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

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.

Functional monosomy of 6q27-qter and functional disomy of Xpter-p22.11 due to X;6 translocation with an atypical X-inactivation pattern

Pattern of X chromosome inactivation (XCI) is typically random in females. However, chromosomal rearrangements affecting the X chromosome can result in XCI skewing due to cell growth disadvantage. In case of an X;autosome translocation, this usually leads to an XCI pattern of 100:0 with the derivative X being the active one in the majority of females. A de novo balanced X;6 translocation [46,X,t(X;6)(p22.1;q27)] and a completely skewed XCI pattern (100:0) were detected in a female patient with microcephaly, cerebellar vermis hypoplasia, heart defect, and severe developmental delay. We mapped the breakpoint regions using fluorescence in situ hybridization and found the X-linked gene POLA1 to be disrupted. POLA1 codes for the catalytic subunit of the polymerase α-primase complex which is responsible for initiation of the DNA replication process; absence of POLA1 is probably incompatible with life. Consequently, by RBA banding we determined which of the X chromosomes was the active one in the patient. In all examined lymphocytes the wild-type X chromosome was active. We propose that completely skewed XCI favoring the normal X chromosome resulted from death of cells with an active derivative X that was caused by a non-functional POLA1 gene. In summary, we conclude that functional monosomy of 6q27-qter and functional disomy of Xpter-p22.11 are responsible for the clinical phenotype of the patient. This case demonstrates the importance of determining which one of the X chromosomes underwent inactivation to correlate clinical features of a female with an X;autosome translocation with the nature of the genetic alteration.

Phenotype in novel Xp duplication

A novel duplication of Xp is described. A 20-year-old man had minor anomalies ichthyosis, congenital heart defect, varicose veins, and hypogonadotropic hypogonadism. He had an interstitial duplication of approximately 2.8 Mb from chromosome region Xp22.31p22.2. His similarly affected brother and asymptomatic mother were shown to carry the same duplication. Knowledge about this duplication and its resultant phenotype will add to our understanding of the role of X chromosome duplications.

Scope for more genetic testing in learning disability. Case report of an inherited duplication on the X-chromosome

There have been major advances in the past few years in our understanding of the X-linked learning disabilities. The most common of these is the fragile-X syndrome, but the number of other gene defects that are now recognised to be linked with learning disability is increasing year on year. We describe one family displaying a family displaying a rare X-linked abnormality. Repeat genetic testing was requested for a family member with mild learning disability when, following chromosomal analysis for her brother, it became known that he had a genetic defect. The genetic defect 46, Xdup(X) (p22.13 p22.31) was identified. To our knowledge this is the first time this precise configuration has been demonstrated. We conclude that genetic testing for individuals with learning disability is worthwhile, even when there may be only a low index of suspicion.

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.

Tall stature, gonadal dysgenesis, and stigmata of Turner's syndrome caused by a structurally altered X chromosome

Genetic analysis in a tall 14-year-old girl with gonadal dysgenesis and some stigmata of Turner's syndrome revealed a duplication of the short arm in a monocentric X chromosome with partial loss of Xq. We suggest that triple gene dosage of SHOX and estrogen deficiency caused the unique overgrowth.

Severe phenotype resulting from an active ring X chromosome in a female with a complex karyotype: characterisation and replication study

We report on the characterisation of a complex chromosome rearrangement, 46,X,del(Xq)/47,X,del(Xq),+r(X), in a female newborn with multiple malformations. Cytogenetic and molecular methods showed that the del(Xq) contains the XIST locus and is non-randomly inactivated in all metaphases. The tiny r(X) chromosome gave a positive FISH signal with UBE1, ZXDA, and MSN cosmid probes, but not with a XIST cosmid probe. Moreover, it has an active status, as shown by a very short (three hour) terminal BrdU pulse followed by fluorescent anti-BrdU antibody staining. The normal X is of paternal origin and both rearranged chromosomes originate from the same maternal chromosome. We suggest that both abnormal chromosomes result from the three point breakage of a maternal isodicentric idic(X)(q21.1). Finally, the phenotype of our patient is compared to other published cases and, despite the absence of any 45,X clone, it appears very similar to those with a 45,X/46,X,r(X) karyotype where the tiny r(X) is active.