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

Subtelomeric rearrangements in Indian children with idiopathic intellectual disability/developmental delay: Frequency estimation & clinical correlation using fluorescence in situ hybridization (FISH)

Background & objectives:

Subtelomeres are prone to deleterious rearrangements owing to their proximity to unique sequences on the one end and telomeric repetitive sequences, which increase their tendency to recombine, on the other end. These subtelomeric rearrangements resulting in segmental aneusomy are reported to contribute to the aetiology of idiopathic intellectual disability/developmental delay (ID/DD). We undertook this study to estimate the frequency of subtelomeric rearrangements in children with ID/DD.

Methods:

One hundred and twenty seven children with idiopathic ID/DD were tested for subtelomeric rearrangements using karyotyping and FISH. Blood samples were cultured, harvested, fixed and GTG-banded using the standard protocols.

Results:

Rearrangements involving the subtelomeres were observed in 7.8 per cent of the tested samples. Detection of rearrangements visible at the resolution of the karyotype constituted 2.3 per cent, while those rearrangements detected only with FISH constituted 5.5 per cent. Five deletions and five unbalanced translocations were detected. Analysis of parental samples wherever possible was informative regarding the inheritance of the rearrangement.

Interpretation & conclusions:

The frequency of subtelomeric rearrangements observed in this study was within the reported range of 0-35 per cent. All abnormal genotypes were clinically correlated. Further analysis with array technologies presents a future prospect. Our results suggest the need to test individuals with ID/DD for subtelomeric rearrangements using sensitive methods such as FISH.

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.

A terminal 3p26.3 deletion is not associated with dysmorphic features and intellectual disability in a four-generation family

Terminal deletions of the distal part of the short arm of chromosome 3 cause a wide range of phenotypes from normal to dysmorphic including microcephaly, developmental delay and intellectual disability. We studied the clinical consequences of a terminal deletion of the short arm of chromosome 3 in four generations of a family. The index patient is a14-month-old boy with microcephaly, corpus callosum dysgenesis, and minor dysmorphic features. Single Nucleotide Polymorphism (SNP) array analysis detected a duplication on the long arm of chromosome 6. His apparently healthy mother carries the same 6q duplication, but as an unexpected finding a terminal deletion of 2.9 Mb of the short arm of chromosome 3 was observed. Further co-segregation analysis in the family for the chromosome 3 deletion showed that with the exception of the sister of the index who has autism, speech delay, and learning problems, family members in four generations of this family are carrier of this 3p deletion and apparently healthy. To our knowledge, this is the first report of a study of this terminal 3p deletion in four generations. In this report, we review the literature on terminal 3p deletions and discuss the importance of molecular testing and reporting of copy number variants to achieve accurate genetic counseling in prenatal and postnatal screening.

Pure trisomy 2p syndrome in two siblings with an unbalanced translocation and minimal terminal 12q monosomy characterized by high-density microarray

Pure partial trisomy 2p patients have rarely been reported. Oligonucleotide array analysis has proved to be important for examining 2p rearrangements to delineate the involved segment and to rule out additional imbalances modifying the phenotype. Here, we report 2 siblings with an unbalanced translocation that led to a partial trisomy 2p (p22.3pter) and a terminal deletion of 12q (q24.33qter). This finding was characterized by the molecular karyotyping of both siblings. The 12q loss spanned approximately 300 kb and did not yield clinical features in our patients. The trisomic region in the short arm of chromosome 2 spanned 32.8 Mb and yielded phenotypic features of pure distal 2p trisomy, notably facial anomalies, growth failure, and psychomotor delay. The clinical features of our patients help to delineate the phenotype of the pure trisomy 2p syndrome. Patient 2 also showed a horseshoe kidney which is a previously unrecognized defect associated with this syndrome.

Developmental abnormalities and mental retardation: diagnostic strategy

Intellectual disability formerly called mental retardation (MR) is defined as having an IQ score below 70; the term "developmental delay" (DD) is preferred for young children. A detailed clinical history including a three-generation pedigreee and physical examination are the fundamental steps in achieving an etiological diagnosis in MR. Physical examination should be performed with special emphasis on dysmorphological and neurological exam. Genetic studies have priority in the laboratory investigation of a child with MR. Routine karyotyping is recommended regardless of the degree of MR. Fragile X studies are strongly recommended in both females and males with unexplained MR, especially in patients with a positive family history and typical physical and behavioral features. FISH analysis of subtelomeric regions should be reserved for selected patients. Inborn errors of metabolism are seldom seen as the causes of isolated MR but should be considered in the differential diagnosis of patients with MR/DD in populations where the rate of consanguineous marriages is high. Neuroimaging studies should be performed on an indication basis such as abnormal brain size or neurological findings. It is essential to diagnose the underlying etiology of MR for recognition of treatable disorders, determining prognosis, family counseling, and providing prenatal diagnosis when possible.

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.

Absence of subtelomeric rearrangements in selected patients with mental retardation as assessed by multiprobe T FISH

Background

Mental retardation (MR) is a heterogeneous condition that affects 2-3% of the general population and is a public health problem in developing countries. Chromosomal abnormalities are an important cause of MR and subtelomeric rearrangements (STR) have been reported in 4-35% of individuals with idiopathic MR or an unexplained developmental delay, depending on the screening tests and patient selection criteria used. Clinical checklists such as that suggested by de Vries et al. have been used to improve the predictive value of subtelomeric screening.

Findings

Fifteen patients (1–20 years old; five females and ten males) with moderate to severe MR from a genetics outpatient clinic of the Gaffrée and Guinle Teaching Hospital (HUGG) of the Federal University of Rio de Janeiro State (UNIRIO) were screened with Multiprobe T FISH after normal high resolution karyotyping. No subtelomeric rearrangements were detected even though the clinical score of the patients ranged from four to seven.

Conclusion

In developing countries, FISH-based techniques such as Multiprobe T FISH are still expensive. Although Multiprobe T FISH is a good tool for detecting STR, in this study it did not detect STR in patients with unexplained MR/developmental delay even though these patients had a marked chromosomal imbalance. Our findings also show that clinical scores are not reliable predictors of STR.

Phenotypic variant of Brachydactyly-mental retardation syndrome in a family with an inherited interstitial 2q37.3 microdeletion including HDAC4

Deletions of the chromosomal region 2q37 cause brachydactyly-mental retardation syndrome (BDMR), also known as Albright hereditary osteodystrophy-like syndrome. Recently, histone deacetylase 4 (HDAC4) haploinsufficiency has been postulated to be the critical genetic mechanism responsible for the main clinical characteristics of the BDMR syndrome like developmental delay and behavioural abnormalities in combination with brachydactyly type E (BDE). We report here on the first three generation familial case of BDMR syndrome with inheritance of an interstitial microdeletion of chromosome 2q37.3. The deletion was detected by array comparative genomic hybridization and comprises the HDAC4 gene and two other genes. The patients of this pedigree show a variable severity of psychomotor and behavioural abnormalities in combination with a specific facial dysmorphism but without BDE. Given that only about half of the patients with 2q37 deletions have BDE; we compared our patients with other patients carrying 2q37.3 deletions or HDAC4 mutations known from the literature to discuss the diagnostic relevance of the facial dysmorphism pattern in 2q37.3 deletion cases involving the HDAC4 gene. We conclude that HDAC4 haploinsufficiency is responsible for psychomotor and behavioural abnormalities in combination with the BDMR syndrome-specific facial dysmorphism pattern and that these clinical features have a central diagnostic relevance.

"Familial" versus "sporadic" intellectual disability: contribution of subtelomeric rearrangements

Background

Cryptic subtelomeric rearrangements have been proposed as a significant cause of sporadic intellectual disability (ID) but the role of such aberrations in familial ID has not yet been studied. As positive family history of ID had been proposed as an important and significant predicting factor of subtelomeric rearrangements, it was assumed that the contribution of subtelomeric aberrations in familial ID would be much more than the sporadic ones. Three hundred and twenty two patients from 102 unrelated families with more than two ID patients in the first degree relatives have been investigated. Assessment of subtelomeric rearrangements were carried out using Multiplex Ligation-Dependent Probe Amplification (MLPA) technique. Detected aberrations were then confirmed by Fluorescence in Situ Hybridization (FISH) method.

Results

Among the families studied, 27.4% had 4-12, 36.3% had 3 and 36.3% had 2 affected individuals in the first degree relatives. One unbalanced translocation and 4 polymorphic changes were detected. The prevalence of clinically significant subtelomeric rearrangements was 0.98%.

Conclusion

This is the first investigation of subtelomeric aberrations in a large sample set of familial ID patients. Our results show that the contribution of subtelomeric rearrangements to familial ID is not as much as what had been determined for sporadic ones in the literature. Moreover, this study shows that the positive family history by alone, cannot be the most important and determining indicator of subtelomeric aberrations while it would be a good predicting factor when associated with dysmorphism or congenital malformations. These findings propose that other cryptic chromosomal abnormalities or even single gene disorders may be the main cause of familial ID rather than subtelomeric aberrations.

Intelligenzminderung

Schwachsinn Der Gebrauch des Terminus »Schwachsinn« ist wegen seines globalen und wenig präzisen Charakters und durch seine historisch und umgangssprachlich bedingte sozial diskriminierende Tönung inzwischen in der wissenschaftlichen Literatur zu Recht weitgehend aufgegeben worden. In der Rechtsprechung speziell in der Forensik ist Schwachsinn als eine schuldausschließende bzw. schuldminderende juristische Kategorie ein nach wie vor gebräuchlicher Begriff.

To determine the frequency of subtelomeric abnormalities in children with idiopathic mental retardation

BACKGROUND

Cross-sectional study was carried out to determine the frequency of subtelomeric abnormalities in children with idiopathic mental retardation (MR).

METHOD

Multiplex ligation-dependant probe amplification technique was used to detect subtelomeric abnormalities.

RESULTS

Out of 35 children, 21 (60%) were males. Family history of MR was present in 23%. Main clinical features included speech delay in all motor delay cases (83%) and non-specific dysmorphic features (77%).

CONCLUSION

Associated clinical features were more in children with intelligence quotient (IQ) < 50 (P < 0.05). Subtelomeric deletion (4q35) was observed in one child.

Delineation of subtelomeric deletion of the long arm of chromosome 6

Pure subtelomeric deletion of the long arm of chromosome 6 is rare. The frequency of this deletion accounts for approximately 0.05% of subjects with intellectual disability and developmental delay with or without dysmorphic features. Common phenotypes associated with this deletion include intellectual disability, developmental delay, dysmorphic features, seizure, hypotonia, microcephaly and hypoplasia of the corpus callosum. The smallest overlapped region is approximately 0.4 Mb, and contains three known genes. Of these genes, TBP has been considered as a plausible candidate gene for the phenotype in patients with a subtelomeric 6q deletion. Analysis of the breakpoints in 14 cases revealed a potential common breakpoint interval 8.0-9.0 Mb from the chromosome 6q terminus where the FRA6E fragile site exists and the PARK2 gene is located. This suggests that breakage at the FRA6E fragile site may be the mechanism behind chromosome 6q subtelomeric deletion in some of the cases.

Molecular characterization of a new patient with a non-recurrent inv dup del 2q and review of the mechanisms for this rearrangement

We report on newborn baby with microcephaly, facial anomalies, congenital heart defects, hypotonia, wrist contractures, long fingers, adducted thumbs, and club feet. Cytogenetic studies revealed an inverted duplication with terminal deletion (inv dup del) of 2q in the patient and a paternal 2qter deletion polymorphism. Microsatellite markers demonstrated that the inv dup del was maternal in origin and intrachromosomal. Intra or interchromosomal rearrangements may cause this aberration either by a U-type exchange (end-to-end fusion), an unequal crossover between inverted repeats (non-allelic homologous recombination: NAHR), or through breakage-fusion-bridge (BFB) cycles leading to a sister chromatid fusion by non-homologous end joining (NHEJ). A high-resolution oligo array-CGH (244 K) defined the breakpoints and did not detect a single copy region with a size exceeding 12.93 Kb in the fusion site. The size of the duplicated segment was 38.75 Mb, extending from 2q33.1 to 2q37.3 and the size of the terminal deletion was 2.85 Mb in 2q37.3. Our results indicate that the inv dup del (2q) is likely a non-recurrent chromosomal rearrangement generated by a NHEJ mechanism. The major clinical characteristics associated with this 2q rearrangement overlap with those commonly found in patients with 2q duplication reported in the literature.

Value for money? Array genomic hybridization for diagnostic testing for genetic causes of intellectual disability

Array genomic hybridization (AGH) provides a higher detection rate than does conventional cytogenetic testing when searching for chromosomal imbalance causing intellectual disability (ID). AGH is more costly than conventional cytogenetic testing, and it remains unclear whether AGH provides good value for money. Decision analytic modeling was used to evaluate the trade-off between costs, clinical effectiveness, and benefit of an AGH testing strategy compared to a conventional testing strategy. The trade-off between cost and effectiveness was expressed via the incremental cost-effectiveness ratio. Probabilistic sensitivity analysis was performed via Monte Carlo simulation. The baseline AGH testing strategy led to an average cost increase of $217 (95% CI $172-$261) per patient and an additional 8.2 diagnoses in every 100 tested (0.082; 95% CI 0.044-0.119). The mean incremental cost per additional diagnosis was $2646 (95% CI $1619-$5296). Probabilistic sensitivity analysis demonstrated that there was a 95% probability that AGH would be cost effective if decision makers were willing to pay $4550 for an additional diagnosis. Our model suggests that using AGH instead of conventional karyotyping for most ID patients provides good value for money. Deterministic sensitivity analysis found that employing AGH after first-line cytogenetic testing had proven uninformative did not provide good value for money when compared to using AGH as first-line testing.

Cryptic subtelomeric rearrangements and X chromosome mosaicism: a study of 565 apparently normal individuals with fluorescent in situ hybridization

Five percent of patients with unexplained mental retardation have been attributed to cryptic unbalanced subtelomeric rearrangements. Half of these affected individuals have inherited the rearrangement from a parent who is a carrier for a balanced translocation. However, the frequency of carriers for cryptic balanced translocations is unknown. To determine this frequency, 565 phenotypically normal unrelated individuals were examined for balanced subtelomeric rearrangements using Fluorescent In Situ hybridization (FISH) probes for all subtelomere regions. While no balanced subtelomeric rearrangements were identified, three females in this study were determined to be mosaic for the X chromosome. Mosaicism for XXX cell lines were observed in the lymphocyte cultures of 3 in 379 women (0.8%), which is a higher frequency than the 1 in 1000 (0.1%) reported for sex chromosome aneuploidies. Our findings suggest that numerical abnormalities of the X chromosome are more common in females than previously reported. Based on a review of the literature, the incidence of cryptic translocation carriers is estimated to be approximately 1/8,000, more than ten-fold higher than the frequency of visible reciprocal translocations.

Identification of subtelomeric genomic imbalances and breakpoint mapping with quantitative PCR in 296 individuals with congenital defects and/or mental retardation

Background

Submicroscopic imbalances in the subtelomeric regions of the chromosomes are considered to play an important role in the aetiology of mental retardation (MR). The aim of the study was to evaluate a quantitative PCR (qPCR) protocol established by Boehm et al. (2004) in the clinical routine of subtelomeric testing.

Results

296 patients with MR and a normal karyotype (500–550 bands) were screened for subtelomeric imbalances by using qPCR combined with SYBR green detection. In total, 17 patients (5.8%) with 20 subtelomeric imbalances were identified. Six of the aberrations (2%) were classified as causative for the symptoms, because they occurred either de novo in the patients (5 cases) or the aberration were be detected in the patient and an equally affected parent (1 case). The extent of the deletions ranged from 1.8 to approximately 10 Mb, duplications were 1.8 to approximately 5 Mb in size. In 6 patients, the copy number variations (CNVs) were rated as benign polymorphisms, and the clinical relevance of these CNVs remains unclear in 5 patients (1.7%). Therefore, the overall frequency of clinically relevant imbalances ranges between 2% and 3.7% in our cohort.

Conclusion

This study illustrates that the qPCR/SYBR green technique represents a rapid and versatile method for the detection of subtelomeric imbalances and the option to map the breakpoint. Thus, this technique is highly suitable for genotype/phenotype studies in patients with MR/developmental delay and/or congenital defects.

Screening of subtelomeric rearrangements in 100 Korean Pediatric patients with unexplained mental retardation and anomalies using subtelomeric FISH (fluorescence in situ hybridization)

Rearrangements of the subtelomeric regions of chromosomes account for a significant proportion of the underlying genetic defects in both idiopathic mental retardation (MR) and multiple congenital anomalies. To detect the rearrangements, a set of subtelomeric fluorescence in situ hybridization (FISH) probes has been developed. The aim of this study was to reveal the frequency of subtelomeric rearrangements in Korean patients with MR or multiple anomalies. We performed a FISH study using a commercially available subtelomeric FISH probes on a series of unrelated Korean pediatric patients with MR or multiple anomalies without identifiable causes. We used a checklist to evaluate the developmental delay and/or MR. Patients who were shown to have chromosome abnormalities, metabolic disorders, or recognizable dysmorphic syndromes by clinical and laboratory findings were excluded. As a result, 100 patients were eligible for the Subtelomeric FISH study, and a total of 29 patients (29%) were suspected to have subtelomeric rearrangements on initial screening by the multiprobe FISH kit. Among theses, confirmatory FISH studies by using single locus-specific FISH probes were performed in 24 patients. One patient (a 10- yr-old girl) was confirmed to have rearrangement, deletion of the telomeric portion of the short arm of chromosome 4 (4p). Her clinical manifestation was compatible with Wolf-Hirschhorn syndrome, which is known to be caused by 4p deletion. The frequency of subtelomeric rearrangements in this study was 1.1% (1/95), lower than those previously reported (0.5-16.3%). We suggest that subtelomeric FISH test is a useful screening tool for patients with idiopathic MR and/or dysmorphism regardless of its false positive value.

Deletion 2q37: an identifiable clinical syndrome with mental retardation and autism

Terminal deletion of the long arm of chromosome 2 is a rare chromosomal disorder characterized by low birth weight, delayed somatic and mental development, craniofacial defects, short neck, heart and lung congenital defects, and autistic features. We report on a girl with 46,XX.ish del(2)(q37.1) de novo karyotype, mental retardation, dysmorphic features, gastrointestinal anomalies, and autistic traits and compare her clinical manifestations with patients with the same deletion previously described in literature.

Genetic evaluation of intellectual disabilities

All children with an intellectual disability (mental retardation) or global developmental delay should have a comprehensive evaluation to establish the etiology of the disability. A specific etiologic diagnosis offers the opportunity to discuss treatment, prognosis, and genetic recurrence risk. A diagnosis also avoids unnecessary testing and can lead to opportunities for improved health and functional outcomes. The key elements of the diagnostic evaluation are the medical and developmental history, 3-generation family history, dysmorphologic examination, neurologic examination, and judicious use of the laboratory and neuroimaging. All published guidelines for the evaluation of children with intellectual disability acknowledge that there is a substantial percentage of patients who are undiagnosed after a comprehensive evaluation and who deserve ongoing follow-up for the purpose of establishing a diagnosis. Recently, studies of the clinical application of array comparative genomic hybridization (aCGH) to individuals with intellectual disability indicate that this approach provides a diagnosis in as much as 10% of patients and that this technique is replacing the use of fluorescent in situ hybridization for subtelomere imbalances now used for such patients when the standard karyotype is normal. The literature suggests that history and examination by an expert clinician will lead to a diagnosis in 2 of 3 patients in whom a diagnosis is made. Laboratory studies alone, including neuroimaging, provide a diagnosis in the remaining one third. The approach to the evaluation of the patient in whom an etiologic diagnosis is not suspected after the history and physical examinations includes a standard karyotype, Fragile X molecular genetic testing, aCGH, and neuroimaging, based on the evidence to date. One can expect rapid changes in the microarray technology in the near future.

Chromosome 2q37 deletion: clinical and molecular aspects

Terminal deletions of chromosome 2 with breakpoints at or within band 2q37, ranging from visible abnormalities to cryptic, subtelomeric deletions, have been recognized with increasing frequency among children with mild-moderate mental retardation, characteristic facial appearance, and behavioral manifestations which often place them on the autism spectrum. The stereotypic facial characteristics include prominent forehead, thin, highly arched eyebrows, depressed nasal bridge, full cheeks, deficient nasal alae and prominent columella, thin upper lip, and various minor anomalies of the pinnae. Abnormal nipples, including inverted nipples, have been reported in a number of cases. CNS, ocular, cardiac, gastrointestinal, renal, and other GU anomalies have been noted in nearly one-third of patients. Of note, coarctation or hypoplasia of the aorta has been described in several affected children. Wilms tumor, renal dysplasia, and tracheomalacia have been reported only with the most proximal breakpoint at band 2q37.1 while a range of GI anomalies, pyloric stenosis, and diaphragmatic defects have been reported with breakpoints throughout the region. A subset of patients with the most distal deletion present phenotypic features which mimic Albright hereditary osteodystrophy (AHO). In addition to the AHO-like phenotype, later onset findings include seizures and cystic kidneys. Timely diagnosis of this recognizable syndrome provides a basis for genetic counseling, appropriate surveillance, and intervention, and avoids unnecessary and expensive diagnostic testing.

Genotype/phenotype correlations in two patients with 12q subtelomere deletions

Subtelomeric imbalances have been implicated in developmental delay and mental retardation (MR) and described for most chromosomes. This study reports the first detailed description of two individuals with de novo 12q subtelomere deletions and high-resolution mapping of their deletion size with oligonucleotide array CGH for genotype/phenotype comparisons. Patient 1 is an 8-year-old male with borderline mild MR, food-seeking behavior, obesity, no significant dysmorphic facial features, abnormal hair whorl pattern, brachydactyly and mild clinodactyly. Patient 2 is a 12-year-old male with mild MR, food-seeking behavior, obesity, short stature, mild dysmorphic facial features, multicystic kidney and unilateral cryptorchidism. Both patients share a deleted region of approximately 1.6 Mb, including 14 known genes, which perhaps contributed to their similar phenotypes. However, Patient 2 has more severe MR and organ system involvement, possibly due to the larger deletion size ( approximately 4.5 Mb) including an additional eight genes, although it is difficult to make phenotype/genotype correlations based on only two patients. Due to the relatively mild presentation of both of our patients, we propose that a proportion of individuals with subtelomeric imbalances may go undetected and therefore, recommend subtelomeric studies be carried out for cases of unexplained mild MR or isolated learning disability (LD) with behavioral problems in the absence of major dysmorphic features or birth defects. In addition, 12q subtelomeric deletions should be considered in the differential diagnosis of patients presenting with food-seeking behavior and resultant obesity, as well as those referred to rule out Prader-Willi syndrome.

Epidemiology and Etiology of Mental Retardation

Mental retardation (MR) is a manifestation of a heterogeneous set of impairments and conditions that result in cognitive limitation. It is a condition of medical, educational, and social importance. Physicians identify profound, severe, and moderate MR but rarely diagnose mild MR unless it is associated with a genetic or medical syndrome. From a medical perspective, the quest for etiology and the possibility of medical or surgical intervention to minimize deterioration are paramount. Educators, on the other hand are less concerned with causation than with academic achievement and school success. The majority of cases of mild MR is identified in school settings. Finally, the public uses the label to describe poor adaptive skills. Adults with MR who hold jobs, live independently, and participate in society are not always described as having MR. Thus some individuals characterized in childhood or adolescence as having mild MR become indistinguishable from the general population in adulthood.

Subtelomeric rearrangements and 22q11.2 deletion syndrome in anomalous growth-restricted fetuses with normal or balanced G-banded karyotype

OBJECTIVE

To determine the frequencies of cryptic subtelomeric rearrangements and 22q11.2 deletion in anomalous growth-restricted fetuses with normal or balanced G-banded karyotypes.

METHODS

This was a study of 27 consecutive fetuses at a median gestational age of 26 (range, 19-33) weeks, that had intrauterine growth restriction (IUGR) as well as at least one major structural anomaly, and a normal or balanced G-banded karyotype. The median maternal age was 29 (range, 17-39) years. Fluorescence z in-situ hybridization (FISH) diagnosis of the cultured amniocytes with the probe TUPLE 1, and then the Chromoprobe Multiprobe-T system were used, respectively, to screen for the frequency of 22q11.2 deletion syndrome and subtelomeric rearrangements involving the 41 unique chromosome ends (i.e. excluding the five short arms of acrocentric autosomes (no. 13, 14, 15, 21 and 22)). Those that had suspected deleted subtelomeres were reanalyzed with a specific subtelomeric probe, TelVysion.

RESULTS

Of the 27 fetuses, three (11%) were affected with 22q11.2 deletion syndrome and two (7.4%) had subtelomeric deletions (one monosomy 21q22.3, one monosomy 1p36.3). Of the 11 fetuses with congenital heart defects, three (27.3%) had 22q11.2 deletion syndrome and one (9.1%) had monosomy 1p36.3. In the remaining 16 fetuses without congenital heart defects, none had 22q11.2 deletion syndrome. However, one (6.3%) had cryptic rearrangement involving subtelomeres.

CONCLUSION

Prenatal subtelomeric FISH screening is technically feasible using cultured amniocytes. We propose that 22q11.2 deletion syndrome and cryptic subtelomere rearrangements may be important etiologies of fetuses with IUGR and at least one structural anomaly, along with a normal karyotype or one that is balanced by traditional G-banding. Fetuses with congenital heart defects and IUGR should undergo FISH to exclude 22q11.2 deletion syndrome. In fetuses with IUGR and at least one major structural anomaly but without congenital heart defects, screening of subtelomeric rearrangements may contribute to further elucidation of the underlying etiology.

Diagnostic yield of various genetic approaches in patients with unexplained developmental delay or mental retardation

The underlying cause of mental retardation remains unknown in up to 80% of patients. As chromosomal aberrations are the most common known cause of mental retardation, several new methods based on FISH, PCR, and array techniques have been developed over recent years to increase detection rate of subtle aneusomies initially of the gene rich subtelomeric regions, but nowadays also genome wide. As the reported detection rates vary widely between different reports and in order to compare the diagnostic yield of various investigations, we analyzed the diagnostic yield of conventional karyotyping, subtelomeric screening, molecular karyotyping, X-inactivation studies, and dysmorphological evaluation with targeted laboratory testing in unselected patients referred for developmental delay or mental retardation to our cytogenetic laboratory (n = 600) and to our genetic clinic (n = 570). In the cytogenetic group, 15% of patients showed a disease-related aberration, while various targeted analyses after dysmorphological investigation led to a diagnosis in about 20% in the genetic clinic group. When adding the patients with a cytogenetic aberration to the patient group seen in genetic clinic, an etiological diagnosis was established in about 40% of the combined study group. A conventional cytogenetic diagnosis was present in 16% of combined patients and a microdeletion syndrome was diagnosed in 5.3%, while subtelomeric screening revealed only 1.3% of causes. Molecular karyotyping with a 10 K SNP array in addition revealed 5% of underlying causes, but 29% of all diagnoses would have been detectable by molecular karyotyping. In those patients without a clear diagnosis, 5.6% of mothers of affected boys showed significant (>95%) skewing of X-inactivation suggesting X-linked mental retardation. The most common diagnoses with a frequency of more than 0.5% were Down syndrome (9.2%), common microdeletion 22q11.2 (2.4%), Williams-Beuren syndrome (1.3%), Fragile-X syndrome (1.2%), Cohen syndrome (0.7%), and monosomy 1p36.3 (0.6%). From our data, we suggest the following diagnostic procedure in patients with unexplained developmental delay or mental retardation: (1) Clinical/dysmorphological investigation with respective targeted analyses; (2) In the remaining patients without an etiological diagnosis, we suggest conventional karyotyping, X-inactivation screening in mothers of boys, and molecular karyotyping, if available. If molecular karyotyping is not available, subtelomeric screening should be performed.

Clinical genetic evaluation of the child with mental retardation or developmental delays

This clinical report describes the clinical genetic evaluation of the child with developmental delays or mental retardation. The purpose of this report is to describe the optimal clinical genetics diagnostic evaluation to assist pediatricians in providing a medical home for children with developmental delays or mental retardation and their families. The literature supports the benefit of expert clinical judgment by a consulting clinical geneticist in the diagnostic evaluation. However, it is recognized that local factors may preclude this particular option. No single approach to the diagnostic process is supported by the literature. This report addresses the diagnostic importance of clinical history, 3-generation family history, dysmorphologic examination, neurologic examination, chromosome analysis (> or =650 bands), fragile X molecular genetic testing, fluorescence in situ hybridization studies for subtelomere chromosome rearrangements, molecular genetic testing for typical and atypical presentations of known syndromes, computed tomography and/or magnetic resonance brain imaging, and targeted studies for metabolic disorders.

Agenesis of the corpus callosum: clinical and genetic study in 63 young patients

This study reports the clinical features of 63 patients with agenesis of the corpus callosum who received in-depth genetic, clinical, and laboratory testing with the aim to contribute to a better description of the large spectrum of associated malformations and to assist clinicians in the diagnosis. Thirty patients manifested complete agenesis and 33 patients displayed partial agenesis. Other associated nervous system malformations were detected in 14 patients with partial agenesis of the corpus callosum (mostly correlated to posterior fossa malformations) and in 10 patients with complete agenesis (more frequently associated with malformations of cortical development). Involvement of organs and apparatus other than the nervous system was present in 41 patients (ascribed to known syndromes in 21 cases). Cytogenetically detectable chromosomal abnormalities (7 patients) and subtelomeric rearrangements (3 patients) were found. Neuromotor skills were impaired in almost all cases (58/63). Mental retardation of different severity was present in 52 cases, whereas 2 patients were borderline and 9 patients had normal intelligence quotient. This study demonstrates that there is no unique prognosis for agenesis of the corpus callosum as this condition is associated with a broad range of clinical manifestations, oscillating between the limits of the norm and severe psychomotor delay.

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.

Frequency of truly cryptic subtelomere abnormalities--a study of 534 patients and literature review

Frequency of truly cryptic subtelomere abnormalities - a study of 534 patients and literature review. Unbalanced subtelomere chromosome rearrangements are a significant cause of mental retardation with approximately 5% of over 3000 affected individuals tested worldwide having a chromosome rearrangement of this type. Many of these abnormalities are detectable using routine karyotyping at the 550 band level and therefore are not considered to be cryptic. The frequency of truly cryptic subtelomere abnormality should be less than 5% but has not been established. In this study, we defined 'cryptic abnormality' as one not detectable at the 550 band level on routine karyotyping. Using this as one of the selection criteria, we have studied 534 individuals with mental retardation/ developmental delay (MR/DD) and referred for subtelomere study by clinical geneticists. We have identified seven cases with cryptic subtelomere abnormalities. The clinical features of the seven abnormal cases are summarized. Literature review identified five publications on the identification of subtelomere abnormalities which used similar recruitment criteria: (a) normal karyotype at the 550 band level and (b) subjects were selected for subtelomere studies. Combining the data from these studies with those of the current study, 1154 patients were tested and 30 subtelomere abnormalities were identified. We estimate the frequency of truly cryptic subtelomere abnormality to be approximately 2.6% (30/1154) in children with MR/DD who are referred for subtelomere study.

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.

Subtelomeric rearrangements in idiopathic mental retardation

OBJECTIVE

To estimate the frequency of subtelomeric rearrangements in patients with sporadic and non-syndromic idiopathic mental retardation (IMR).

METHODS

A total of 18 IMR patients were taken for the study. Selection criteria included no known syndromes or chromosomes abnormalities and known causes of IMR. All patients signed an informed consent to participate. Chromosome analysis was carried out on all patients to rule out gross chromosome abnormalities. Lymphocyte cultures were initiated and harvested using standard protocols. For fluorescence in situ hybridization (FISH), Chromoprobe Multiprobe-T system was used. This system consists of 24 embossed areas with each area having one reversibly bound subtelomere probe for a specific chromosome. The subtelomere probes were differentially labeled with green fluorescence for short arm and orange for the long arm. Hybridization, washing and staining are done using standard protocols. A minimum of 5 metaphases were analyzed per chromosome per patient.

RESULTS

A total of 2 subtelomeric rearrangements were detected (11.1%). Case 1 involved a 17-year-old with severe MR, profound deafness and dysmorphic features with reciprocal translocation t(3;7)(q26.2; p15.1). The second case involved a 4.6-year-old with mild developmental delay and a terminal deletion of the long arm of chromosome 2, del(2) (q37.3). The frequency of abnormalities detected in our study is in agreement with published reports.

CONCLUSION

Subtelomeric screening with FISH is a useful tool for investigation of IMR, however, it is not cost effective in all cases. Conventional chromosome analysis coupled with targeted FISH testing might be the optimal strategy for investigation of IMR.

Subtelomeric study of 132 patients with mental retardation reveals 9 chromosomal anomalies and contributes to the delineation of submicroscopic deletions of 1pter, 2qter, 4pter, 5qter and 9qter

Background

Cryptic chromosome imbalances are increasingly acknowledged as a cause for mental retardation and learning disability. New phenotypes associated with specific rearrangements are also being recognized. Techniques for screening for subtelomeric rearrangements are commercially available, allowing the implementation in a diagnostic service laboratory. We report the diagnostic yield in a series of 132 subjects with mental retardation, and the associated clinical phenotypes.

Methods

We applied commercially available subtelomeric fluorescence in situ hybridization (FISH). All patients referred for subtelomeric screening in a 5-year period were reviewed and abnormal cases were further characterized clinically and if possible molecularly.

Results

We identified nine chromosomal rearrangements (two of which were in sisters) corresponding to a diagnostic yield of approx. 7%. All had dysmorphic features. Five had imbalances leading to recognizable phenotypes.

Conclusion

Subtelomeric screening is a useful adjunct to conventional cytogenetic analyses, and should be considered in mentally retarded subjects with dysmorphic features and unknown cause.

Diagnostic investigations in individuals with mental retardation: a systematic literature review of their usefulness

There are no guidelines available for diagnostic studies in patients with mental retardation (MR) established in an evidence-based manner. Here we report such study, based on information from original studies on the results with respect to detected significant anomalies (yield) of six major diagnostic investigations, and evaluate whether the yield differs depending on setting, MR severity, and gender. Results for cytogenetic studies showed the mean yield of chromosome aberrations in classical cytogenetics to be 9.5% (variation: 5.4% in school populations to 13.3% in institute populations; 4.1% in borderline-mild MR to 13.3% in moderate-profound MR; more frequent structural anomalies in females). The median yield of subtelomeric studies was 4.4% (also showing female predominance). For fragile X screening, yields were 5.4% (cytogenetic studies) and 2.0% (molecular studies) (higher yield in moderate-profound MR; checklist use useful). In metabolic investigations, the mean yield of all studies was 1.0% (results depending on neonatal screening programmes; in individual populations higher yield for specific metabolic disorders). Studies on neurological examination all showed a high yield (mean 42.9%; irrespective of setting, degree of MR, and gender). The yield of neuroimaging studies for abnormalities was 30.0% (higher yield if performed on an indicated basis) and the yield for finding a diagnosis based on neuroradiological studies only was 1.3% (no data available on value of negative findings). A very high yield was found for dysmorphologic examination (variation 39-81%). The data from this review allow conclusions for most types of diagnostic investigations in MR patients. Recommendations for further studies are provided.

The use of subtelomeric probes to study mental retardation

In this chapter, we focus on the genetic basis of mental retardation (MR), specifically the use of subtelomeric probes to provide new diagnoses in idiopathic MR. We discuss both the background to the clinical demand for diagnoses and the technological advances that culminated in the development of subtelomeric testing strategies. We explain the theory behind these strategies and briefly outline the protocols involved, giving the advantages, limitations, and pitfalls of the analyses. Finally, we give an overview of the MR subtelomeric studies to date and how subtelomeric testing has become a widely used tool in clinical diagnostic laboratories, particularly in the diagnosis of unexplained MR, but also in other fields of clinical medicine. The conclusion addresses the overall impact that subtelomeric testing has had on the diagnosis of MR, the implications for patients and their families, and future research avenues for exploring the genetic causes of MR and improving our overall understanding of neurocognitive development.

Chromosome 2q terminal deletion: report of 6 new patients and review of phenotype-breakpoint correlations in 66 individuals

We report a new patient with terminal deletion of chromosome 2 with breakpoint at 2q36 and five additional new patients with 2q terminal deletion with breakpoint at 2q37. Hemidiaphragmatic hernia is a novel finding in one patient with a breakpoint at 2q37.1. In comparing these patients to 60 previously reported individuals with 2q terminal deletions, certain physical abnormalities are loosely associated with positions of breakpoint. For example, facial features (e.g., prominent forehead, depressed nasal bridge, and dysmorphic ears and nose), short stature, and short hands and feet were frequent in patients with breakpoints at or proximal to 2q37.3. Reports of horseshoe kidney and Wilms tumor were limited to patients with a breakpoint at 2q37.1, and structural brain anomalies and tracheal anomalies were reported only in patients with breakpoints at or proximal to 2q37.1. Cleft palate was reported only in patients with the most proximal breakpoints (2q36 or 2q35). Neurological effects including developmental delay, mental retardation, autistic-like behavior, and hypotonia were typical in this patient population but did not stratify in severity according to breakpoint. Terminal deletion of the long arm of chromosome 2 should be considered in the infant with marked hypotonia, poor feeding, gastroesophageal reflux, and growth delay, and the older child with developmental delay, autistic behavior, and the characteristic facial and integumentary features described herein. Assignment of clinical features to specific breakpoints and refinement of predictive value may be useful in counseling.

Subtelomeric rearrangements as neutral genomic polymorphisms

Submicroscopic chromosomal rearrangements affecting telomeres are important aetiological contributors to the development of mental retardation. Results from over 2,500 analysed patients with mental retardation demonstrated that about 5% have a subtelomeric aberration. However, some subtelomeric rearrangements have no phenotypic consequences. Due to the heterogeneity of such rearrangements and to the limited information about which monosomy or trisomy can be tolerated without phenotypic effect, conclusions about the association of a specific aberration and the phenotypical consequences are often hard to draw. We performed a study of subtelomeric aberrations with the aim to provide more insights into the understanding of such rearrangements as neutral genomic polymorphisms. We found two new polymorphisms: a duplication or triplication of the subtelomeric region of the long arm of chromosome 4 and a trisomy of the subtelomeric region of the short arm of chromosome 6 owing to a transposition to chromosome 22. These new data are presented and discussed in the context of the published literature.

Subtelomeric rearrangements in the mentally retarded: A comparison of detection methods

In recent years, subtelomeric rearrangements, e.g., chromosome deletions or duplications too small to be detected by conventional cytogenetic analysis, have emerged as a significant cause of both idiopathic and familial mental retardation. As mental retardation is a common disorder, many patients need to be tested on a routine basis. In this review, we will discuss the different methods that have been applied in laboratories worldwide, including multiprobe fluorescence in situ hybridization (FISH), multiallelic marker analysis, multiplex amplifiable probe hybridization (MAPH), multiplex ligation-dependent probe amplification (MLPA), quantitative real-time PCR, comparative genomic hybridization (CGH), and multicolor FISH, including spectral karyotyping (SKY), subtelomeric combined binary ratio labeling FISH (S-COBRA FISH), multiplex FISH telomere integrity assay (M-TEL), telomeric multiplex FISH (TM-FISH), and primed in situ labeling (PRINS).

A 4q35.2 subtelomeric deletion identified in a screen of patients with co-morbid psychiatric illness and mental retardation

Background

Cryptic structural abnormalities within the subtelomeric regions of chromosomes have been the focus of much recent research because of their discovery in a percentage of people with mental retardation (UK terminology: learning disability). These studies focused on subjects (largely children) with various severities of intellectual impairment with or without additional physical clinical features such as dysmorphisms. However it is well established that prevalence of schizophrenia is around three times greater in those with mild mental retardation. The rates of bipolar disorder and major depressive disorder have also been reported as increased in people with mental retardation. We describe here a screen for telomeric abnormalities in a cohort of 69 patients in which mental retardation co-exists with severe psychiatric illness.

Methods

We have applied two techniques, subtelomeric fluorescence in situ hybridisation (FISH) and multiplex amplifiable probe hybridisation (MAPH) to detect abnormalities in the patient group.

Results

A subtelomeric deletion was discovered involving loss of 4q in a patient with co-morbid schizoaffective disorder and mental retardation.

Conclusion

The precise region of loss has been defined allowing us to identify genes that may contribute to the clinical phenotype through hemizygosity. Interestingly, the region of 4q loss exactly matches that linked to bipolar affective disorder in a large multiply affected Australian kindred.

Unbalanced cryptic 5p deletion/17p duplication identified by subtelomeric FISH in a family with a boy with chimerism and a balanced t(4;5)

The use of subtelomeric FISH probes has greatly supplemented conventional chromosome analysis in detecting cryptic anomalies in patients with mental retardation (MR), dysmorphic features, and congenital malformations. We report a 3-month-old boy who was diagnosed with ambiguous genitalia, dysmorphic features, and developmental delay. Standard chromosome studies on blood revealed a chimeric karyotype of 46,XY,t(4;5)(q31.1;q14)[46]/46,XX[4]. The boy had intra-abdominal gonads that were testicular in origin by biopsy. Multiple dysmorphic features, marked hypotonia, developmental delay, poor growth, and relative macrocephaly were noted on physical exam. His 2.5-year-old sister also presented with hypotonia, developmental delay, relative macrocephaly, and similar dysmorphic stigmata. In addition, she was diagnosed with several internal malformations. Her karyotype was 46,XX. Due to the striking phenotypic similarity, subtelomeric FISH studies were initiated in the siblings. In addition to the known balanced karyotypic abnormalities, the boy was found to have a derivative chromosome 5 with a 5pter deletion and a 17pter duplication. This cryptic abnormality was also detected in his sister. Chromosome analysis of the father revealed a subtle balanced t(5;17)(p15.31;p13.1) which was confirmed by subtelomeric FISH, whereas the mother's chromosome complement was normal. This familial constellation illustrates the usefulness of subtelomeric FISH in the diagnosis of cryptic chromosome abnormalities in patients for whom conventional karyotype does not disclose findings sufficient to explain the observed phenotypic anomalies.

High frequency of subtelomeric rearrangements in a cohort of 92 patients with severe mental retardation and dysmorphism

About 5-10% of patients with dysmorphisms, severe mental retardation, and normal standard karyotype are affected by subtelomeric chromosome rearrangements. Sequence homology between different chromosomes and variability between homologs make these regions more susceptible to breakage and reunion. We analyzed the telomeric regions of 92 of these patients, selected with strict clinical criteria. Fifteen individuals (16.3%) had subtelomeric rearrangements. Nine had a unique anomaly, which in one case had been inherited from a balanced parent. Six subjects had double segmental imbalances, including three de novo imbalances. This study provides further evidence for the plasticity of subtelomeric regions, which often results in cryptic rearrangements, and recommends stringent criteria for selecting patient candidates to telomere analysis.

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.

Subtelomere FISH in 50 children with mental retardation and minor anomalies, identified by a checklist, detects 10 rearrangements including a de novo balanced translocation of chromosomes 17p13.3 and 20q13.33

Submicroscopic or subtle aneusomies at the chromosome ends, typically diagnosed by subtelomere fluorescence in situ hybridization (FISH), are a significant cause of idiopathic mental retardation (MR). Some 20 subtelomere studies, including more than 2,500 subjects, have been reported. The studies are not directly comparable because different techniques and patient ascertainment criteria were used, but an analysis of 14 studies showed that aberrations were detected in 97 out of 1,718 patients (5.8%, range 2-29%; 95% confidence interval (CI) 4.60-6.84%). We performed a subtelomere FISH study of 50 unrelated children ascertained by a checklist that evaluates MR or developmental delay, dysmorphism, growth defect, and abnormal pedigree and found 10 bona fide causal rearrangements (detection rate 20%, 95% CI 10-33.7%). The findings included five unbalanced familial translocations or inversions, two unbalanced de novo translocations, and two de novo deletions. Patient 5 showed multiple anomalies (large head, vision defect, omphalocele, heart defect, enlarged kidneys, moderate MR, speech defect, mild transient homocysteinemia) and a de novo balanced translocation of chromosomes 17p13.3 and 20q13.33. The report of a subtelomeric balanced rearrangement associated with a disease phenotype is a novel one. FISH mapping using panels of overlapping BAC clones identified a number of candidate genes at or near his breakpoints, including ASPA, TRPV3, TRPV1, and CTNS at 17p13.3, and three genes of unknown function at 20q13.33. Only the homocysteinemia could be speculatively linked to one of these genes (CTNS, the gene for cystinosis). Three within the subset of 16 children (18.8%) with mild (IQ, 50-69) or unspecified degree of MR tested positive, suggesting that the checklist approach could be especially useful within this group of patients.