PLP1 duplication at the breakpoint regions of an apparently balanced t(X;22) translocation causes Pelizaeus-Merzbacher disease in a girl.

PLP1 (proteolipid protein1 gene) mutations cause Pelizaeus-Merzbacher disease (PMD), characterized by hypomyelination of the central nervous system, and affecting almost exclusively males. We report on a girl with classical PMD who carries an apparently balanced translocation t(X;22)(q22;q13). By applying array-based comparative genomic hybridization (a-CGH), we detected duplications at 22q13 and Xq22, encompassing 487-546 kb and 543-611 kb, respectively. The additional copies were mapped by fluorescent in situ hybridization to the breakpoint regions, on the derivative X chromosome (22q13 duplicated segment) and on the derivative 22 chromosome (Xq22 duplicated segment). One of the 14 duplicated X-chromosome genes was PLP1.The normal X chromosome was the inactive one in the majority of peripheral blood leukocytes, a pattern of inactivation that makes cells functionally balanced for the translocated segments. However, a copy of the PLP1 gene on the derivative chromosome 22, in addition to those on the X and der(X) chromosomes, resulted in two active copies of the gene, irrespective of the X-inactivation pattern, thus causing PMD. This t(X;22) is the first constitutional human apparently balanced translocation with duplications from both involved chromosomes detected at the breakpoint regions.

Constitutional haploinsufficiency of tumor suppressor genes in mentally retarded patients with microdeletions in 17p13.1.

Chromosome microdeletions or duplications are detected in 10-20% of patients with mental impairment and normal karyotypes. A few cases have been reported of mental impairment with microdeletions comprising tumor suppressor genes. By array-CGH we detected 4 mentally impaired individuals carrying de novo microdeletions sharing an overlapping segment of approximately 180 kb in 17p13.1. This segment encompasses 18 genes, including 3 involved in cancer, namely KCTD11/REN, DLG4/PSD95, and GPS2. Furthermore, in 2 of the patients, the deletions also included TP53, the most frequently inactivated gene in human cancers. The 3 tumor suppressor genes KCTD11, DLG4, and GPS2, in addition to the GABARAP gene, have a known or suspected function in neuronal development and are candidates for causing mental impairment in our patients. Among our 4 patients with deletions in 17p13.1, 3 were part of a Brazilian cohort of 300 mentally retarded individuals, suggesting that this segment may be particularly prone to rearrangements and appears to be an important cause (approximately 1%) of mental retardation. Further, the constitutive deletion of tumor suppressor genes in these patients, particularly TP53, probably confers a significantly increased lifetime risk for cancer and warrants careful oncological surveillance of these patients. Constitutional chromosome deletions containing tumor suppressor genes in patients with mental impairment or congenital abnormalities may represent an important mechanism linking abnormal phenotypes with increased risks of cancer.

Chromosome imbalances in syndromic hearing loss.

The cause of hearing impairment has not been elucidated in a large proportion of patients. We screened by 1-Mb array-based comparative genomic hybridization (aCGH) 29 individuals with syndromic hearing impairment whose clinical features were not typical of known disorders. Rare chromosomal copy number changes were detected in eight patients, four de novo imbalances and four inherited from a normal parent. The de novo alterations define candidate chromosome segments likely to harbor dosage-sensitive genes related to hearing impairment, namely 1q23.3-q25.2, 2q22q23, 6p25.3 and 11q13.2-q13.4. The rare imbalances also present in normal parents might be casually associated with hearing impairment, but its role as a predisposition gene remains a possibility. Our results show that syndromic deafness is frequently associated with chromosome microimbalances (14-27%), and the use of aCGH for defining disease etiology is recommended.

High frequency of submicroscopic chromosomal imbalances in patients with syndromic craniosynostosis detected by a combined approach of microsatellite segregation analysis, multiplex ligation-dependent probe amplification and array-based comparative genome hybridisation.

We present the first comprehensive study, to our knowledge, on genomic chromosomal analysis in syndromic craniosynostosis. In total, 45 patients with craniosynostotic disorders were screened with a variety of methods including conventional karyotype, microsatellite segregation analysis, subtelomeric multiplex ligation-dependent probe amplification) and whole-genome array-based comparative genome hybridisation. Causative abnormalities were present in 42.2% (19/45) of the samples, and 27.8% (10/36) of the patients with normal conventional karyotype carried submicroscopic imbalances. Our results include a wide variety of imbalances and point to novel chromosomal regions associated with craniosynostosis. The high incidence of pure duplications or trisomies suggests that these are important mechanisms in craniosynostosis, particularly in cases involving the metopic suture.

Clinical and molecular delineation of the 17q21.31 microdeletion syndrome.

BACKGROUND: The chromosome 17q21.31 microdeletion syndrome is a novel genomic disorder that has originally been identified using high resolution genome analyses in patients with unexplained mental retardation. AIM: We report the molecular and/or clinical characterisation of 22 individuals with the 17q21.31 microdeletion syndrome. RESULTS: We estimate the prevalence of the syndrome to be 1 in 16,000 and show that it is highly underdiagnosed. Extensive clinical examination reveals that developmental delay, hypotonia, facial dysmorphisms including a long face, a tubular or pear-shaped nose and a bulbous nasal tip, and a friendly/amiable behaviour are the most characteristic features. Other clinically important features include epilepsy, heart defects and kidney/urologic anomalies. Using high resolution oligonucleotide arrays we narrow the 17q21.31 critical region to a 424 kb genomic segment (chr17: 41046729-41470954, hg17) encompassing at least six genes, among which is the gene encoding microtubule associated protein tau (MAPT). Mutation screening of MAPT in 122 individuals with a phenotype suggestive of 17q21.31 deletion carriers, but who do not carry the recurrent deletion, failed to identify any disease associated variants. In five deletion carriers we identify a <500 bp rearrangement hotspot at the proximal breakpoint contained within an L2 LINE motif and show that in every case examined the parent originating the deletion carries a common 900 kb 17q21.31 inversion polymorphism, indicating that this inversion is a necessary factor for deletion to occur (p<10(-5)). CONCLUSION: Our data establish the 17q21.31 microdeletion syndrome as a clinically and molecularly well recognisable genomic disorder.

Array-CGH detection of micro rearrangements in mentally retarded individuals: clinical significance of imbalances present both in affected children and normal parents.

BACKGROUND: The underlying causes of mental retardation remain unknown in about half the cases. Recent array-CGH studies demonstrated cryptic imbalances in about 25% of patients previously thought to be chromosomally normal. OBJECTIVE AND METHODS: Array-CGH with approximately 3500 large insert clones spaced at approximately 1 Mb intervals was used to investigate DNA copy number changes in 81 mentally impaired individuals. RESULTS: Imbalances never observed in control chromosomes were detected in 20 patients (25%): seven were de novo, nine were inherited, and four could not have their origin determined. Six other alterations detected by array were disregarded because they were shown by FISH either to hybridise to both homologues similarly in a presumptive deletion (one case) or to involve clones that hybridised to multiple sites (five cases). All de novo imbalances were assumed to be causally related to the abnormal phenotypes. Among the others, a causal relation between the rearrangements and an aberrant phenotype could be inferred in six cases, including two imbalances of the X chromosome, where the associated clinical features segregated as X linked recessive traits. CONCLUSIONS: In all, 13 of 81 patients (16%) were found to have chromosomal imbalances probably related to their clinical features. The clinical significance of the seven remaining imbalances remains unclear. The limited ability to differentiate between inherited copy number variations which cause abnormal phenotypes and rare variants unrelated to clinical alterations currently constitutes a limitation in the use of CGH-microarray for guiding genetic counselling.

Whole-genome array-CGH screening in undiagnosed syndromic patients: old syndromes revisited and new alterations.

We report array-CGH screening of 95 syndromic patients with normal G-banded karyotypes and at least one of the following features: mental retardation, heart defects, deafness, obesity, craniofacial dysmorphisms or urogenital tract malformations. Chromosome imbalances not previously detected in normal controls were found in 30 patients (31%) and at least 16 of them (17%) seem to be causally related to the abnormal phenotypes. Eight of the causative imbalances had not been described previously and pointed to new chromosome regions and candidate genes for specific phenotypes, including a connective tissue disease locus on 2p16.3, another for obesity on 7q22.1-->q22.3, and a candidate gene for the 3q29 deletion syndrome manifestations. The other causative alterations had already been associated with well-defined phenotypes including Sotos syndrome, and the 1p36 and 22q11.21 microdeletion syndromes. However, the clinical features of these latter patients were either not typical or specific enough to allow diagnosis before detection of chromosome imbalances. For instance, three patients with overlapping deletions in 22q11.21 were ascertained through entirely different clinical features, i.e., heart defect, utero-vaginal aplasia, and mental retardation associated with psychotic disease. Our results demonstrate that ascertainment through whole-genome screening of syndromic patients by array-CGH leads not only to the description of new syndromes, but also to the recognition of a broader spectrum of features for already described syndromes. Furthermore, on the technical side, we have significantly reduced the amount of reagents used and costs involved in the array-CGH protocol, without evident reduction in efficiency, bringing the method more within reach of centers with limited budgets.

Notes on the population genetics of fragile X syndrome.

Our analysis of fragile X-inactivation in normal and mentally retarded heterozygotes led us to conclude that a fraction of female carriers of the imprinted (fully mutated) allele is phenotypically normal as a consequence of X-inactivation. Taking this into account, we derived equilibrium equations for the fragile X [fra(X)] genotype frequencies. We also showed that small variations in the value of s (selection coefficient of affected heterozygotes) and r (imprinting rate during oogenesis) affect genotype ratios significantly.

Effect of X inactivation on fragile X frequency and mental retardation.

The probability of a heterozygote being affected was estimated from the distribution of frequencies of early-replicating fragile X [fra(X)] chromosome in normal and mentally retarded heterozygotes, taking into account the prior probabilities of 0.35 for mental retardation and 0.65 for normality. The estimated probability of a heterozygote with 100% early-replicating fra(X) being mentally retarded was 78%, which coincides with the value of penetrance in males. Therefore, the manifestation of retardation in females seems to differ from that in males due solely to X inactivation. The frequencies of early-replicating fra(X) were significantly increased among the heterozygotes with the highest frequencies of fra(X) both in the normal group and in the mentally retarded. The mean frequencies of early-replicating fra(X) were 0.42 and 0.68 for normal and mentally retarded heterozygotes, respectively. Considering the overall frequency of retarded heterozygotes as 0.35, the mean frequency of early-replicating fra(X) obtained for all heterozygotes was 0.51, which is in accordance with the hypothesis of random X inactivation. Thus the fragile site appears to have equal chances of being detected when located either on the early- or on the late-replicating X. This leads to the conclusion that the frequency of the fragile site is a consequence of the proportion of cells with the active Martin-Bell syndrome (MBS) gene and not the result of a better visualization of the site on the early-replicating X.

The number of CGG repeats of the FMR1 locus in premutated and fully mutated heterozygotes and their offspring: implications for the origin of mosaicism.

The size of the CGG repeat of the FMR1 gene was investigated with probe StB12.3 in 154 transmissions to the offspring of heterozygotes for the premutation and the full mutation. Among the 135 offspring of premutated heterozygotes there were three decreases in size of the repeats: in two of these cases a full mutation was present along with the decreased premutation, and in a third mosaic (46,fra(X)(q27.3),Y), a normal allele was observed. In the 19 offspring of fully mutated females with no detected mosaicism, there were three mosaics and three individuals who had full mutations that included a number of repeats smaller than those present in their mothers. Among the 32 offspring who received a premutation from their premutated mothers, 27 alleles were increased in size and 5 remained unaltered. Among 11 mosaic offspring of premutated mothers, the premutation increased in 4, decreased in 3, and was unchanged in 4. In contrast to the trend of an increasing premutation size in the non-mosaic offspring, the premutation present in mosaics can be smaller, larger, or of unaltered size with approximately equal frequencies. These data suggest that the premutations present in mosaics result from mitotic instability of the inherited full mutations. This is further supported by the finding of a mosaic male with a normal sized allele.

Relationship of expansion of CGG repeats and X-inactivation with expression of fra(X)(q27.3) in heterozygotes.

Expression of the fragile site Xq27.3 was investigated in 82 heterozygotes (58 normal and 24 mentally impaired) diagnosed by DNA analysis. EcoRI and EagI DNA digests were probed with StB12.3. This allowed the detection of the expansion of the CGG repeat of the FMR1 gene and the methylation pattern of the adjacent CpG island. Heterozygotes with delta < or = 400 bp (52/82) were all mentally normal and manifested fra(X) in less than 3% of the cells or did not express it. Unmethylated mutant alleles were always observed. About two thirds of females with delta > 500 bp (21/30) showed fra(X) frequencies above 3% (3 normal and 18 mentally impaired). Lower frequencies of fra(X) or negative results were observed in the remaining 9 females (3 normal and 6 affected). The large mutant alleles were always methylated. Therefore, while delta < or = 400 bp is always associated with negative or low expression of fra(X), larger expansions are not present exclusively in heterozygotes with high frequencies of fra(X). In 25 of 30 heterozygotes with delta > 500 bp, active and inactive normal alleles were observed. Three fra(X)-negative or low manifesting heterozygotes showed completely skewed X-inactivation, with the normal allele either active or inactive. Two females with high frequencies of fra(X) always had the normal allele inactivated. Densitometry studies showed no difference in the inactivation of the normal allele between heterozygotes who manifested fra(X) or not. Thus fra(X) expression does not seem to be influenced by X-inactivation.

Brief clinical report: duplication of distal 17q: report of an observation.

We describe a boy with the syndrome due to dup(17q) resulting from a paternal balanced t(12;17) (q24;q23). The comparison of the clinical findings in our patient with those previously reported shows that the dup(17q23----qter) is associated with a clinically recognizable syndrome. Anomalies present in greater than or equal to 75% of the patients were severe psychomotor retardation; short stature; microcephaly; frontal bossing and temporal retraction; widow's peak; narrow palpebral fissures; flat nasal bridge; thin upper lip overlapping thin lower lip; downturned corners of the mouth; apparently low-set, posteriorly angulated and malformed ears; low posterior hairline; widely spaced nipples; cryptorchidism; proximal limb shortness; and hyperlaxity of limb joints. The translocation carrier father of our patient had a Poland anomaly.

Phenotypic spectrum of 45,X/46,XY individuals.

We report on five patients with 45,X/46,XY mosaicism. In these subjects, as well as in 58 individuals from the literature with a similar chromosome constitution, we did not find a preponderance of 46,XY cells among patients showing ambiguous to abnormal male external genitalia when compared to those patients with slight or no virilization. However, the average frequency of 46,XY cells in blood in these mosaic individuals suggests that this sample includes mainly individuals whose mosaicism originated early in embryonic cell division. Those individuals whose mosaicism originated later are not significantly represented in this sample and would have higher frequencies of 46,XY cells. These individuals would be excluded from an intersex sample if they had well-virilized genitalia. This ascertainment bias suggests that the degree of virilization depends on the frequency of 46,XY cells.

Duchenne muscular dystrophy in a girl with a 45,X/46,XX/47,XXX chromosome constitution.

We report on a 4-year-old girl with Duchenne muscular dystrophy (DMD). One of her sisters had grossly elevated serum creatine-kinase and pyruvate-kinase levels, and one of her maternal great uncles was presumptively affected by DMD. Cytogenetic analysis showed a 45,X/46,XX/47,XXX chromosome constitution. The maternally inherited DMD gene is presumed to be present on the single X of the 45,X cell line.

Partial aniridia, cerebellar ataxia, and mental deficiency (Gillespie syndrome) in two brothers.

We report on two brothers (in a sibship of three) with partial aniridia, cerebellar ataxia, and moderate mental retardation, with normal G-banded chromosomes. Both present cerebellum hypoplasia; the younger also has congenital pulmonic stenosis. A review of the literature is presented. Cause is unknown, although the possibility of an autosomal recessive gene cannot be ruled out.

FRAXA premutation associated with premature ovarian failure.

A family is described in which six females in three generations experienced premature ovarian failure (POF). In three of them a FRAXA premutation was documented and the carrier status of a fourth female could be inferred, because her son had the fragile X syndrome. These findings provide further evidence for a nonrandom association between POF and the FRAXA premutation.

DXS548/FRAXAC1 haplotypes in fragile X chromosomes in the Brazilian population.

In order to investigate the origin of the fragile X mutation in the Brazilian population, we assessed the size of the microsatellite markers DXS548, FRAXAC1 and FRAXAC2 in 72 X chromosomes from unrelated affected males and 64 control chromosomes. We found a significantly different distribution of alleles between fragile X and controls for loci DXS548 and FRAXAC1, but no apparent linkage disequilibrium was detected for the sequence FRAXAC2. The most frequent DXS548/FRAXAC1 haplotypes in affected males were haplotypes 204/158 bp (2-1) and 196/152 bp (6-4). These findings are in accordance with the proposed two main mutational pathways for the generation of FMR-1 alleles that predispose to instability and hyperexpansion.

Fragile X frequency in a mentally retarded population in Brazil.

Seventy-five male and 50 female students from 2 special schools for mildly, moderately retarded, or borderline individuals were screened clinically and cytogenetically in order to estimate the contribution of fragile X [fra(X)] syndrome to the cause of mental retardation in Brazil. We found 6 males (8%) from 4 families and 2 unrelated females (4%) with fra(X) chromosomes. One male and one female were isolated cases. The estimated frequency of Martin-Bell [fra(X)] syndrome among mentally impaired individuals in Brazil was similar to that previously reported in other countries.

Neuroblastoma in a boy with MCA/MR syndrome, deletion 11q, and duplication 12q.

Deletion 11q23-->qter and duplication 12q23-->qter are described in a boy with neuroblastoma, multiple congenital anomalies, and mental retardation. The patient has clinical manifestations of 11q deletion and 12q duplication syndromes. The possible involvement of the segment 11q23-->24 in the cause of the neuroblastoma is discussed.