Inherited partial X chromosome duplication in a mentally retarded male

CNV Analysis through Exome Sequencing Reveals a Large Duplication Involved in Sex Reversal, Neurodevelopmental Delay, Epilepsy and Optic Atrophy

BACKGROUND

Duplications on the short arm of chromosome X, including the gene NR0B1, have been associated with gonadal dysgenesis and with male to female sex reversal. Additional clinical manifestations can be observed in the affected patients, depending on the duplicated genomic region. Here we report one of the largest duplications on chromosome X, in a Lebanese patient, and we provide the first comprehensive review of duplications in this genomic region.

CASE PRESENTATION

A 2-year-old female patient born to non-consanguineous Lebanese parents, with a family history of one miscarriage, is included in this study. The patient presents with sex reversal, dysmorphic features, optic atrophy, epilepsy, psychomotor and neurodevelopmental delay. Single nucleotide variants and copy number variants analysis were carried out on the patient through exome sequencing (ES). This showed an increased coverage of a genomic region of around 23.6 Mb on chromosome Xp22.31-p21.2 (g.7137718-30739112) in the patient, suggestive of a large duplication encompassing more than 60 genes, including the NR0B1 gene involved in sex reversal. A karyotype analysis confirmed sex reversal in the proband presenting with the duplication, and revealed a balanced translocation between the short arms of chromosomes X and 14:46, X, t(X;14) (p11;p11) in her/his mother.

CONCLUSIONS

This case highlights the added value of CNV analysis from ES data in the genetic diagnosis of patients. It also underscores the challenges encountered in announcing unsolicited incidental findings to the family.

An Xp21.3p11.4 duplication observed in a boy with intellectual deficiency and speech delay and his asymptomatic mother

BACKGROUND

Interstitial Xp duplications have been rarely described, especially in males. Male patients show intellectual deficiency (ID) and variable congenital malformations depending on the size and the position of the duplication.

METHODS

Cytogenetic and molecular analyses using standard G-banding, R-banding, fluorescence in situ hybridization, and an array comparative genomic hybridization analysis for copy number variation detection were performed in the propositus and his mother.

RESULTS

A 12,168,283 bp interstitial duplication of the Xp21.3p11.4 region was detected in the boy with ID and speech delay and his asymptomatic mother.

CONCLUSION

An Xp21.3p11.4 duplication was characterized at the molecular level in a boy with ID and speech delay. Genotype-phenotype correlations of interstitial Xp duplications were performed by comparing previously reported cases and our patient.

Pure de-novo 5 Mb duplication at Xp11.22-p11.23 in a male: phenotypic and molecular characterization

Males with duplications within the short arm of the X chromosome are rare and most cases are inherited from a maternal heterozygote. Here we describe the first detailed characterization of a de-novo Xp duplication delineated to Xp11.22-->Xp11.23 in a 15-year-old male with moderate mental impairment, autistic-like behaviour, short stature, and mild dysmorphic features. Chromosome analysis (550 band resolution) was normal and comparative genomic hybridization (CGH) analysis on metaphase spreads detected duplication on Xp11. Further characterization of the duplication by array CGH, FISH experiments with specific BAC probes, and genotyping with microsatellite markers helped to determine proximal and distal breakpoints giving a size of the duplication of approximately 5 Mb. As far as we are aware this is the first described male with isolated microduplication on Xp11.22-Xp11.23. Among the genes included within the duplicated region, and particularly those which are outside copy number polymorphisms, we discuss the relationship of FTSJ1, PQBP1 and HDAC6 with the clinical symptoms of our patient.

Regulation of sexual dimorphism in mammals

Sexual dimorphism in humans has been the subject of wonder for centuries. In 355 BC, Aristotle postulated that sexual dimorphism arose from differences in the heat of semen at the time of copulation. In his scheme, hot semen generated males, whereas cold semen made females (Jacquart, D., and C. Thomasset. Sexuality and Medicine in the Middle Ages, 1988). In medieval times, there was great controversy about the existence of a female pope, who may have in fact had an intersex phenotype (New, M. I., and E. S. Kitzinger. J. Clin. Endocrinol. Metab. 76: 3-13, 1993.). Recent years have seen a resurgence of interest in mechanisms controlling sexual differentiation in mammals. Sex differentiation relies on establishment of chromosomal sex at fertilization, followed by the differentiation of gonads, and ultimately the establishment of phenotypic sex in its final form at puberty. Each event in sex determination depends on the preceding event, and normally, chromosomal, gonadal, and somatic sex all agree. There are, however, instances where chromosomal, gonadal, or somatic sex do not agree, and sexual differentiation is ambiguous, with male and female characteristics combined in a single individual. In humans, well-characterized patients are 46, XY women who have the syndrome of pure gonadal dysgenesis, and a subset of true hermaphrodites are phenotypic men with a 46, XX karyotype. Analysis of such individuals has permitted identification of some of the molecules involved in sex determination, including SRY (sex-determining region Y gene), which is a Y chromosomal gene fulfilling the genetic and conceptual requirements of a testis-determining factor. The purpose of this review is to summarize the molecular basis for syndromes of sexual ambiguity seen in human patients and to identify areas where further research is needed. Understanding how sex-specific gene activity is orchestrated may provide insight into the molecular basis of other cell fate decisions during development which, in turn, may lead to an understanding of aberrant cell fate decisions made in patients with birth defects and during neoplastic change.

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.

Partial disomy of Xp and the presence of SRY in a phenotypic female

We present a study of a mentally retarded and mildly dysmorphic female in whom initial cytogenetic studies identified the karyotype 46,X, + mar. Further characterisation of the structurally abnormal chromosome by fluorescence in situ hybridisation (FISH) showed that it is composed of both X and Y chromosome material with a centromere originating from the Y chromosome. The presence of the DMD gene and the absence of the XIST gene was shown by FISH using locus specific probes. The Y segment included the SRY and ZFY genes. Based on these findings, the karyotype was defined as 46, X,der(Y)t(X;Y) (p21.1;q11). This case illustrates male to female sex reversal owing to a partial duplication of the short arm of the X chromosome in the presence of SRY.

Partial X chromosome trisomy with functional disomy of Xp due to failure of X inactivation

A 5-month-old girl with mild phenotypic abnormalities, developmental delay, and seizures was found to have the de novo karyotype 46,XX,-13,+der(13)t(X;13)(p21.2;p11.1). The partial trisomy of Xp21.2-->pter was confirmed with fluorescence in situ hybridization, using an X chromosome painting probe and several cosmid and YAC probes for Xp sequences. Replication banding showed that one of the structurally normal X chromosomes was late-replicating, but that the Xp segment of the der(13) was early-replicating in all cells examined. Since segments of the X chromosome separated from the X inactivation center in Xq13.2 cannot undergo X inactivation, the result is functional disomy of distal Xp. As the loss of short arm material from chromosome 13 is not considered to be clinically significant, the genomic imbalance of Xp expressed in this patient most likely accounts for her abnormal phenotype.

The biochemical role of SRY in sex determination

The human sex-determining gene on the Y chromosome, termed SRY, has recently been isolated by positional cloning; compelling evidence now exists equating SRY with the testis-determining factor, TDF. The SRY gene product is an HMG box protein whose DNA-binding activity is vital for testis formation as sex-reversed patients with SRY mutations lack this activity in vitro. The in vivo DNA target for SRY, however, remains elusive. Here, we show, by gel retardation analysis, that SRY recognises specific DNA sequences and that such sequences exist upstream of the AMH promoter, a potential downstream target for SRY. We also describe the DNA bending and cruciform DNA-binding functions of SRY and propose a model for the potential action of SRY in the "HMG-1-rich" mammalian nucleus.

A dosage sensitive locus at chromosome Xp21 is involved in male to female sex reversal

Male to female sex reversal has been observed in individuals with duplications of the short arm of the X chromosome. Here we demonstrate that sex reversal results from the presence of two active copies of an Xp locus rather than from its rearrangement and that alterations at this locus constitute one of the causes of sex reversal in individuals with a normal 46,XY karyotype. We have named this locus DSS (Dosage Sensitive Sex reversal) and localized it to a 160 kilobase region of chromosome Xp21, adjacent to the adrenal hypoplasia congenita locus. The identification of male individuals deleted for DSS suggests that this locus is not required for testis differentiation. We propose that DSS has a role in ovarian development and/or functions as a link between ovary and testis formation.

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

We describe a male infant with severe mental retardation and autism with a duplication of the short arm of the X chromosome. Chromosome painting confirmed the origin of this X duplication. Molecular cytogenetic analysis with fluorescence in situ hybridization (FISH) identified one copy of the zinc finger protein on the X chromosome (ZFX) and two copies of the steroid sulfatase gene (STS), further delineating the breakpoints. Based on cytogenetic and molecular comparisons of cases from the literature of sex-reversal in dup(X),Y patients and our patient, we suggest that a possible secondary sex-influencing gene involved in the regulation of sex determination or testis morphogenesis is present at the distal Xp21.1 to p21.2 region.

SRVX, a sex reversing locus in Xp21.2-->p22.11

Duplication within Xp21 causes female or intersexual development in human embryos with an XY chromosome complement. We have mapped the responsible gene, SRVX (sex reversal X), in XY-sex-reversed maternal half siblings who had inherited the duplication from their mother. The limited size of the duplication in our cases, relative to its extent in other similar cases, allows assignment of the SRVX locus to Xp21.2-->p22.11. We infer that SRVX is part of a pathway of sex-determining genes that includes SRY and SRA1, the latter recently assigned to chromosome 17q. If mutation of SRA1 or SRVX can reverse the sex of the XY fetus, this would explain why mutation within SRY is found only sporadically in women with XY gonadal dysgenesis.

Duplication of the short arm of the X chromosome in mother and daughter

An 11-year-old girl with short stature, mental retardation, and mild dysmorphic features was found to have an inverted duplication of most of the short arm of the X chromosome [dic inv dup(X)(qter-->p22.3::p22.3-->cen:)]. Her mother, who is also short and retarded, carries the same duplication. Fluorescence in situ hybridization with an X chromosome library, and with X centromere-specific alpha satellite and telomere probes, was useful in characterizing the duplication. In most females with structurally abnormal X chromosomes, the abnormal chromosome is inactivated. Although the duplicated X was consistently late replicating in the mother, X chromosome inactivation studies in the proband indicated that in 11% of her lymphocytes the duplicated X was active.

A complex rearrangement associated with sex reversal and the Wolf-Hirschhorn syndrome: a cytogenetic and molecular study

We report a male infant referred with multiple congenital abnormalities consistent with the Wolf-Hirschhorn syndrome. Cytogenetic analysis showed a chromosome complement of 46,XX with a deletion of 4p15.2----4pter and its replacement by material of unknown origin. The patient was positive for a number of Yp probes including SRY, the testis determining factor, and in situ hybridisation localised the Yp material to the tip of the short arm of one X chromosome. Using pDP230, a probe for the pseudoautosomal region, and M27 beta, which recognises a locus in proximal Xp, the material translocated on to 4p was identified as originating from the short arm of the paternal X chromosome. The most reasonable explanation for this complex rearrangement is two separate exchange events involving both chromatids of Xp during paternal meiosis. An aberrant X-Y interchange gave rise to the sex reversal and an X;4 translocation resulted in additional, apparently active Xp material and a deletion of 4p which produced the Wolf-Hirschhorn phenotype.

Sex reversal in a child with a 46,X,Yp+ karyotype: support for the existence of a gene(s), located in distal Xp, involved in testis formation

We report on a sex reversed Japanese child with a 46,X,Yp+ karyotype, minor dysmorphic features, and no testicular development. The Yp+ chromosome was derived by translocation of an Xp fragment (Xp21-Xp22.3) to Yp11.3. This has resulted in deletion of distal part of the Y chromosome pseudoautosomal region (DXYS15-telomere) and duplication of the X specific region (DXS84-PABX) and proximal part of the pseudoautosomal region (MIC2-DXYS17). No deletion of the Y specific region was detected nor was any mutation found in SRY. Cytogenetic analysis suggests that the proximal part of the Xp fragment is the most distal part of the short arm of the Yp+ chromosome (Xp21----Xp 22.3::Yp11.3----Yqter). No chromosomal mosaicism was detected. These results are similar to previous reports of sex reversal in four subjects with a 46,Y,Xp+ karyotype. We conclude that the sex reversal is a direct, or indirect, consequence of having two active copies of the distal part of Xp and may indicate the presence of a gene(s) which acts in the testis determination or differentiation pathway.

Partial duplication of Xp: a case report and review of previously reported cases

We report clinical and cytogenetic findings on a 24-year-old woman with short stature, irregular menses, and other anomalies suggestive of Ullrich-Turner syndrome (UTS). Chromosome analysis documented a de novo duplication of Xp21 without any apparent microscopic deletion. DNA studies showed that part of band Xp22.1 is also duplicated. The clinical findings are compared with 5 other patients with dup(Xp).

Duplications of the X chromosome in males: evidence that most parts of the X chromosome can be active in two copies

We have analysed two duplications of the X chromosome in male patients using chromosome replication and DNA methylation patterns as determinants of the functional status of the duplicated segments. In both cases, the large duplicated regions, Xq12-q22 and Xq26.3-qter, were not inactivated. A review of previously reported male cases revealed that these duplications were also not subject to inactivation. Taken together, the examined duplications cover almost the entire X chromosome except the pericentromeric region and Xq25-26. Thus, most regions of the X chromosome can be present in two functional copies without lethal consequences.

Prenatal diagnosis of inv(X)(q12q28) in a male fetus

Amniocentesis and prenatal chromosome analysis were performed for advanced maternal age. The fetus was male with a paracentric inversion in the long arm of the X chromosome. The mother and a brother also carried the inversion. The pregnancy continued to term and the infant is developing normally at one year of age.

Inherited X-chromosome inverted tandem duplication in a male traced to a grandparental mitotic error

A male infant was referred for cytogenetic evaluation because of dysmorphic features and developmental delay. In both lymphocytes and skin fibroblasts, a modal number of 46 chromosomes was obtained with an obvious elongation of the long arm of the X chromosome (Xq+). Studies of seven members in 3 generations of this family showed that the proband's mother, sister, and maternal grandmother were phenotypically normal carriers of this abnormal X chromosome. High resolution GTG- and RBG-banding defined the extra chromatin material as an inverted duplication of Xq21----Xq24. This was supported by an approximate twofold increase in alpha-galactosidase A activity, localized to Xq21----q24, observed in the proband's lymphocytes and fibroblasts. BrdU-incorporation studies of the mother's lymphocytes showed the abnormal X to be late replicating in all 100 cells studied and normal alpha-galactosidase A levels. Cytogenetic analysis of the maternal grandmother revealed cytogenetic mosaicism with one cell line containing the abnormal X (37%), and the other, a normal female karyotype (63%). This family is instructive since: (1) it represents only the second case of a dysmorphic male demonstrating a confirmed interstitial partial Xq duplication, and (2) the origin of this familial structural rearrangement has been traced to a grandparental mitotic error.

Inherited tandem duplication dup(X) (q131-q212) in a male proband

A tandem duplication dup(X) (q131-q212) has been diagnosed neonatally because of the peculiar appearance. Family investigation demonstrated that the duplication has segregated through phenotypically normal female carriers for at least three generations. Inactivation studies showed that the aberrant X was preferentially late replicating. The difficulties related to prenatal diagnosis of minor X chromosome aberrations in males are discussed.