are not easily visible by FISH can be accurately detected using aCGH. Because aCGH allows simultaneous interrogation of hundreds to thousands of DNA probes and is more amenable to automation, it offers an efficient and high-throughput alternative for detecting and calibrating unbalanced rearrangements, both of the telomere region, as well as other genomic locations.

Unexplained mental retardation: is brain MRI useful?

Mental retardation (MR), defined as an IQ below 70, is a frequent cause of consultation in paediatrics. To evaluate the yield of brain MRI in the diagnostic work-up of unexplained MR in children. The MRI features and clinical data of 100 patients (age 1-18 years) affected with non-progressive MR of unknown origin were compared to an age-matched control group (n=100). Two radiologists conducted an independent review of the MRI scans. Univariate and multivariate analyses showed a higher incidence of brain anomalies in the MR group than in the control group (53 vs 17, OR=5.7 [2.9-11.1]), for signal abnormalities within the periventricular white matter (OR=20.3 [2.6-155.3]), lateral ventricular dilatation (OR=15.6 [2.0-124]), mild corpus callosum abnormalities (shortness, atrophy) (OR=6.8 [1.8-25.6]) and subtle cerebellar abnormalities, including fissure enlargement (OR=5.2 [1.1-26.2]). The diagnostic value of MRI abnormalities was considered good in 5% of patients (Alexander disease n=1, diffuse cortical malformation n=1, leukomalacia n=1, vermian agenesis n=1, commissural agenesis n=1), and weak in 48% of patients, in whom non-specific abnormalities did not lead to a diagnosis. Some clinical features resulted in a significantly higher percentage of abnormal MRI scans: abnormal neurological examination (82% vs 47%, P=0.008), abnormal skull circumference (66% vs 49%, P=0.04). Motor delay was associated with cerebellar abnormalities (P=0.01). This study confirms the weak diagnostic yield of MRI in mentally retarded children. The use of a control group has enabled us to identify the neuroimaging markers frequently associated with MR. Subgrouping patients according to neuroimaging markers and clinical signs should help identify those who would benefit from molecular studies.

Brain-Thyroid-Lung syndrome: a patient with a severe multi-system disorder due to a de novo mutation in the thyroid transcription factor 1 gene

A 23-year-old man was diagnosed with pulmonary alveolar proteinosis at the age of 11 months, and primary hypothyroidism gradually developed during infancy. He had delayed developmental milestones and severe hypotonia that evolved into non-progressive chorea during childhood. He died from large cell lung carcinoma at the age of 23 years. A de novo heterozygous insertion mutation 859-860insC in the TITF-1 gene was demonstrated. TITF-1 gene mutations should be considered in paediatric and adult patients with unexplained (combinations of) chorea, mental retardation, primary hypothyroidism, and chronic lung disease. Introduction of a name for the disorder, e.g. Brain-Thyroid-Lung syndrome, would probably facilitate further recognition. Whether the TITF-1 gene mutation in this patient predisposed to the development of lung cancer remains speculative.

Biochemical and clinical characteristics of creatine deficiency syndromes.

Creatine deficiency syndromes are a newly described group of inborn errors of creatine synthesis (arginine:glycine amidinotransferase (AGAT) deficiency and guanidinoacetate methyltransferase (GAMT) deficiency) and of creatine transport (creatine transporter (CRTR) deficiency). The common clinical feature of creatine deficiency syndromes is mental retardation and epilepsy suggesting main involvement of cerebral gray matter. The typical biochemical abnormality of creatine deficiency syndromes is cerebral creatine deficiency, which is demonstrated by in vivo proton magnetic resonance spectroscopy. Measurement of guanidinoacetate in body fluids may discriminate between the GAMT (high concentration), AGAT (low concentration) and CRTR (normal concentration) deficiencies. Further biochemical characteristics include changes in creatine and creatinine concentrations in body fluids. GAMT and AGAT deficiency are treatable by oral creatine supplementation, while patients with CRTR deficiency do not respond to this type of treatment. The creatine deficiency syndromes are underdiagnosed, so their possibility should be considered in all children affected by unexplained mental retardation, seizures and speech delay.

Screening for subtelomeric rearrangements in 210 patients with unexplained mental retardation using multiplex ligation dependent probe amplification (MLPA)

Background: Subtelomeric rearrangements contribute to idiopathic mental retardation and human malformations, sometimes as distinct mental retardation syndromes. However, for most subtelomeric defects a characteristic clinical phenotype remains to be elucidated....

Chromosome subtelomeric analysis by FISH in patients with mental retardation

To assess subtelomeric chromosome anomalies in patients with idiopathic mental retardation (MR). Subtelomeric screening was performed in 46 patients with undiagnosed mental retardation. The patients were selected based on the following criteria: (1) MR with two or more of the following conditions: dysmorphic features, prenatal growth retardation, postnatal growth abnormalities, a suggestive family history; (2) chromosome karyotype at the level >450 bands being normal; (3) exclusion of other identified genetic or environmental diagnosis. Fluorescence in situ hybridization (FISH) was performed using ToTelVysion DNA probes. Abnormal findings were confirmed by FISH with a specific subtelomeric probes and family studies were carried out to determine its inheritance. Clinically significant aberrations were detected in two cases with 6q and 2q terminal microdeletion. The deletion in one case was inherited from a similarly affected father. Subtle chromosomal subtelomeric abnormalities occurred with a frequency of 7.6% in children with moderate to severe mental retardation and of 3.0% in the children with mild retardation. The results suggest that cryptic abnormalities of the ends of chromosomes might represent a significant cause of mental retardation, and screening for subtelomeric rearrangements might be warranted in children with unexplained mental retardation.

Biochemical and clinical characteristics of creatine deficiency syndromes.

Creatine deficiency syndromes are a newly described group of inborn errors of creatine synthesis (arginine:glycine amidinotransferase (AGAT) deficiency and guanidinoacetate methyltransferase (GAMT) deficiency) and of creatine transport (creatine transporter (CRTR) deficiency). The common clinical feature of creatine deficiency syndromes is mental retardation and epilepsy suggesting main involvement of cerebral gray matter. The typical biochemical abnormality of creatine deficiency syndromes is cerebral creatine deficiency, which is demonstrated by in vivo proton magnetic resonance spectroscopy. Measurement of guanidinoacetate in body fluids may discriminate between the GAMT (high concentration), AGAT (low concentration) and CRTR (normal concentration) deficiencies. Further biochemical characteristics include changes in creatine and creatinine concentrations in body fluids. GAMT and AGAT deficiency are treatable by oral creatine supplementation, while patients with CRTR deficiency do not respond to this type of treatment. The creatine deficiency syndromes are underdiagnosed, so their possibility should be considered in all children affected by unexplained mental retardation, seizures and speech delay.

Use of subtelomeric fluorescence in situ hybridization in cytogenetic diagnosis.

During the last few years there has been an increasing number of reports of chromosomal abnormalities identified by subtelomeric fluorescence in situ hybridization testing in children with unexplained mental retardation. As more children are identified with subtelomeric deletions, duplications, and cryptic unbalanced rearrangements by this testing, questions have arisen regarding the appropriate use of this new technology. A review of current knowledge regarding the clinical phenotypes seen in these patients as well as of newer information regarding the use of this new cytogenetic test in areas outside clinical genetics may help to determine which patients would benefit from its use.

MECP2 analysis in mentally retarded patients: implications for routine DNA diagnostics.

Rett syndrome (RTT) is one of the most common neurodevelopmental disorders in females. The disease is caused by mutations in the methyl-CpG-binding protein 2 gene (MECP2), and various mutations have been reported. The phenotypic spectrum in both female and male patients is diverse, ranging from very mild to congenital encephalopathy and prenatal lethality. In this study, the question was addressed as to whether implementation of systematic screening of MECP2 in patients with an unexplained mental retardation in DNA diagnostics would be reasonable, and the spectrum of phenotypes resulting from mutations in this gene was further explored. Mutational analysis of MECP2 was performed in mentally retarded female patients who were negative for FMR1 CGG repeat expansion, in male and female patients with clinical features suggestive of either Angelman or Prader-Willi syndrome without methylation defects on chromosome 15q11-q13. In the cohort of females negative for the molecular Fragile-X studies (N=92), one nonsense mutation (p.Q406X) was found. In the cohort of Angelman-negative patients (N=63), two missense mutations (p.R133C in a female patient and a mosaic p.T158M in a male patient) were found, which have been reported many times in patients with classical RTT syndrome. In the Prader-Willi-negative group (N=98), no pathogenic mutations were found. The results support testing of patients with features suggestive of Angelman syndrome, but without methylation defects on chromosome 15q11-q13 for mutations in MECP2. In the remaining patients with unexplained mental retardation, additional clinical features should determine whether analysis of MECP2 is indicated.

Submicroscopic deletion 9(q34.4) and duplication 19(p13.3): Identified by subtelomere specific FISH probes

Submicroscopic rearrangements involving chromosome ends are responsible for the unexplained mental retardation and multiple congenital anomalies observed in a number of patients. We have studied a patient with mental retardation, significant microcephaly, alopecia universalis, and other anomalies who carries an unbalanced segregant from a cryptic reciprocal translocation involving chromosomes 9 and 19. FISH studies using subtelomere specific probes revealed a derivative chromosome 9 in which the 9q subtelomeric sequence has been replaced by 19p subtelomeric sequence. As a result, the patient has partial monosomy 9q and partial trisomy 19p. The patient inherited the derivative 9 from his father, who carries a cryptic apparently balanced reciprocal translocation involving the terminal regions of 9q and 19p. This case is exceptional in that reports of rearrangements involving distal chromosome 9q and 19p are rare. This study demonstrates the utility of subtelomere specific FISH probes for detecting cryptic subtelomeric rearrangements in patients with idiopathic mental retardation and normal appearing karyotypes.

Molecular screening of FRAXA and FRAXE in Indian patients with unexplained mental retardation.

Fragile-X mental retardation is the commonest form of inherited mental retardation. We have studied 146 Indian patients (174 X chromosomes) with unexplained mental retardation by molecular methods. All study subjects were unrelated. Three of the 118 males were found to have the FMR1 full mutation. None of the patients tested were positive for the FMR2 full mutation. The Fragile X prevalence was 2.5% among males, which is lower than previously reported in Indian mentally retarded patients. Screening for Fragile X among patients with nonspecific mental retardation is important, even if there is no family history of mental retardation or typical behavioral or physical features associated with the Fragile-X phenotype. Identification of positive cases is also very important for the families, because of the high recurrence risk of the disease. Large multicenter screening programs with uniform criteria would be worthwhile to determine the prevalence of Fragile-X mental retardation in the Indian population.

Prospective screening for subtelomeric rearrangements in children with mental retardation of unknown aetiology: the Amsterdam experience

Objective: The frequency of subtelomeric rearrangements in patients with unexplained mental retardation (MR) is uncertain, as most studies have been retrospective and case retrieval may have been biased towards cases...

Automated fluorescent genotyping detects 10% of cryptic subtelomeric rearrangements in idiopathic syndromic mental retardation

Recent studies have shown that cryptic unbalanced subtelomeric rearrangements contribute to a significant proportion of idiopathic syndromic mental retardation cases. Using a fluorescent genotyping based strategy, we found a 10%...

Detection of submicroscopic aberrations in patients with unexplained mental retardation by fluorescence in situ hybridization using multiple subtelomeric probes

PurposeTo further assess the frequency of subtelomeric aberrations in a selected population and to examine the feasibility of a clinical testing. MethodsPatients were selected based on the following criteria: (1) mental retardation (IQ < 70) or developmental delay with dysmorphic features; (2) a normal karyotype at the level of resolution of 450 to 500 bands; and (3) exclusion of other possible etiologies by a full genetic assessment and relevant tests. Fluorescence in situ hybridization (FISH) was performed using multiple subtelomeric probes. Abnormal findings were confirmed by 24-color spectral karyotyping or FISH with a specific subtelomeric probe, and family studies were carried out to determine inheritance. ResultsClinically significant aberrations were detected in 6 of 150 proband patients (4%), while deletion of the 2q subtelomeric region appeared to be a common variant (6%). ConclusionsFISH with multiple subtelomeric probes is a valuable clinical test for establishing a definitive diagnosis for patients with unexplained mental retardation/developmental disorders.

Use of primed in situ labeling (PRINS) for the detection of telomeric deletions associated with mental retardation

Rearrangements involving the telomeric regions of human chromosomes are often associated with mental retardation. These rearrangements, however, are difficult to detect using conventional cytogenetic techniques. We propose the use of primed in situ (PRINS) labeling as an alternative to fluorescence in situ hybridization because it is very fast, reproducible, and simple to perform. Sixty-five children with unexplained mental retardation were studied using PRINS technology; two of them were shown to have a telomeric deletion.

Multiplex FISH telomere integrity assay identifies an unbalanced cryptic translocation der(5)t(3;5)(q27;p15.3) in a family with three mentally retarded individuals.

Cryptic rearrangements involving the terminal regions of chromosomes are suspected to be the cause of idiopathic mental retardation in a significant number of cases. This finding highlights the necessity of a primary screening test for such chromosome aberrations. Here we present a multiplex fluorescence in situ hybridization telomere integrity assay which allows the detection of submicroscopic aberrations in the telomeric regions of all chromosomes. This novel approach identified an unbalanced cryptic translocation der(5)t(3;5)(q27;p15.3) in a family with three cases of unexplained mental retardation and dysmorphic features. The symptoms of the patients represent neither the classical dup(3q)- nor cri du chat syndrome, although all affected individuals demonstrate several features of both syndromes. The identification of two balanced translocation carriers emphasizes the significance of the telomere integrity assay for genetic counseling and prenatal diagnosis.

Detection of a cryptic translocation in a family with mental retardation using FISH and telomere region-specific probes

Cryptic rearrangements involving the telomeres are thought to account for a substantial number of patients with unexplained mental retardation and multiple congenital anomalies, although the exact incidence of these rearrangements is still unclear. With the advent of chromosome-specific telomeric probes and the use of FISH (fluorescence in situ hybridization), it is now possible to identify submicroscopic rearrangements of the distal ends of chromosomes that may otherwise go undetected using conventional cytogenetic studies. We report on a 4 1/2 year-old girl with severe mental retardation and minor anomalies who inherited the unbalanced product of a cryptic translocation involving chromosomes 2 and 17 from her father. The family history was significant for early pregnancy losses, stillbirths, and mental retardation in many other family members, suggesting segregation of a familial translocation. This translocation was detected using chromosome-specific telomere FISH probes, and not visible using conventional cytogenetic methods. Collectively, this case and those previously reported clearly demonstrate the value of a systematic search for cryptic chromosome rearrangements in patients with unexplained mental retardation with previously reported normal chromosome studies; and in particular those with a family history of mental retardation, birth defects, or early pregnancy losses.