Molecular cytogenetic analysis of a duplication Xp in a male: further delineation of a possible sex influencing region on the X chromosome

Mutation screening in the Greek population and evaluation of NLGN3 and NLGN4X genes causal factors for autism

Molecular and neurobiological evidence for the involvement of neuroligins (particularly NLGN3 and NLGN4X genes) in autistic disorder is accumulating. However, previous mutation screening studies on these two genes have yielded controversial results. The present study explores, for the first time, the contribution of NLGN3 and NLGN4X genetic variants in Greek patients with autistic disorder. We analyzed the full exonic sequence of NLGN3 and NLGN4X genes in 40 patients strictly fulfilling the Diagnostic and Statistical Manual of Mental Disorders, 4th ed. criteria for autistic disorder. We identified nine nucleotide changes in NLGN4X--one probable causative mutation (p.K378R) previously reported by our research group, one novel variant (c.-206G>C), one nonvalidated single nucleotide polymorphism (SNP, rs111953947), and six known human SNPs reported in the SNP database--and one known human SNP in NLGN3 also reported in the SNP database. The variants identified are expected to be benign. However, they should be investigated in the context of variants in interacting cellular pathways to assess their contribution to the etiology of autism.

De novo duplication of Xq22.1→q24 with a disruption of the NXF gene cluster in a mentally retarded woman with short stature and premature ovarian failure

OBJECTIVE

To present molecular cytogenetic characterization of a de novo duplication of Xq22.1→q24 in a mentally retarded woman with short stature and premature ovarian failure.

MATERIALS AND METHODS

A 19-year-old woman presented with psychomotor retardation, developmental delay, mental retardation, short stature, low body weight, general muscle hypotonia, distal muscle hypotrophy of the lower extremities, elongated digits, scanty pubic and axillary hair, hypoplastic external female genitalia, and secondary amenorrhea but no clinical features of Pelizaeus-Merzbacher disease. Conventional cytogenetic analysis revealed a karyotype of 46,X,dup(X)(q22.1q24). Fluorescence in situ hybridization determined a direct duplication with a linear tandem orientation. Array comparative genomic hybridization demonstrated partial trisomy Xq [arr cgh Xq22.1q24 (101,490,234-119,070,188 bp)×3] with a 17.6-Mb duplication.

RESULTS

The duplicated region contained NXF2B, NXF4, NXF3, PLP1, and PGRMC1 genes. There was a disruption of the NXF gene cluster of Xcen-NXF5-NXF2-NXF2B-NXF4-NXF3-Xqter.

CONCLUSION

A duplication of Xq22.1→q24 with a disruption of the NXF gene cluster in female patients can be associated with clinical manifestations of mental retardation in addition to short stature and premature ovarian failure.

First reported case of intrachromosomal cryptic inv dup del Xp in a boy with developmental retardation

We report here on a 6-year-old boy referred to the laboratory for karyotyping and SHOX microdeletion testing. The most significant clinical findings in this boy were small stature, Madelung deformity, facial dysmorphism, mild mental retardation and behavioral problems. R-, G- and RTBG-banding chromosome analysis showed a normal male karyotype. Fine molecular characterization, by FISH, of terminal Xp microdeletion revealed an associated partial duplication. Further refinement of the molecular analysis indicated an inverted duplication of the Xp22.31-Xp22.32 (13.7 Mb) region including the STS, VCX-A and KAL1 genes, associated with a terminal Xp deletion Xp22.33-Xpter (3.6 Mb) encompassing the SHOX and ARSE genes. Such rearrangements have been characterized for other chromosomal pairs, but this is the first reported male patient involving the short arm of the X chromosome. Molecular analysis of the maternal and patient's microsatellite markers showed interchromatid mispairing leading to non-allelic homologous recombination to be the most likely mechanism underlying this rearrangement. This case highlights the importance of clinically driven FISH investigations in order to uncover cryptic micro-rearrangements.

Brief report: non-random X chromosome inactivation in females with autism

Autism is a heterogeneous neurodevelopmental disorder with a 3-4 times higher sex ratio in males than females. X chromosome genes may contribute to this higher sex ratio through unusual skewing of X chromosome inactivation. We studied X chromosome skewness in 30 females with classical autism and 35 similarly aged unaffected female siblings as controls using the polymorphic androgen receptor (AR) gene. Significantly, increased X chromosome skewness (e.g., >80:20%) was detected in our autism group (33%) compared to unaffected females (11%). X chromosome skewness was also seen in 50% of the mothers with autistic daughters. No mutation was seen in the promoter region of the XIST gene reported to be involved in X chromosome inactivation in our subjects. X chromosome skewness has been reported in female carriers of other neurological disorders such as X-linked mental retardation, adrenoleukodystrophy and Rett syndrome.

Cytogenetic abnormalities and fragile-X syndrome in Autism Spectrum Disorder

BACKGROUND

Autism is a behavioral disorder with impaired social interaction, communication, and repetitive and stereotypic behaviors. About 5-10 % of individuals with autism have 'secondary' autism in which an environmental agent, chromosome abnormality, or single gene disorder can be identified. Ninety percent have idiopathic autism and a major gene has not yet been identified. We have assessed the incidence of chromosome abnormalities and Fragile X syndrome in a population of autistic patients referred to our laboratory.

METHODS

Data was analyzed from 433 patients with autistic traits tested using chromosome analysis and/or fluorescence in situ hybridization (FISH) and/or molecular testing for fragile X syndrome by Southern and PCR methods.

RESULTS

The median age was 4 years. Sex ratio was 4.5 males to 1 female [354:79]. A chromosome (cs) abnormality was found in 14/421 [3.33 %] cases. The aberrations were: 4/14 [28%] supernumerary markers; 4/14 [28%] deletions; 1/14 [7%] duplication; 3/14 [21%] inversions; 2/14 [14%] translocations. FISH was performed on 23 cases for reasons other than to characterize a previously identified cytogenetic abnormality. All 23 cases were negative. Fragile-X testing by Southern blots and PCR analysis found 7/316 [2.2 %] with an abnormal result. The mutations detected were: a full mutation (fM) and abnormal methylation in 3 [43 %], mosaic mutations with partial methylation of variable clinical significance in 3 [43%] and a permutation carrier [14%]. The frequency of chromosome and fragile-X abnormalities appears to be within the range in reported surveys (cs 4.8-1.7%, FRAX 2-4%). Limitations of our retrospective study include paucity of behavioral diagnostic information, and a specific clinical criterion for testing.

CONCLUSIONS

Twenty-eight percent of chromosome abnormalities detected in our study were subtle; therefore a high resolution cytogenetic study with a scrutiny of 15q11.2q13, 2q37 and Xp23.3 region should be standard practice when the indication is autism. The higher incidence of mosaic fragile-X mutations with partial methylation compared to FRAXA positive population [50% vs 15-40%] suggests that faint bands and variations in the Southern band pattern may occur in autistic patients.

Functional disomy of Xp including duplication ofDAX1gene with sex reversal due to t(X;Y)(p21.2;p11.3)

Translocations involving the short arms of the X and Y in human chromosomes are uncommon. One of the best-known consequences of such exchanges is sex reversal in 46,XX males and some 46,XY females, due to exchange in the paternal germline of terminal portions of Xp and Yp, including the SRY gene. Translocations of Xp segments to the Y chromosome result in functional disomy of the X chromosome with an abnormal phenotype and sex reversal if the DSS locus, mapped in Xp21, is present. We describe a 7-month-old girl with severe psychomotor retardation, minor anomalies, malformations, and female external genitalia. Cytogenetic analysis showed a 46,X,mar karyotype. The marker was identified as a der(Y)t(Xp;Yp) by fluorescence in situ hybridisation analysis. Further studies with specific locus probes of X and Y chromosomes made it possible to clarify the break points and demonstrated the presence of two copies of the DAX1 gene, one on the normal X chromosome and one on the der(Y). The karyotype of the child was: 46,X,der(Y)t(X;Y)(p21.2;p11.3). The syndrome resulted from functional disomy Xp21.2-pter, with sex reversal related to the presence of two active copies of the DAX1 gene located in Xp21. Few cases of Xp disomy with sex reversal have been reported, primarily related to Xp duplications with 46,XY karyotype, and less often to Xp;Yq translocations. To our knowledge, our patient with sex reversal and a t(Xp;Yp) is the second reported case.

Gastrin-releasing peptide receptor (GRPR) locus in Japanese subjects with autism

Gastrin-releasing peptide receptor (GRPR) gene is considered a candidate locus for infantile autism for several reasons. The present study investigated two polymorphic sites (C/450/T and C/661/T) in the second exon of the GRPR gene in Japanese patients with autism (DSM-IV) and healthy subjects. The two polymorphic sites were at high linkage disequilirium, consistent with a previous study in a North American population. The C450-C661 allele, which was observed in one-third of the chromosomes from the North American subjects, was less frequent (6-7%) in the Japanese subjects, suggesting a large ethnic difference in the frequency of the polymorphism. The allele frequencies and genotype distributions were not significantly different between the patients and controls. However, further studies are required to exclude the GRPR locus as a candidate locus for autism, considering the low frequency of the polymorphism in the Japanese subjects.

Autism and the X chromosome: no linkage to microsatellite loci detected using the affected sibling pair method

The etiology of autism spectrum disorders (ASDs) is poorly understood, although it is clear that genetic factors play a major role. ASDs appear to be a heterogeneous group of disorders, making genetic analysis difficult in the absence of etiologically definable subgroups. The excess of males in the affected population has led to suggestions that an X-linked locus could play a role in the causation of autism or a related pervasive developmental disorder. To examine this, we have investigated the genotypes of 31 families with two or more affected boys, at a series of 16 highly polymorphic loci distributed along the X chromosome with an average interlocus distance of 12 cM, in order to identify regions of significantly increased concordance among pairs of affected brothers. No locus tested showed a significant increase in concordance, supporting findings by others that there are no genes of major effect located on the X chromosome that contribute to increased susceptibility to ASD.

Chromosomal abnormalities in a clinic sample of individuals with autistic disorder

We examined data from the largest reported sample of autistic individuals who have been karyotyped with the aim of providing additional information in the search for autism disease genes. Individuals seen in the University of Iowa's Child and Adolescent Psychiatry Clinic since 1980 who had been diagnosed with autism were cross-referenced with the University of Iowa's Cytogenetics Laboratory database. We determined the number of individuals referred for cytogenetic testing and, of these, the number found to have gross cytological abnormalities. Medical records were reviewed for all cases with such abnormalities. Between 1980 and 1998, 898 subjects seen in the clinic were diagnosed with autism. Of these, 278 (30.1%) were referred for cytological studies; 25 (9.0%) of these were found to have chromosomal abnormalities. The most common chromosomal abnormalities were Fragile X, other sex chromosome anomalies, and chromosome 15 abnormalities. These data support the contribution of chromosomal abnormalities to a small but significant number of cases of autism, and highlight the involvement of chromosome 15 and the sex chromosomes.

The HOPA gene dodecamer duplication is not a significant etiological factor in autism

A recent study has suggested that a dodecamer duplication in the HOPA gene in Xq13 may occur in a significant portion of male patients with autism. We have determined the incidence of this duplication in 202 patients from the South Carolina Autism Study. The incidence of the duplication was not significantly different between patients and controls. Three of the female patients inherited the duplication from nonautistic fathers. In addition, there was no systematic skewing of X inactivation in the female patients with the duplication, or in nonautistic mothers and sisters with the duplication. These findings suggest that the dodecamer duplication in the HOPA gene does not play a significant role in the etiology of autism.

Chromosomal disorders and autism

Many cases of autism appear to be caused by several abnormal genes acting in concert. The literature on chromosomal aberrations in autism is reviewed, with a view to finding potential gene markers for the neuropsychiatric disorder. Most of the chromosomes have been implicated in the genesis of autism. However, aberrations on the long arm of Chromosome 15 and numerical and structural abnormalities of the sex chromosomes have been most frequently reported. These chromosomes appear to hold particular promise in the search for candidate genes.

Intersitial deletion of 20p: new candidate region for Hirschsprung disease and autism?

We describe a patient with Hirschsprung disease and autism. High-resolution karyotyping indicated that the patient has an interstitial deletion of 20p11.22-p11.23. Microsatellite analysis showed a deletion involving a 5-6 cM region from the maternally derived chromosome 20. The deleted region is proximal to, and does not overlap, the recently characterized Alagille syndrome region. This region of 20p has not yet been implicated in Hirschsprung disease or autism. However, this region contains several genes that could plausibly contribute to any phenotype that includes abnormal neural development.

Molecular cytogenetic identification of four X chromosome duplications

Four cases with previously unidentified X-chromosome abnormalities were studied by standard cytogenetic techniques and FISH in order to demonstrate the origin of the extra segment on the abnormal X chromosomes. All cases were identified as X-chromosome duplications by using a chromosome-specific painting probe. Application of appropriate locus-specific DNA probes as an adjunct to GTG- and RBG-banding proved useful in defining the breakpoints and the extent of the duplications. Although the duplicated X chromosome in female cases was selectively inactivated, as demonstrated by its late-replicating pattern, abnormal clinical findings were manifested in 3 female patients.

A duplication of distal Xp associated with hypogonadotrophic hypogonadism, hypoplastic external genitalia, mental retardation, and multiple congenital abnormalities

An unusual familial case of three sibs with a partial duplication of distal Xp sequences is described. The proband, an 18 year old boy, showed mental retardation, severe dysmorphic features, hypogonadotrophic hypogonadism (HHG), and hypoplastic external genitalia. His karyotype was 46,Y,inv dup(X) (p22.11-->p 22.32). The proband has two sisters each with the same inv dup(Xp) chromosome. Both sisters presented with short stature but were otherwise phenotypically normal. The abnormal X chromosome was inactive in the majority of cells examined. Southern blot dosage analysis indicated a duplication of distal Xp sequences. The proximal breakpoint is located between DXS28 and DXS41, and is therefore at least 2 Mb distal to the DSS locus. The relationship between the phenotype and the Xp duplication is discussed.

Sex determining gene on the X chromosome short arm: dosage sensitive sex reversal

The present review article summarizes current knowledge concerning the sex determining gene on Xp21, termed DSS (dosage sensitive sex reversal). The presence of DSS has been based on the finding that, in the presence of SRY, partial active Xp duplications encompassing the middle part of Xp result in sex reversal, whereas those of the distal or proximal part of Xp permit male sex development. Because Klinefelter patients develop as males, it is believed that DSS is normally subject to X-inactivation, and that two active copies of DSS override the function of SRY, resulting in gonadal dysgenesis because of meiotic pairing failure. It may be possible that DSS encodes a target sequence for repressing function of SRY or that DSS is involved in an X chromosome-counting mechanism. Molecular approaches have localized DSS to a 160 kb region and isolated candidate genes such as DAX-1 and MAGE-Xp, but there has been no formal evidence equating the candidate gene with DSS. In addition to its clinical importance, the exploration of DSS must provide a useful clue to phylogenetic studies of sex chromosomes and dosage compensation.

Hypomelanosis of Ito and X;autosome translocations: a unifying hypothesis

Hypomelanosis of Ito is a sporadic multisystem disorder known to be associated in many cases with chromosomal mosaicism. While no particular pattern is generally evident for the specific chromosomes involved in such patients, a subgroup of female patients exists in whom the common factor is the presence of a balanced, constitutional X;autosome translocation, with a cytogenetic breakpoint in the pericentromeric region of the X. It is argued here that the phenotype in these cases results not from the interruption of X linked genes but from the presence of mosaic functional disomy of X sequences above the breakpoint.

Xp-duplications with and without sex reversal

Duplications in Xp including the DSS (dosage sensitive sex reversal) region cause male to female sex reversal. We investigated two patients from families with Xp duplications. The first case was one of two sisters with karyotype 46,XY,der(22),t(X;22)(p11.3;p11)mat and unambiguous female genitalia. The living sister was developmentally retarded, and showed multiple dysmorphic features and an acrocallosal syndrome. The second case was a boy with a maternally inherited direct duplication of Xp21.3-pter with the breakpoint close to the DSS locus. He had multiple abnormalities and micropenis, but otherwise unambiguous male genitalia. We performed quantitative Southern blot analysis with probes from Xp22.13 to p21.2 to define the duplicated region. Clinical, cytogenetic, and molecular data from both patients were compared with those of previously reported related cases. A comparison of the extragenital symptoms revealed no differences between patients with or without sex reversal. In both cases, the symptoms were non-specific. Among 22 patients with a duplication in Xp, nine had unambiguous female genitalia and a well-documented duplication of the DSS region. Two patients with duplication of DSS showed ambiguous external genitalia. From these data, we conclude that induction of testicular tissue may start in these patients, but that the type of genitalia depends on the degree of subsequent degeneration by a gene in DSS.

The genetic basis of murine and human sex determination: a review

Determination of mammalian sex depends on the presence or absence of a functional testis. Testes are determined by the activity of the testis determining factor encoded by the sex determining gene, Y (SRY) located on the Y chromosome. Considerable evidence suggests that the SRY gene is the only gene on the Y chromosome that is both necessary and sufficient to initiate testis determination. Other steps in the mammalian sex determining pathway are unknown, although recent advances have shown that mutations in X chromosome and autosomal loci are also associated with sex reversal, suggesting the presence of at least one other sex determining gene. Duplications of sequences on the short arm of the human X chromosome, including the DAX-1 (DSS-AHC critical region on the X chromosome, gene 1) gene, are occasionally associated with XY male-to-female sex reversal. In addition, mutations in the SRY-related gene SOX9 (SRY-related box) are associated with a failure of human testicular determination. Furthermore, the occurrence of inherited sex reversed conditions in both mice and men indicate the presence of at least one other sex determining gene. Breeding the Y chromosome from certain Mus musculus domesticus strains into the laboratory mouse strain C57BL/6J results in XY male-to-female sex reversal. This suggests both allelic variation of the Sry gene and the presence of autosomal sex determining genes. In humans, familial cases of SRY-negative XX males occur. Analysis of the transmission of the trait indicates the segregation of an autosomal or X-linked recessive mutation. The mutation may be in a gene whose wild-type function is to inhibit male sex determination. SRY may trigger male sex determination by repressing or functionally antagonizing the product of this gene.

Agonadism in two sisters with XY gonosomal constitution, mental retardation, short stature, severely retarded bone age, and multiple extragenital malformations: a new autosomal recessive syndrome

We report on 12- and 14-year old sisters with a 46, XY chromosome constitution, normal female external genitalia, and absence of gonadal tissue. Except for omphalocele, right renal agenesis and malrotation of the colon in the elder sister, the internal organs were normal. Both were mentally retarded, of short stature, and had extremely retarded bone age. In addition, they had an almost identical pattern of minor anomalies: peculiar face, hypodontia, short neck, inverted nipples, thoracolumbar scoliosis, "dysplastic" hips, partial clino-/syndactyly of toes. The occurrence of a basically similar set of malformations in two sisters and the first cousin consanguinity of the parents suggests autosomal recessive inheritance. The conserved region of the SRY gene ([high mobility group] HMG box) was sequenced in the elder sib and was normal. No consistent malformations are observed at present in agonadal patients. This supports the idea that several autosomal genes have the potential of influencing the sequence of events of sex determination.