Advances in molecular cytogenetics for the evaluation of mental retardation

6q13q14.3 Microdeletion Syndrome with Severe Hypotonia and Facial Dysmorphism: Genotype–Phenotype Correlation

Hypotonia is a symptom of diminished tone of skeletal muscle and can be nongenetic or a part of genetic syndrome. Hypotonia, developmental delay, and facial dysmorphism are nonspecific findings observed in many genetic syndromes mostly in chromosomal microdeletion and duplication. Here we report a case with severe hypotonia and facial dysmorphism, diagnosed with deletion at 6q13q14.3 by array comparative genomic hybridization (CGH) at very early age. Recent genetic diagnostic technologies such as array CGH may enable clinicians to diagnose chromosomal abnormalities earlier and provide appropriate medical management

Screening for Subtelomeric Rearrangements in Thai Patients with Intellectual Disabilities Using FISH and Review of Literature on Subtelomeric FISH in 15,591 Cases with Intellectual Disabilities

We utilized fluorescence in situ hybridization (FISH) to screen for subtelomeric rearrangements in 82 Thai patients with unexplained intellectual disability (ID) and detected subtelomeric rearrangements in 5 patients. Here, we reported on a patient with der(20)t(X;20)(p22.3;q13.3) and a patient with der(3)t(X;3)(p22.3;p26.3). These rearrangements have never been described elsewhere. We also reported on a patient with der(10)t(7;10)(p22.3;q26.3), of which the same rearrangement had been reported in one literature. Well-recognized syndromes were detected in two separated patients, including 4p deletion syndrome and 1p36 deletion syndrome. All patients with subtelomeric rearrangements had both ID and multiple congenital anomalies (MCA) and/or dysmorphic features (DF), except the one with der(20)t(X;20), who had ID alone. By using FISH, the detection rate of subtelomeric rearrangements in patients with both ID and MCA/DF was 8.5%, compared to 2.9% of patients with only ID. Literature review found 28 studies on the detection of subtelomeric rearrangements by FISH in patients with ID. Combining data from these studies and our study, 15,591 patients were examined and 473 patients with subtelomeric rearrangements were determined. The frequency of subtelomeric rearrangements detected by FISH in patients with ID was 3%. Terminal deletions were found in 47.7%, while unbalanced derivative chromosomes were found in 47.9% of the rearrangements.

Genotype/phenotype correlation in a female patient with 21q22.3 and 12p13.33 duplications

Many chromosomal rearrangements that lead to copy-number gains or losses have been shown to cause distinctive and recognizable clinical phenotypes. Conventional cytogenetic analysis can detect many, but not all, rearrangements depending on its power of resolution. The wide use of whole-genome array-based comparative genomic hybridization (array-CGH) techniques has allowed the detection of novel syndromes and to establish genotype-phenotype correlations by delineating at high resolution the regions involved in specific chromosomal aberrations. We report on a two and half-year-old female patient with intellectual disability and distinctive phenotypic features resulting from a de novo duplication of about 0.3 Mb in 21q22.3 associated with duplication of about 0.3 Mb in 12p13.33. The patient's chromosomal abnormalities were identified at the cytogenetic molecular level, using SNP array analysis, while GTG banding technique revealed a normal karyotype. Clinical findings of the patient were compared with Down syndrome and 12p duplication syndrome. This study suggests that an area of contiguous genes on the distal part of chromosome 21 (21q22.3) contribute to the Down syndrome phenotype and indicates that genes in the distal region of 12p (12p13.33) account for many facial characteristics and hypotonia of trisomy 12p syndrome.

Analysis of genomic aberrations using comparative genomic hybridization of metaphase chromosomes

Comparative genomic hybridization (CGH) allows the global screening of copy number aberrations within a sample. Specifically, large (>20 mb) deletions and amplifications are detected, based on utilization of test and reference (karyotypically normal) DNA. These samples are whole-genome amplified by DOP-PCR and then differentially labeled with fluorophores via nick translation. Test and reference samples are competitively hybridized to normal metaphase chromosomes. The relative amount of each DNA that binds to a chromosomal locus is indicative of the abundance of that DNA. Thus, if a chromosomal region is amplified, the test DNA will out-compete the reference DNA for binding and fluorescence will indicate amplification. Conversely, if a region is deleted, more reference DNA will bind and fluorescence will indicate a deletion. The following chapter outlines the protocols used for CGH analysis of metaphase chromosomes. These protocols include metaphase chromosome slide preparation, DNA extraction (from blood, cell lines, and microdissected formalin-fixed paraffin-embedded tissue), DOP-PCR, nick translation, in situ hybridization, and fluorescence microscopy and image analysis.

Identification of Chromosome Abnormalities in Subtelomeric Regions Using Multiplex Ligation Dependent Probe Amplification (MLPA) Technique in 100 Iranian Patients With Idiopathic Mental Retardation

Background

Mental retardation/Developmental delay (MR/DD) is present in 1 - 3% of the general population (1, 2). MR is defined as a significant impairment of both cognitive (IQ < 70) and social adaptive functions, with onset before 18 years of age.

Objectives

The purpose was to determine the results of subtelomeric screening by the Multiplex Ligation Dependent Probe Amplification (MLPA) Technique in 100 selected patients with idiopathic mental retardation (IMR) in Iran.

Materials and Methods

A number of 100 patients with IMR, normal karyotypes and negative fragile-X and metabolic tests were screened for subtelomeric abnormalities using MLPA technique.

Results

Nine of 100 patients showed subtelomeric abnormalities with at least one of the two MLPA kits. Deletion in a single region was found in 3 patients, and in two different subtelomeric regions in 1 patient. Duplication was only single and was present in 2 patients. Three patients were found to have both a deletion and duplication.MLPA testing in the parental samples of 7 patients which was accessible showed that 4 patients were de novo, 2 patients had inherited from a clinically normal mother, and one had inherited from a clinically normal father. Screening with the two MLPA kits (SALSA P036 and SALSA P070) proved abnormality in only five of the 9 patients.

Conclusions

So, the prevalence rate of abnormal subtelomeres using MLPA technique in patients with idiopathic MR in our study was 5 - 9%, the higher limit referring to the positive results of one of the two MLPA kits, and the lower limit representing the results of positive double-checking with the two MLPA kits.

Cytogenetic findings in mentally retarded Iranian patients

We conducted a cytogenetic study on 865 individuals with idiopathic mental retardation (MR) who were admitted to the Cytogenetics Department of the Iran Blood Transfusion Organisation (IBTO) Research Centre, Tehran, Iran; these were performed on blood samples using conventional staining methods. Chromosome anomalies were identified in 205 of the patients (23.6%). The majority were Down's syndrome cases (n = 138). In 33 males, a positive fragile X anomaly was found. The remainder (n = 34) had other chromosomal abnormalities including structural chromosome aberrations (n = 23), marker chromosomes with an unknown origin (n = 3), sex chromosome aneuploidy (n = 6) and trisomy 18 (n = 2). The contribution of chromosome aberrations to the cause of MR in this group of patients is discussed.

Severe intellectual disability, omphalocele, hypospadia and high blood pressure associated to a deletion at 2q22.1q22.3: case report

Background

Recently, array-comparative genomic hybridization (aCGH) platforms have significantly improved the resolution of chromosomal analysis allowing the identification of genomic copy number gains and losses smaller than 5 Mb. Here we report on a young man with unexplained severe mental retardation, autism spectrum disorder, congenital malformations comprising hypospadia and omphalocele, and episodes of high blood pressure. An ~ 6 Mb interstitial deletion that includes the causative genes is identified by oligonucleotide-based aCGH.

Results

Our index case exhibited a de novo chromosomal abnormality at 2q22 [del(2)(q22.1q22.3)dn] which was not visible at the 550 haploid band level. The deleted region includes eight genes: HNMT, SPOPL, NXPH2, LOC64702, LRP1B, KYNU, ARHGAP15 and GTDC1.

Discussion

aCGH revealed an ~ 6 Mb deletion in 2q22.1 to 2q22.3 in an as-yet unique clinical case associated with intellectual disability, congenital malformations and autism spectrum disorder. Interestingly, the deletion is co-localized with a fragile site (FRA2K), which could be involved in the formation of this chromosomal aberration. Further studies are needed to determine if deletions of 2q22.1 to 2q22.3 define a new microdeletion syndrome.

Familial 3q29 microdeletion syndrome providing further evidence of involvement of the 3q29 region in bipolar disorder

The 3q29 microdeletion syndrome is caused by a recurrent 1.6 Mb deletion of the 3q subtelomeric region. Though sometimes visible on routine microscopy, the deletion is detected more reliably using subtelomeric fluorescence in-situ hybridization (FISH) or molecular karyotyping. The clinical features associated with a 3q29 microdeletion are variable and include developmental delay, autistic features, skeletal abnormalities and dysmorphic facial features with a relatively long face, long nose with a high bridge and broad tip, short philtrum and large ears. Orofacial clefting, cardiac defects, ocular anomalies and genitourinary malformations have been reported occasionally. We report a three generation family where four individuals were confirmed to have a 3q29 microdeletion and compare their clinical features to those of previously reported patients. This family shows that the learning difficulties associated with a 3q29 deletion may be relatively mild. The history of a severe depressive disorder commencing in adulthood in the affected grandmother also supports previous studies linking the 3q29 region to bipolar disorder and links with the observation of Digilio et al. (2009) who also reported a history of depression in an adult woman with a similar deletion.

Submicroscopic subtelomeric aberrations in Chinese patients with unexplained developmental delay/mental retardation

BACKGROUND

Subtelomeric imbalance is widely accepted as related to developmental delay/mental retardation (DD/MR). Fine mapping of aberrations in gene-enriched subtelomeric regions provides essential clues for localizing critical regions, and provides a strategy for identifying new candidate genes. To date, no large-scale study has been conducted on subtelomeric aberrations in DD/MR patients in mainland China.

METHODS

This study included 451 Chinese children with moderate to severe clinically unexplained DD/MR. The subtelomere-MLPA (multiplex ligation dependent probe amplification) and Affymetrix human SNP array 6.0 were used to determine the subtelomeric copy number variations. The exact size and the breakpoint of each identified aberration were well defined.

RESULTS

The submicroscopic subtelomeric aberrations were identified in 23 patients, with a detection rate of 5.1%. 16 patients had simple deletions, 2 had simple duplications and 5 with both deletions and duplications. The deletions involved 14 different subtelomeric regions (1p, 2p, 4p, 6p, 7p, 7q, 8p, 9p, 10p, 11q, 14q, 15q, 16p and 22q), and duplications involved 7 subtelomeric regions (3q, 4p, 6q, 7p, 8p, 12p and 22q). Of all the subtelomeric aberrations found in Chinese subjects, the most common was 4p16.3 deletion. The sizes of the deletions varied from 0.6 Mb to 12 Mb, with 5-143 genes inside. Duplicated regions were 0.26 Mb to 11 Mb, with 6-202 genes inside. In this study, four deleted subtelomeric regions and one duplicated region were smaller than any other previously reported, specifically the deletions in 11q25, 8p23.3, 7q36.3, 14q32.33, and the duplication in 22q13. Candidate genes inside each region were proposed.

CONCLUSIONS

Submicroscopic subtelomeric aberrations were detected in 5.1% of Chinese children with clinically unexplained DD/MR. Four deleted subtelomeric regions and one duplicated region found in this study were smaller than any previously reported, which will be helpful for further defining the candidate dosage sensitive gene associated with DD/MR.

Analysis of genomic aberrations using comparative genomic hybridization of metaphase chromosomes

Comparative genomic hybridization (CGH) allows the global screening of copy number aberrations within a sample. Specifically, large (>20 mb) deletions and amplifications are detected, which are likely to indicate regions harboring tumor suppressor and oncogenes. CGH involves the extraction of test and reference (karyotypically normal) DNA. These samples are whole-genome amplified by DOP-PCR and then differentially labeled with fluorophores via nick translation. Test and reference samples are competitively hybridized to normal metaphase chromosomes. The relative amount of each DNA that binds to a chromosomal locus is indicative of the abundance of that DNA. Thus, if a chromosomal region is amplified, the test DNA will outcompete the reference DNA for binding and fluorescence will indicate amplification. Conversely, if a region is deleted, more reference DNA will bind and fluorescence will indicate a deletion. The following chapter outlines the protocols used for CGH analysis of metaphase chromosomes. These protocols include metaphase chromosome slide preparation, DNA extraction (from blood, cell lines and microdissected formalin-fixed paraffin-embedded tissue), DOP-PCR, nick translation, in situ hybridization and fluorescence microscopy and image analysis.

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.

Multiplex PCR/liquid chromatography assay for screening of subtelomeric rearrangements

In idiopathic or nonspecific mental retardation, the overall rate of cryptic subtelomeric rearrangements is estimated to be about 5%. Development of cost-effective screening for subtelomeric deletions would help clinical geneticists to make specific diagnoses in children with idiopathic mental retardation. Current screening modalities include fluorescence in situ hybridization (FISH) using subtelomeric probes and PCR-based quantitative analyses. Reductions in the cost and turnaround time will make the complete screening of subtelomeric rearrangements more widely used in clinical settings. Recently, a versatile method, called the multiplex PCR/liquid chromatography assay (MP/LC), was developed to assess copy numbers in this assay. Multiple genomic regions are amplified using unlabeled primers, then separated by ion-pair reversed-phase high-performance liquid chromatography. In the present study, we developed an MP/LC-based subtelomeric screening system that involves 21 multiple reactions and validated the protocol by analyzing 16 publicly available cell lines with known cytogenetic abnormalities involving at least one subtelomere per patient. To confirm the validity of the MP/LC method, we analyzed these cell lines concurrently with array-based comparative genomic hybridization (array-CGH), which gives higher resolution than the conventional G-banding technique. Among those 16 samples, the results from MP/LC and array-CGH agreed with each other perfectly. In 2 of the 16 samples, MP/LC correctly revealed subtelomeric duplications that were detected by array-CGH but were undetected by conventional cytogenetics, demonstrating the sensitivity of the MP/LC assay. This system is expected to be useful for making specific diagnoses and in genetic counseling for children with idiopathic mental retardation, a sizable fraction of whom have subtelomeric rearrangements.

Dedicator of cytokinesis 8 is disrupted in two patients with mental retardation and developmental disabilities

We have identified disruptions in the dedicator of cytokinesis 8 gene, DOCK8, in two unrelated patients with mental retardation (MR). In one patient, a male with MR and no speech, we mapped a genomic deletion of approximately 230 kb in subtelomeric 9p. In the second patient, a female with mental retardation and ectodermal dysplasia and a balanced translocation, t(X;9) (q13.1;p24), we mapped the 9p24 breakpoint to a region overlapping with the centromeric end of the 230-kb subtelomeric deletion. We characterized the DOCK8 gene from the critical 9p deletion region and determined that the longest isoform of the DOCK8 gene is truncated in both patients. Furthermore, the DOCK8 gene is expressed in several human tissues, including adult and fetal brain. Recently, a role for DOCK8 in processes that affect the organization of filamentous actin has been suggested. Several genes influencing the actin cytoskeleton have been implicated in human cognitive function and thus a possibility exists that the rare mutations in the DOCK8 gene may contribute to some cases of autosomal dominant mental retardation.

Array-based comparative genomic hybridization for investigating chromosomal abnormalities in patients with learning disability: Systematic review meta-analysis of diagnostic and false-positive yields

PURPOSE

Array-based comparative genomic hybridization is increasingly being used in patients with learning disability, in addition to existing cytogenetic techniques. This paper reports the results of an evaluation of this emerging technology and discusses the challenges faced in conducting the evaluation.

METHODS

Systematic review and meta-analysis of studies investigating patients with learning disability and dysmorphic features in whom conventional cytogenetic analysis has proven negative. Conventional indices of clinical validity could not be calculated, and we use an alternative, based on the extent to which array-based comparative genomic hybridization met its clinical objectives.

RESULTS

Seven studies (462 patients) were included. The overall diagnostic yield of causal abnormalities was 13% (95% confidence interval: 10-17%; heterogeneity test statistic I = 0%), and the overall number needed to test was eight (95% confidence interval: 6-10). The false-positive yield of noncausal abnormalities ranged from 5% to 67%, although this range was only 5% to 10% in six of the studies.

CONCLUSION

Although promising, there is insufficient evidence to recommend introduction of this test into routine clinical practice. A number of important technical questions need answering, such as optimal array resolution, which clones to include, and the most appropriate platforms. A thorough assessment of clinical utility and cost-effectiveness compared with existing tests is also required.

Partial tandem duplication ofGRIA3 in a male with mental retardation

The genetic factors underlying mental retardation (MR) are very heterogeneous. Recent studies have identified a number of genes involved in MR, several of which lie on the X-chromosome, but the current understanding of the monogenic causes of MR is far from complete. Investigation of chromosomal rearrangements in patients with MR has proven particularly informative in the search for novel genes. Using array-based comparative genomic hybridization analysis, we identified a small copy number gain at Xq25, which was undetectable by conventional G-band analysis, in a boy with unexplained MR. Further characterization revealed a partial tandem duplication of GRIA3, an alteration also present on one allele in his mother. RT-PCR analysis of lymphoblastoid cell RNA revealed remarkably reduced GRIA3 transcript levels in the patient. The mother, whose cognitive level is normal, also demonstrated remarkably reduced GRIA3 transcript levels in lymphoblastoid cells, and X-chromosome inactivation (XCI) was completely skewed in her peripheral lymphocytes. It is possible that XCI in the brain is not completely skewed and that GRIA3 expression from the normal allele may account for the mother's normal cognitive function. Taken together with previous findings of GRIA3 disruptions in the patients with MR, our study strengthens the idea that GRIA3 is a candidate gene for X-linked MR and that severely reduced GRIA3 expression results in MR.

Additional chromosomal abnormalities in patients with a previously detected abnormal karyotype, mental retardation, and dysmorphic features

The detection of chromosomal abnormalities in patients with mental retardation (MR) and dysmorphic features increases with improvements of molecular cytogenetic methods. We report on six patients referred for detailed characterization of chromosomal abnormalities (four translocations, one inversion, one deletion) detected by conventional cytogenetics, in whom metaphase CGH revealed imbalances not involved in the initially detected rearrangements. The detected abnormalities were validated by real-time PCR. Parents were investigated by CGH in four cases. The genomic screening revealed interstitial deletions of 2q33.2-q34, 3p21, 4q12-q13.1, 6q25, 13q22.2-q31.1, and 14q12. The estimated minimum sizes of the deletions ranged from 2.65 to 9.27 Mb. The CGH assay did not reveal imbalances that colocalized with the breakpoints of the inversion or the translocations. The deletion of 6q included ESR1, in which polymorphisms are associated with variation of adult height. FOXG1B, known to be involved in cortical development, was located in the 14q deletion. The results illustrate that whole-genome molecular cytogenetic analysis of phenotypically affected patients with abnormal conventional karyotypes may detect inapparent molecular cytogenetic abnormalities in patients with microscopic chromosomal abnormalities and that these data provide additional information of clinical importance.

Brief Report: Visual-Spatial Deficit in a 16-year-old Girl with Maternally Derived Duplication of Proximal 15q

Duplications of chromosome 15 may be one of the most common single genetic causes of autism spectrum disorders (ASD), aside from fragile X. Most of the cases are associated with maternally derived interstitial duplication involving 15q11-13. This case report describes a female proband with a maternally derived interstitial duplication of proximal 15q. She did not exhibit any symptoms of ASD apart from some developmental delay. By adolescence, she showed mild dysmorphism, a discrepant profile on the Wechsler Intelligence Scale for Children (Verbal IQ = 87; Performance IQ = 65) and a major deficit in visual-spatial abilities affecting fine motor skills, mathematical reasoning, visual memory and some global reading tasks. This is one of the first reports of a child with a maternal duplication who exhibits a visual-spatial deficit without ASD.

Spectral karyotyping of human, mouse, rat and ape chromosomes--applications for genetic diagnostics and research

Spectral karyotyping (SKY) is a widely used methodology to identify genetic aberrations. Multicolor fluorescence in situ hybridization using chromosome painting probes in individual colors for all metaphase chromosomes at once is combined with a unique spectral measurement and analysis system to automatically classify normal and aberrant chromosomes. Based on countless studies and investigations in many laboratories worldwide, numerous new chromosome translocations and other aberrations have been identified in clinical and tumor cytogenetics. Thus, gene identification studies have been facilitated resulting in the dissection of tumor development and progression. For example, different translocation partners of the TEL/ETV6 transcription factor that is specially required for hematopoiesis within the bone marrow were identified. Also, the correct classification of complex karyotypes of solid tumors supports the prognostication of cancer patients. Important accomplishments for patients with genetic diseases, leukemias and lymphomas, mesenchymal tumors and solid cancers are summarized and exemplified. Furthermore, studies of disease mechanisms such as centromeric DNA breakage, DNA double strand break repair, telomere shortening and radiation-induced neoplastic transformation have been accompanied by SKY analyses. Besides the hybridization of human chromosomes, mouse karyotyping has also contributed to the comprehensive characterization of mouse models of human disease and for gene therapy studies.

Subtelomeric trisomy 21q: a new benign chromosomal variant

The diagnosis of a subtelomeric rearrangement has immediate impact on counseling, particularly in the case of familial rearrangements. However, the existence of subtelomeric imbalances with absent phenotypic effects may hamper genetic counseling, particularly when the rearrangement has not been previously described. We report on a new subtelomeric polymorphism, consisting of a familial subtelomeric rearrangement of chromosome 19 resulting in distal trisomy for 21q, detected in a child with Angelman Syndrome (AS) due to an UBE3A mutation. This report shows that new, previously unknown, benign subtelomeric variants may complicate the correct clinical diagnosis.

Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation

The cause of mental retardation in one-third to one-half of all affected individuals is unknown. Microscopically detectable chromosomal abnormalities are the most frequently recognized cause, but gain or loss of chromosomal segments that are too small to be seen by conventional cytogenetic analysis has been found to be another important cause. Array-based methods offer a practical means of performing a high-resolution survey of the entire genome for submicroscopic copy-number variants. We studied 100 children with idiopathic mental retardation and normal results of standard chromosomal analysis, by use of whole-genome sampling analysis with Affymetrix GeneChip Human Mapping 100K arrays. We found de novo deletions as small as 178 kb in eight cases, de novo duplications as small as 1.1 Mb in two cases, and unsuspected mosaic trisomy 9 in another case. This technology can detect at least twice as many potentially pathogenic de novo copy-number variants as conventional cytogenetic analysis can in people with mental retardation.

[Autism: genetics]

Autism is a strongly genetic disorder, with an estimated heritability of greater than 90%. A combination of phenotypic heterogeneity and the likely involvement of multiple interacting loci have hampered efforts at gene discovery. As a consequence, the genetic etiology of the spectrum of autism related disorders remains largely unknown. Over the past several years, the convergence of rapidly advancing genomic technologies, the completion of the human genome project, and increasingly successful collaborative efforts to increase the number of patients available for study have led to the first solid clues to the biological origins of these disorders. This paper will review the literature to date summarizing the results of linkage, cytogenetic, and candidate gene studies with a focus on recent progress. In addition, promising avenues for future research are considered.

The yield of subtelomeric FISH analysis in the evaluation of autistic spectrum disorders

To assess the frequency of cryptic subtelomeric rearrangements in children and adolescents with autism spectrum disorders, blood samples were studied using a complete set of subtelomeric FISH probes in 72 children with autism spectrum disorders. All children had normal high resolution karyotype, DNA fra-X analysis, brain MRI, metabolic work-up, and physical/neurological examination. Subtelomeric analysis did not detect abnormalities in any of the subjects, suggesting the uselessness of such investigations in individuals with primary autism spectrum disorders.

Etiologic yield of autistic spectrum disorders: A prospective study

Studies addressing etiologic yield in childhood developmental disabilities have mainly looked at individuals with developmental delay/mental retardation. The few studies addressing the question of etiologic yield in patients with pervasive developmental disorders (PDDs) had a major drawback, in that the enrolled subjects were diagnosed as having the autistic spectrum disorders based only on history and clinical examination, and/or on unspecified instruments. In addition, only some of these patients underwent a complete laboratory evaluation. To investigate the etiologic yield of PDDs, we undertook a large prospective study on subjects selected according to very strict criteria and diagnosed as having PDD based on the present "gold standard" (ADI-R and ADOS-G), and a clinical diagnosis made by a child psychiatrist. Eighty-five (85) patients with PDD and their first degree relatives participated in this study. These patients were selected from a sample of 236 subjects who had received a clinical diagnosis of PDD at the Stella Maris Institute between March 2002 and 2005. Selection criteria for entering the study were: (1) a diagnosis of PDD (with exclusion of the Rett syndrome) confirmed after the administration of the ADI-R (autism diagnostic interview-revised) and the ADOS-G (autism diagnostic observation schedule-generic). In addition, a clinical diagnosis was made by the child psychiatrist, on the basis of presence or absence of DSM-IV symptoms of autism; (2) chronological age between 4 and 18 years; (3) IQ>30; (4) availability of both biologic parents. Patients, 65/85 (76.5%), had autism, 18/85 (21.2%) had PDD-NOS, and the remaining 2/85 (2.3%) had Asperger syndrome. Ages varied between 4 years 2 months and 12 years 5 months (mean 7.6 years), and there was a marked male preponderance (68/85). All subjects underwent various laboratory studies and neuroimaging. With respect to possible etiologic determination, a detailed history and physical examination in this group of patients with PDD was informative in 10.5% (9/85). HRB karyotype was diagnostic in one, and molecular fragile X studies in one child. Brain MRI was informative in two children (2.3%) with relative macrocrania but no neurological features; and EEG was helpful in one child, identifying a Landau-Kleffner disorder. Audiometry and brainstem auditory evoked potentials (BAEPs) showed a bilateral sensorineural loss in another child. Metabolic evaluation gave normal results in all subjects. The results suggest an evaluation paradigm with reference to etiologic determination for individuals with PDDs that does not presently justify metabolic or neuroimaging on a screening basis. Recurrence risk, treatment implications, and significant and long-lasting emotional relief for the parents suggest that serious consideration be given to clinical genetic examination, genetic testing, EEG study (during wakefulness and sleep), and audiometry, despite a relatively low yield.

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.

Chromosome analysis: what and when to request

Chromosome abnormalities have long been recognised as an important cause of learning disability and multiple malformation syndromes; 0.8% of live born infants have numerical or structural chromosomal anomalies resulting in an abnormal phenotype. The identification of such anomalies is important, both clinically and for accurate genetic counselling. Recently, the human genome sequence has enabled higher resolution screens for chromosome anomalies using both molecular cytogenetic and array based techniques. This review suggests a simple algorithm for the targeted use of diagnostic cytogenetic tools in specific patient groups commonly seen in paediatric practice.

Addressing health disparities through promoting equity for individuals with intellectual disability

Intellectual disabilities (ID) are conditions originating before the age of 18 that result in significant limitations in intellectual functioning and conceptual, social and practical adaptive skills. IDs affect 1 to 3% of the population. Persons with ID are more likely to have physical disabilities, mental health problems, hearing impairments, vision impairments and communication disorders. These co-existing disabilities, combined with the limitations in intellectual functioning and in adaptive behaviours, make this group of Canadians particularly vulnerable to health disparities. The purpose of this synthesis article is to explore potential contributory factors to health vulnerabilities faced by persons with ID, reveal the extent and nature of health disparities in this population, and examine initiatives to address such differences. The review indicates that persons with ID fare worse than the general population on a number of key health indicators. The factors leading to vulnerability are numerous and complex. They include the way society has viewed ID, the etiology of ID, health damaging behaviours, exposure to unhealthy environments, health-related mobility and inadequate access to essential health and other basic services. For persons with ID there are important disparities in access to care that are difficult to disentangle from discriminatory values and practice. Policy-makers in the United States, England and Scotland have recently begun to address these issues. It is recommended that a clear vision for health policy and strategies be created to address health disparities faced by persons with ID in Canada.

X chromosome array-CGH for the identification of novel X-linked mental retardation genes

Array-CGH technology for the detection of submicroscopic copy number changes in the genome has recently been developed for the identification of novel disease-associated genes. It has been estimated that submicroscopic genomic deletions or duplications will be present in 5-7% of patients with idiopathic mental retardation (MR). Since 30% more males than females are diagnosed with MR, we have developed a full coverage X chromosome array-CGH with a theoretical resolution of 82 kb, for the detection of copy number alterations in patients with suspected X-linked mental retardation (XLMR). First, we have validated the genomic location of X-derived clones through male versus female hybridisations. Next, we validated our array for efficient and reproducible detection of known alterations in XLMR patients. In all cases, we were able to detect the deletions and duplications in males as well as females. Due to the high resolution of our X-array, the boundaries of the genomic aberrations could clearly be identified making genotype-phenotype studies more reliable. Here, we describe the production and validation of a full coverage X-array-CGH, which will allow for fast and easy screening of submicroscopic copy number alterations in XLMR patients with the aim to identify novel MR genes or mechanisms involved in a deranged cognitive development.

Detection of chromosomal abnormalities by comparative genomic hybridization

PURPOSE OF REVIEW

Comparative genomic hybridization (CGH) is a modified in-situ hybridization technique. In this type of analysis, two differentially labeled genomic DNAs (study and reference) are cohybridized to normal metaphase spreads or to microarray. Chromosomal locations of copy number changes in the DNA segments of the study genome are revealed by a variable fluorescence intensity ratio along each target chromosome. Thus, CGH allows detection and mapping of DNA sequence copy differences between two genomes in a single experiment.

RECENT FINDINGS

Since its development, comparative genomic hybridization has been applied mostly as a research tool in the field of cancer cytogenetics to identify genetic changes in many previously unknown regions. It is also a powerful tool for detection and identification of unbalanced chromosomal abnormalities in prenatal, postnatal and preimplantation diagnostics.

SUMMARY

The development of comparative genomic hybridization and increase in resolution analysis by using the microarray-based technique offer new information on chromosomal pathologies and thus better management of patients.

Specific Genetic Disorders and Autism: Clinical Contribution Towards their Identification

Autism is a heterogeneous disorder that can reveal a specific genetic disease. This paper describes several genetic diseases consistently associated with autism (fragile X, tuberous sclerosis, Angelman syndrome, duplication of 15q11-q13, Down syndrome, San Filippo syndrome, MECP2 related disorders, phenylketonuria, Smith-Magenis syndrome, 22q13 deletion, adenylosuccinate lyase deficiency, Cohen syndrome, and Smith-Lemli-Opitz syndrome) and proposes a consensual and economic diagnostic strategy to help practitioners to identify them. A rigorous initial clinical screening is presented to avoid unnecessary laboratory and imaging studies. Regarding psychiatric nosography, the concept of "syndromal autism"--autism associated with other clinical signs should be promoted because it may help to distinguish patients who warrant a multidisciplinary approach and further investigation.

4p terminal deletion and 11p subtelomeric duplication detected by genomic microarray in a patient with Wolf-Hirschhorn syndrome and an atypical phenotype

We report a de novo cryptic 11p duplication found by genomic microarray with a cytogenetically detected 4p deletion. Terminal 4p deletions cause Wolf-Hirschhorn syndrome, but the phenotype probably was modified by the paternally derived 11p duplication. This emphasizes the clinical utility of genomic microarray.

New trends in chromosomal investigation in children with cardiovascular malformations

We investigated a group of 376 children, seen over a period of 7 years with different types of congenital cardiovascular defects, to assess the presence of chromosomal aberrations. The diagnostic approach, achieved in 3 consecutive steps, revealed conventional chromosomal aberrations in 30 of the patients (8%) excluding trisomies 13, 18, 21. Fluorescence in situ hybridisation for microdeletions showed 51 microdeletions (15%), with 43 patients having deletions of 22q11.2, 7 patients with deletion of 7q11.23, and 1 patient with deletion of 4p16.3. In 23 patients with additional clinical abnormalities, we carried out a subtelomeric screening. This revealed, in two cases (9%), different subtelomeric aberrations, namely deletions of 1p and of 1q. Thus, subtelomeric screening proved to be a very valuable as a new diagnostic approach. Our approach to genetic investigation in three phases makes it possible to detect a high rate of pathologic karyotypes in patients with congenital cardiovascular malformations, thus guaranteeing more effective genetic counselling of the families, and a more precise prognosis for the patient.

Neuropsychiatric syndromes in adults with intellectual disability: issues in assessment and treatment

The purpose of this article is to present a survey of important neuropsychiatric issues and recent findings regarding the evaluation and treatment of neuropsychiatric symptoms and syndromes in patients with intellectual disability (ID). The cause of ID, environmental or genetic, can be determined in few patients. Etiology is idiopathic in most patients. ID and psychiatric illness are not mutually exclusive; individuals with ID have increased rates of psychiatric illness. Although recognition of significant axis I psychopathology is important, not all challenging behaviors in persons with ID will have a clear axis I diagnosis. Psychologic, behavioral, and environmental treatments are appropriate measures, but pharmacotherapy often is needed. Our experience has shown us that the more severe, disruptive, and dangerous the behavior, the stronger the indication for empirical drug treatment trials. Community-based models of support with neuropsychiatric intervention can be a potent therapeutic combination in the management of challenging behaviors in individuals with ID.

[The future of cytogenetics after the sequencing of the human genome]

Since the fundamental discovery in 1956 that normal human cell contain 46 chromosomes, human cytogenetics has been transformed by technological advance that have greatly improved resolution and sensibility, first with the introduction of banding and high resolution technologies and, latter, with the fluorescent in situ hybridization (FISH). These latest technique allow to detect extremely subtle alterations in chromosome constitution and had made possible to evaluate the karyotype of non-dividing cells. The latest transformation of cytogenetics came with the technique of comparative genome hybridization which allows genome-wide screens for the loss or gain of chromosomal material in test samples relative to normal controls. Nevertheless, only the conventional cytogenetics techniques are able to detect balanced chromosomals rearrangements particularly in phenotypically abnormal patients in whom candidate genes may be disrupted or functionally altered. Thus, Cytogenetics will still play a central role in our understanding of the molecular basis of human hereditary diseases.

Dysmorphology diagnosis

A patient with multiple malformations poses a diagnostic dilemma to the pediatrician. There are thousands of malformation syndromes described and diagnosis of a syndrome appears a daunting task. An approach to diagnosis of a malformation syndrome is presented. Relevant details in the history and examination, important investigations, the process of differential diagnosis, and search engines used to aid in diagnosis of a malformation syndrome are described.

Rapid detection of subtelomeric deletion/duplication by novel real-time quantitative PCR using SYBR-green dye

Telomeric chromosome rearrangements may cause mental retardation, congenital anomalies, miscarriages, and hematological malignancies. Automated detection of subtle deletions and duplications involving telomeres is essential for high-throughput screening procedures, but impractical when conventional cytogenetic methods are used. Novel real-time PCR quantitative genotyping of subtelomeric amplicons using SYBR-green dye allows high-resolution screening of single copy number gains and losses by their relative quantification against a diploid genome. To assess the applicability of the technique in the screening and diagnosis of subtelomeric imbalances, we describe here a blinded study in which DNA from 20 negative controls and 20 patients with known unbalanced cytogenetic abnormalities involving at least one or more telomeres were analyzed using a novel human subtelomere-specific primer set, producing altogether 86 amplicons, in the SYBR-green I-based real-time quantitative PCR screening approach. Screening of the DNA samples from 20 unrelated controls for copy number polymorphism do not detect any polymorphism in the set of amplicons, but single-copy-number gains and losses were accurately detected by quantitative PCR in all patients, except the copy number alterations of the subtelomeric p-arms of the acrocentric chromosomes in two cases. Furthermore, a detailed mapping of the deletion/translocation breakpoint was demonstrated in two cases by novel real-time PCR "primer-jumping." Because of the simplicity and flexibility of the SYBR-green I-based real-time detection, the primer-set can easily be extended, either to perform further detailed molecular characterization of breakpoints or to include amplicons for the detection and/or analysis of syndromes that are associated with genomic copy number alterations, e.g., deletion/duplication-syndromes and malignant cancers.

A comparison of different metaphase CGH methods for the detection of cryptic chromosome aberrations of defined size

An increasing body of evidence indicates that submicroscopic gene dose alterations may cause mental impairment and malformations. During the last decade, comparative genomic hybridization (CGH) has become a useful tool in the detection and mapping of chromosome aberrations. Modifications of CGH with increased resolution down to 3-5 Mb have been reported and CGH is now offered as a diagnostic procedure in the evaluation of patients with idiopathic mental retardation (MR). In order to increase the resolution, we modified the CGH protocol using freshly prepared high-quality metaphase slides and chemical labeling, and tested the method on a set of patients with well-defined submicroscopic chromosome abnormalities with confirmed size 1.3-20.5 Mb. Subsequently, a completely blinded test was performed to compare the performance of the chemical labeling CGH to the commercially available HR-CGH. Using the two different CGH methods, we were able to detect chromosome imbalances down to 2-3 Mb approximately. The HR-CGH method detected all aberrations >6 Mb and a few smaller, while the modified CGH method was able to detect all but three aberrations >1.8 Mb. The modified CGH method was superior in the detection of terminal imbalances, while the HR-CGH software was more successful in the detection of imbalances located very close to the centromeric regions. In conclusion, the resolution of metaphase CGH may be as high as 2-3 Mb but is most likely depending on the chromosomal region involved, a clear limitation when used as a screening method for chromosome aberrations in patients with idiopathic MR.

Prospective study comparing HR-CGH and subtelomeric FISH for investigation of individuals with mental retardation and dysmorphic features and an update of a study using only HR-CGH

In a prospective study 94 individuals with mental retardation (MR) and dysmorphic features with normal conventional karyotypes were investigated by both subtelomeric FISH and high resolution CGH (HR-CGH) in order to compare the potential of the two techniques in this application. A total of 9.6% abnormalities were found with HR-CGH and subtelomeric FISH, with HR-CGH detecting 8.5% (95% CI: 4.4-15.9) and FISH 3.2% (95% CI: 1.2-9.0). Thus, the techniques complemented each other, however, the diagnostic yield appeared higher of HR-CGH than of subtelomeric FISH, as most aberrations were interstitial. Another 330 individuals with MR and dysmorphic features with normal conventional karyotypes were investigated by HR-CGH on a routine basis. When added to the analyses of the prospective study a total of 51/424 (12%; 95% CI: 9.3-15.5) abnormalities were found, of which the majority were interstitial. We conclude that HR-CGH is well suited for routine screening for cryptic chromosomal imbalances in patients with MR and dysmorphic features. It is likely that the use of the technique in this application will reinforce the effort of defining new syndromes.

Sox3 is required for gonadal function, but not sex determination, in males and females

Sox3 is expressed in developing gonads and in the brain. Evolutionary evidence suggests that the X-chromosomal Sox3 gene may be the ancestral precursor of Sry, a sex-determining gene, and Sox3 has been proposed to play a role in sex determination. However, patients with mutations in SOX3 exhibit normal gonadal determination but are mentally retarded and have short stature secondary to growth hormone (GH) deficiency. We used Cre-LoxP targeted mutagenesis to delete Sox3 from mice. Null mice of both sexes had no overt behavioral deficits and exhibited normal GH gene expression. Low body weight was observed for some mice; overgrowth and misalignment of the front teeth was observed consistently. Female Sox3 null mice (-/-) developed ovaries but had excess follicular atresia, ovulation of defective oocytes, and severely reduced fertility. Pituitary (luteinizing hormone and follicle-stimulating hormone) and uterine functions were normal in females. Hemizygous male null mice (-/Y) developed testes but were hypogonadal. Testis weight was reduced by 42%, and there was extensive Sertoli cell vacuolization, loss of germ cells, reduced sperm counts, and disruption of the seminiferous tubules. We conclude that Sox3 is not required for gonadal determination but is important for normal oocyte development and male testis differentiation and gametogenesis.

Diagnostic evaluation of developmental delay/mental retardation: An overview

Mental retardation (MR) is one of the few clinically important disorders for which the etiopathogenesis is still poorly understood. It is a condition of great concern for public health and society. MR is currently defined as a significant impairment of cognitive and adaptive functions, with onset before age 18 years. It may become evident during infancy or early childhood as developmental delay (DD), but it is best diagnosed during the school years. MR is estimated to occur in 1-10% of the population, and research on its etiology has always been a challenge in medicine. The etiopathogenesis encompasses so many different entities that the attending physician can sometimes feel a "virtual panic," starting a wide-range diagnostic evaluation. The Consensus Conference of the American College of Medical Genetics has recently established guidelines regarding the evaluation of patients with MR [Curry et al., 1997], emphasizing the high diagnostic utility of cytogenetic studies and neuroimaging in certain clinical settings. However, since then there has been substantial progress in molecular cytogenetics and neuroimaging techniques, the use of which has allowed recognition and definition of new disorders, thus increasing the diagnostic yield. This review will focus on the most appropriate investigations shown to be, at present, necessary to define the etiology of DD/MR, in the context of recommendations for the clinical evaluation of the patient with undiagnosed MR.