Trisomy of the short stature homeobox-containing gene (SHOX) due to duplication/deletion of the X chomosome: clinical implications on the stature

SHOX Duplication and Tall Stature in a Patient with Xq Deletion and Vascular Disease

The anomalies of X chromosome are classified as numerical or structural. Concomitant structural anomalies in this chromosome that associate partial loss of its long arm with duplications in its short arm are uncommon. Only a few cases have been published and in most of them the reported patients present ovarian dysfunction, tall stature, and overdosage of the SHOX gene with locus Xp22.33. Considering these reports, we evaluated the case of a woman with a deletion in the long arm of the X chromosome, premature ovarian failure, tall stature, and multiple arterial vascular disease. With the aim to find a relationship between karyotype and phenotype, we explored associated anomalies in Xp and certified the overdosage of the SHOX gene in this case by MLPA. Also, taking into account the fact that the gene locus of the angiotensin-converting enzyme type 2 (ACE2) is located in Xp, our goal was to investigate the influence of this gene in the development of cardiovascular disease. The detection of the gene product of ACE2 by ELISA was undetectable. We have proposed that cytogenetic anomalies in X chromosome could contribute to decrease this protein synthesis in this gender.

A 105 kb interstitial insertion in the Xq27.1 palindrome from pseudoautosomal region PAR1 causes a novel X-linked recessive compound phenotype

BACKGROUND

Genomic disorders present a wide spectrum of unrelated clinical entities that result from genomic rearrangements. Interstitial insertions requiring three points of breakage are rare genomic rearrangement events. The pseudoautosomal region PAR1, homologous between the Xp22 and Yp11 loci, has a high crossover and recombination rate. A 180 bp human-specific palindrome at Xq27.1 appears to be a hotspot for genomic rearrangement, and several genetic diseases/phenotypes associated with Xq27.1 palindrome-driven genomic rearrangement have been reported. Here we investigate a Chinese family with an extremely rare X-linked compound phenotype that remains undiagnosed. We attempt to identify underlying genetic causes by an integrated genome analysis.

METHODS

A five-generation Chinese family with a distinct X-linked compound phenotype was recruited. Peripheral blood samples were collected and genomic DNA was extracted. Systemic physical and lab examinations were performed to evaluate the phenotype. An integrated genomic analysis was performed. Genotyping and linkage analysis were conducted to map the disease locus. Whole exome sequencing was performed to detect mutations in coding region. Whole genome sequencing was used to detect single nucleotide variations, small insertions, small deletions, or large structural variations. Copy number variation scanning was also performed on the genome scale. Interstitial insertion was confirmed by gap-PCR and quantitative-PCR, and breakpoint junctions were identified by genome walking and direct sequencing. Expression of products of genes nearby to the Xq27.1 palindrome was measured in peripheral blood from patients and unrelated controls via quantitative-PCR.

RESULTS

The identified compound phenotype of genu varum, cubitus valgus, and everted lipsdoes not match any reported clinical entities. Fine mapping and linkage analysis identified a candidate interval of 4 Mb on the X chromosome. No potential coding region mutations were detected. A 105 kb genomic fragment of PAR1 containing no coding genes was duplicated and inserted into the center of a human-specific palindrome at Xq27.1. The interstitial insertion fully cosegregated with the family phenotype. No expression of FGF13 or SOX3 was detected in peripheral blood from the proband or unrelated controls.

CONCLUSION

We report an extremely rare phenotype associated with an infrequently-seen genomic rearrangement. The novel compound phenotype is X-linked and characterized by genu varum, cubitus valgus, and everted lips. A 105 kb interstitial insertion of a PAR1 fragment into the Xq27.1 palindrome is associated with the phenotype in the family. The present study identified the underlying genetic cause of the phenotype, expanding the spectrum of known human-specific Xq27.1 palindrome insertion events and associated phenotypes.

Short stature homeobox-containing gene duplications in 3.7% of girls with tall stature and normal karyotypes

AIM

The short stature homeobox-containing gene (SHOX) plays an important role in short stature, but has not been explored in detail in a tall stature population before. This study explored the prevalence of SHOX aberrations in girls diagnosed with idiopathic tall stature with a normal karyotype.

METHODS

We studied SHOX aberrations in 81 girls with a median age of 10.43 (7.17-12.73) years diagnosed with tall stature who were referred to our clinic at Copenhagen University Hospital, Denmark, between 2003 and 2013. SHOX copy variations were analysed by quantitative polymerase chain reaction, and aberrations were confirmed by multiplex ligation probe-dependent amplification.

RESULTS

One extra SHOX copy was found in three (3.7%) of the 81 girls with tall stature, and their heights were 2.87, 3.71 and 3.98 standard deviation scores (SDS) and above the median height SDS of the girls with two SHOX copies. Their sitting height/height ratios (-3.08, -2.00 and -2.18 SDS) were all lower than the population mean. Despite these SHOX duplications, the three girls were clinically and biochemically comparable to the 78 girls with two SHOX copies.

CONCLUSION

This study was the first to demonstrate SHOX duplications in three girls with tall stature and normal karyotypes.

Turner syndrome caused by rare complex structural abnormalities involving chromosome X

Turner syndrome (TS) is a phenotypic heterogeneous genetic disorder caused by the loss of an X-chromosome or X-structural abnormalities in the X-chromosome, and affects approximately 1 in every 2,500 females. The affected individuals may develop diverse clinical features, including short stature, ovarian dysgenesis, skeletal dysplasia, facial abnormalities and other disorders. A constitutional karyotype of 45, X accounts for nearly 50% of TS patients, while X-mosaicism and other X-chromosomal structural abnormalities, including deletions, duplications, ring, isodicentric chromosomes, inversions and translocations, have been reported in other cases. The present study reports the results of chromosome microarray analysis (CMA) in two Chinese female TS patients with idiosyncratic karyotypes. The first patient had a karyotype of 46, X, der(X), and the CMA results demonstrated that the derivative chromosome was an abnormal X-chromosome that consisted of three deletions (Xp21.3-p11.23, Xp11.1-q13.1 and Xq21.31-q28), as well as three duplications (Xp22.33-p21.3, Xp11.23-p11.1 and Xq13.1-q21.31). The karyotype of the second patient was 46, X, der(X) t(X;?)(q 22.1;?),inv(11)(q13.5q21), while CMA revealed an Xq21.2-q27.1 duplication and an Xq27.2-q28 deletion. In conclusion, the current study performed genotype-phenotype correlation analysis in two patients and provided novel insight of the genotype of TS.

Comparison of SHOX and associated elements duplications distribution between patients (Lėri-Weill dyschondrosteosis/idiopathic short stature) and population sample

The effect of heterozygous duplications of SHOX and associated elements on Lėri-Weill dyschondrosteosis (LWD) and idiopathic short stature (ISS) development is less distinct when compared to reciprocal deletions. The aim of our study was to compare frequency and distribution of duplications within SHOX and associated elements between population sample and LWD (ISS) patients. A preliminary analysis conducted on Czech population sample of 250 individuals compared to our previously reported sample of 352 ISS/LWD Czech patients indicated that rather than the difference in frequency of duplications it is the difference in their distribution. Particularly, there was an increased frequency of duplications residing to the CNE-9 enhancer in our LWD/ISS sample. To see whether the obtained data are consistent across published studies we made a literature survey to get published cases with SHOX or associated elements duplication and formed the merged LWD, the merged ISS, and the merged population samples. Relative frequency of particular region duplication in each of those merged samples were calculated. There was a significant difference in the relative frequency of CNE-9 enhancer duplications (11 vs. 3) and complete SHOX (exon1-6b) duplications (4 vs. 24) (p-value 0.0139 and p-value 0.000014, respectively) between the merged LWD sample and the merged population sample. We thus propose that partial SHOX duplications and small duplications encompassing CNE-9 enhancer could be highly penetrant alleles associated with ISS and LWD development.

X-chromosome gene dosage as a determinant of impaired pre and postnatal growth and adult height in Turner syndrome

OBJECTIVE

Short stature is a key aspect of the phenotype of patients with Turner syndrome (TS). SHOX haploinsufficiency is responsible for about two-thirds of the height deficit. The aim was to investigate the effect of X-chromosome gene dosage on anthropometric parameters at birth, spontaneous height, and adult height (AH) after growth hormone (GH) treatment.

DESIGN

We conducted a national observational multicenter study.

METHODS

Birth parameter SDS for gestational age, height, and AH before and after GH treatment respectively, and height deficit with respect to target height (SDS) were classified by karyotype subgroup in a cohort of 1501 patients with TS: 45,X (36%), isoXq (19%), 45,X/46,XX (15%), XrX (7%), presence of Y (6%), or other karyotypes (17%).

RESULTS

Birth weight, length (P<0.0001), and head circumference (P<0.001), height and height deficit with respect to target height (SDS) before GH treatment, at a median age of 8.8 (5.3-11.8) years and after adjustment for age and correction for multiple testing (P<0.0001), and AH deficit with respect to target height at a median age of 19.3 (18.0-21.8) years and with additional adjustment for dose and duration of GH treatment (P=0.006), were significantly associated with karyotype subgroup. Growth retardation tended to be more severe in patients with XrX, isoXq, and, to a lesser extent, 45,X karyotypes than in patients with 45,X/46,XX karyotypes or a Y chromosome.

CONCLUSION

These data suggest that haploinsufficiency for an unknown Xp gene increases the risk of fetal and postnatal growth deficit and short AH with respect to target height after GH therapy.

Rare pseudoautosomal copy-number variations involving SHOX and/or its flanking regions in individuals with and without short stature

Pseudoautosomal region 1 (PAR1) contains SHOX, in addition to seven highly conserved non-coding DNA elements (CNEs) with cis-regulatory activity. Microdeletions involving SHOX exons 1-6a and/or the CNEs result in idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis (LWD). Here, we report six rare copy-number variations (CNVs) in PAR1 identified through copy-number analyzes of 245 ISS/LWD patients and 15 unaffected individuals. The six CNVs consisted of three microduplications encompassing SHOX and some of the CNEs, two microduplications in the SHOX 3'-region affecting one or four of the downstream CNEs, and a microdeletion involving SHOX exon 6b and its neighboring CNE. The amplified DNA fragments of two SHOX-containing duplications were detected at chromosomal regions adjacent to the original positions. The breakpoints of a SHOX-containing duplication resided within Alu repeats. A microduplication encompassing four downstream CNEs was identified in an unaffected father-daughter pair, whereas the other five CNVs were detected in ISS patients. These results suggest that microduplications involving SHOX cause ISS by disrupting the cis-regulatory machinery of this gene and that at least some of microduplications in PAR1 arise from Alu-mediated non-allelic homologous recombination. The pathogenicity of other rare PAR1-linked CNVs, such as CNE-containing microduplications and exon 6b-flanking microdeletions, merits further investigation.

Pseudoisodicentric Xp chromosome [46,X,psu idic(X)(q21.1)] and its effect on growth and pubertal development

BACKGROUND

Most isodicentric (Xp) and (Xq) chromosomes occur as a mosaic with a 45,X cell line. Patients with a nonmosaic 46,X,idic(Xq) are rare.

CASES

The first girl was referred at 13 years with a short stature and pubertal delay (M1, P2, A1). Her height was 141.6 cm (-3.1 SDS). Ovarian failure was present. The second girl was referred because of her short stature at 12.5 years. Her height was 142.2 cm (-2.4 SDS). She had spontaneous puberty (M3, P1, A1).

RESULTS

In both girls, conventional karyotyping of lymphocytes revealed an aberrant X chromosome consisting of twice the short arm and a small part of the long arm of the X chromosome [nonmosaic 46,X,psu idic(X)(q21.1)]. FISH analysis of the aberrant X chromosome showed the presence of two centromeres, two copies of the XIST gene and two copies of the SHOX gene.

CONCLUSIONS

The presence of two XIST genes on the isodicentric X chromosome with Xq deletion indicates the inactivation of this chromosome. This inactivation also concerned the pseudoautosomal regions which caused haploinsufficiency of the SHOX genes. The girls were treated with growth hormones. The critical region (Xq23 to Xq28) for the ovarian function was deleted in both patients, but the gonadal function was variable. .

Discovery of a large deletion of KAL1 in 2 deaf brothers

OBJECTIVES

Kallmann syndrome (KS) usually combines an anosmia and a hypogonadotrophic hypogonadism. Hearing impairment was described in a few cases of KS. Our objective is to describe an unusual presentation of KS in 2 cases and to explore the pattern of inheritance in this family.

PATIENTS

Two brothers presented with a sensorineural hearing impairment associated with cryptorchidism and abnormal movements.

RESULTS

Genome-wide array analysis identified a large deletion of KAL1 in both patients confirming the diagnosis of Kallmann syndrome. The absence of familial history has been explained by a somatic mosaicism identified in their mother.

CONCLUSION

The description of a hearing defect in 2 brothers with Kallmann syndrome allows asserting that deafness is part of the clinical features of this disease and must lead the physician to monitor the hearing function of Kallmann patients.

A case of premature ovarian failure in a 33-year-old woman

Objective. To assess aetiology of a POF in a 33-year-old woman and, if possible, plan a cure. Design. Case report. Setting. medical genetics diagnostic unit in a university hospital. Patient. A 33-year-old woman with premature ovarian failure (POF). Intervention(s). Genetic counseling, karyotyping, FISH study. Result(s). Turner-like diagnosis. Conclusion(s). Most cases of POF remain idiopathic. Turner syndrome can occur in very different phenotypes; cytogenetic and molecular profiling can provide a definitive diagnosis in cases with nonclassical phenotype.

Array-CGH characterization of a prenatally detected de novo 46,X,der(Y)t(X;Y)(p22.3;q11.2) in a male fetus

We report on an apparently normal 5-month-old boy with a X;Y complex rearrangement identified first on prenatal diagnosis and found on array-CGH to have a 7.6 Mb duplication of Xp22.3 chromosome and a deletion of Yq chromosome, distal to the AZFa locus. Karyotype analysis on amniotic fluid cell cultures revealed a de novo homogenous chromosome marker that we interpreted as an isochromosome Yp. FISH analysis using SRY probe revealed only one signal on the derivative Y chromosome. The final karyotype was interpreted as 46,X,der(Y)t(X;Y)(p22.31;q11.22). Translocation Xp22;Yq11 in male are very rare event and only 4 cases have been published, all showing mental retardation and malformations. Herein we discussed some possible explanation for this apparent phenotypic variability.