Array based CGH and FISH fail to confirm duplication of 8p22-p23.1 in association with Kabuki syndrome

Novel loci for non-syndromic coarctation of the aorta in sporadic and familial cases

BACKGROUND

Coarctation of the aorta (CoA) accounts for 5-8% of all congenital heart defects. CoA can be detected in up to 20% of patients with Ullrich-Turner syndrome (UTS), in which a part or all of one of the X chromosomes is absent. The etiology of non-syndromic CoA is poorly understood. In the present work, we test the hypothesis that rare copy number variation (CNV) especially on the gonosomes, contribute to the etiology of non-syndromic CoA.

METHODS

We performed high-resolution genome-wide CNV analysis using the Affymetrix SNP 6.0 microarray platform for 70 individuals with sporadic CoA, 3 families with inherited CoA (n=13) and 605 controls. Our analysis comprised genome wide association, CNV burden and linkage. CNV was validated by multiplex ligation-dependent probe amplification.

RESULTS

We identified a significant abundance of large (>100 kb) CNVs on the X chromosome in males with CoA (p=0.005). 11 out of 51 (~ 22%) male cases had these large CNVs. Association analysis in the sporadic cohort revealed 14 novel loci for CoA. The locus on 21q22.3 in the sporadic CoA cohort overlapped with a gene locus identified in all familial cases of CoA (candidate gene TRPM2). We identified one CNV locus within a locus with high multipoint LOD score from a linkage analysis of the familial cases (SEPT9); another locus overlapped with a region implicated in Kabuki syndrome. In the familial cases, we identified a total of 7 CNV loci that were exclusively present in cases but not in unaffected family members.

CONCLUSION

Of all candidate loci identified, the TRPM2 locus was the most frequently implicated autosomal locus in sporadic and familial cases. However, the abundance of large CNVs on the X chromosome of affected males suggests that gonosomal aberrations are not only responsible for syndromic CoA but also involved in the development of sporadic and non-syndromic CoA and their male dominance.

Deletion of KDM6A, a histone demethylase interacting with MLL2, in three patients with Kabuki syndrome

Kabuki syndrome (KS) is a rare genetic disease that causes developmental delay and congenital anomalies. Since the identification of MLL2 mutations as the primary cause of KS, such mutations have been identified in 56%-76% of affected individuals, suggesting that there may be additional genes associated with KS. Here, we describe three KS individuals with de novo partial or complete deletions of an X chromosome gene, KDM6A, that encodes a histone demethylase that interacts with MLL2. Although KDM6A escapes X inactivation, we found a skewed X inactivation pattern, in which the deleted X chromosome was inactivated in the majority of the cells. This study identifies KDM6A mutations as another cause of KS and highlights the growing role of histone methylases and histone demethylases in multiple-congenital-anomaly and intellectual-disability syndromes.

The C20orf133 gene is disrupted in a patient with Kabuki syndrome

Kabuki syndrome (KS) is a rare, congenital mental retardation syndrome. The aetiology of KS remains unknown. Four carefully selected patients with KS were screened for chromosomal imbalances using array comparative genomic hybridisation at 1 Mb resolution. In one patient, a 250 kb de novo microdeletion at 20p12.1 was detected, deleting exon 5 of C20orf133. The function of this gene is unknown. In situ hybridisation with the mouse orthologue of C20orf133 showed expression mainly in brain. The de novo nature of the deletion, the expression data and the fact that C20orf133 carries a macro domain, suggesting a role for the gene in chromatin biology, make the gene a likely candidate to cause the phenotype in this patient with KS. Both the finding of different of chromosomal rearrangements in patients with KS features and the absence of C20orf133 mutations in 19 additional patients with KS suggest that KS is genetically heterogeneous.

Molecular karyotyping in 17 patients and mutation screening in 41 patients with Kabuki syndrome

The Kabuki syndrome (KS, OMIM 147920), also known as the Niikawa-Kuroki syndrome, is a multiple congenital anomaly/mental retardation syndrome characterized by a distinct facial appearance. The cause of KS has been unidentified, even by whole-genome scan with array comparative genomic hybridization (CGH). In recent years, high-resolution oligonucleotide array technologies have enabled us to detect fine copy number alterations. In 17 patients with KS, molecular karyotyping was carried out with GeneChip 250K NspI array (Affymetrix) and Copy Number Analyser for GeneChip (CNAG). It showed seven copy number alterations, three deleted regions and four duplicated regions among the patients, with the exception of registered copy number variants (CNVs). Among the seven loci, only the region of 9q21.11-q21.12 (approximately 1.27 Mb) involved coding genes, namely, transient receptor potential cation channel, subfamily M, member 3 (TRPM3), Kruppel-like factor 9 (KLF9), structural maintenance of chromosomes protein 5 (SMC5) and MAM domain containing 2 (MAMDC2). Mutation screening for the genes detected 10 base substitutions consisting of seven single-nucleotide polymorphisms (SNPs) and three silent mutations in 41 patients with KS. Our study could not show the causative genes for KS, but the locus of 9q21.11-q21.12, in association with a cleft palate, may contribute to the manifestation of KS in the patient. As various platforms on oligonucleotide arrays have been developed, higher resolution platforms will need to be applied to search tiny genomic rearrangements in patients with KS.

Array-CGH in patients with Kabuki-like phenotype: identification of two patients with complex rearrangements including 2q37 deletions and no other recurrent aberration

Background

Kabuki syndrome (KS) is a multiple congenital anomaly syndrome characterized by specific facial features, mild to moderate mental retardation, postnatal growth delay, skeletal abnormalities, and unusual dermatoglyphic patterns with prominent fingertip pads. A 3.5 Mb duplication at 8p23.1-p22 was once reported as a specific alteration in KS but has not been confirmed in other patients. The molecular basis of KS remains unknown.

Methods

We have studied 16 Spanish patients with a clinical diagnosis of KS or KS-like to search for genomic imbalances using genome-wide array technologies. All putative rearrangements were confirmed by FISH, microsatellite markers and/or MLPA assays, which also determined whether the imbalance was de novo or inherited.

Results

No duplication at 8p23.1-p22 was observed in our patients. We detected complex rearrangements involving 2q in two patients with Kabuki-like features: 1) a de novo inverted duplication of 11 Mb with a 4.5 Mb terminal deletion, and 2) a de novo 7.2 Mb-terminal deletion in a patient with an additional de novo 0.5 Mb interstitial deletion in 16p. Additional copy number variations (CNV), either inherited or reported in normal controls, were identified and interpreted as polymorphic variants. No specific CNV was significantly increased in the KS group.

Conclusion

Our results further confirmed that genomic duplications of 8p23 region are not a common cause of KS and failed to detect other recurrent rearrangement causing this disorder. The detection of two patients with 2q37 deletions suggests that there is a phenotypic overlap between the two conditions, and screening this region in the Kabuki-like patients should be considered.

Chorea associated with antiphospholipid antibodies in a patient with Kabuki syndrome

Kabuki syndrome, OMIM 147920 (KS) is a disorder characterized by multi-system abnormalities. These include physical, neurological, endocrine, and autoimmune abnormalities. Multiple autoimmune abnormalities are described in KS such as immune thrombocytopenic purpura (ITP), vitiligo, thyroiditis, hemolytic anemia, and hypogammaglobulinemia. In this report, we describe a patient with KS with sudden onset chorea associated with the presence of anti-phospholipid antibodies (aPLs) in the serum. Chorea in the presence of aPLs has been well described in the literature both in the presence and absence of antiphospholipid syndrome (APS) and systemic lupus erythematosus (SLE). This report of APL in a patient with KS adds to the list of autoimmune disorders seen in patients with KS and also strengthens the hypothesis that patients with this syndrome have an increased incidence of immune dysregulation.

From microscopes to microarrays: dissecting recurrent chromosomal rearrangements

Submicroscopic chromosomal rearrangements that lead to copy-number changes have been shown to underlie distinctive and recognizable clinical phenotypes. The sensitivity to detect copy-number variation has escalated with the advent of array comparative genomic hybridization (CGH), including BAC and oligonucleotide-based platforms. Coupled with improved assemblies and annotation of genome sequence data, these technologies are facilitating the identification of new syndromes that are associated with submicroscopic genomic changes. Their characterization reveals the role of genome architecture in the aetiology of many clinical disorders. We review a group of genomic disorders that are mediated by segmental duplications, emphasizing the impact that high-throughput detection methods and the availability of the human genome sequence have had on their dissection and diagnosis.

Kabuki syndrome in a girl with mosaic 45,X/47,XXX and aortic coarctation

OBJECTIVE

To describe the clinical findings of a patient with mosaic 45,X/47,XXX and aortic coarctation.

DESIGN

Descriptive case study.

SETTING

Tertiary medical center.

PATIENT(S)

A 6-year-old girl with stigmata of Turner syndrome, aortic coarctation, patent ductus arteriosus, and a peculiar facial appearance.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Cytogenetic analysis.

RESULT(S)

The patient manifested a characteristic Kabuki syndrome facial appearance with long palpebral fissures, everted lateral third of lower eyelids, arched eyebrows, a depressed nasal tip, large dysplastic ears and epicanthic folds. She had undergone cardiac surgery for treatment of aortic coarctation and patent ductus arteriosus. Cytogenetic analysis of the blood lymphocytes revealed a karyotype of mos 45,X,9ph [35 cells]/47,XXX,9ph [5 cells].

CONCLUSION(S)

This is the first report of mosaic 45,X/47,XXX associated with Kabuki syndrome. We emphasize that Kabuki syndrome, a peculiar facial appearance and aortic coarctation, should be considered in girls with sex chromosome abnormalities.

The C20orf133 gene is disrupted in a patient with Kabuki syndrome

BACKGROUND

Kabuki syndrome (KS) is a rare, clinically recognisable, congenital mental retardation syndrome. The aetiology of KS remains unknown.

METHODS

Four carefully selected patients with KS were screened for chromosomal imbalances using array comparative genomic hybridisation at 1 Mb resolution.

RESULTS

In one patient, a 250 kb de novo microdeletion at 20p12.1 was detected, deleting exon 5 of C20orf133. The function of this gene is unknown. In situ hybridisation with the mouse orthologue of C20orf133 showed expression mainly in brain, but also in kidney, eye, inner ear, ganglia of the peripheral nervous system and lung.

CONCLUSION

The de novo nature of the deletion, the expression data and the fact that C20orf133 carries a macro domain, suggesting a role for the gene in chromatin biology, make the gene a likely candidate to cause the phenotype in this patient with KS. Both the finding of different of chromosomal rearrangements in patients with KS features and the absence of C20orf133 mutations in 19 additional patients with KS suggest that KS is genetically heterogeneous.

Two classes of low-copy repeats comediate a new recurrent rearrangement consisting of duplication at 8p23.1 and triplication at 8p23.2

We describe a new type of rearrangement consisting of the duplication of 8p23.1 and the triplication of 8p23.2 [dup trp(8p)] in two patients affected by mental retardation and minor facial dysmorphisms. Array-comparative genomic hybridization (CGH), fluorescence in situ hybridization (FISH), and genotyping of polymorphic loci allowed us to demonstrate that this rearrangement is mediated by the combined effects of two unrelated low-copy repeats (LCRs). The first set of LCRs consists of the two clusters of olfactory receptor genes (OR-REPs) lying at 8p23.1. The second type of LCRs consists of a 15-kb segmental duplication, lying in inverted orientation at 8p23.2 and enclosing a nonrepeated sequence of approximately 130 kb, named MYOM2-REP because of its proximity to the MYOM2 gene. The molecular characterization of a third case with a dicentric chromosome 8 demonstrated that the rearrangement had been generated by nonallelic homologous recombination between the two MYOM2-REPs. Based on our findings, we propose a model showing that a second recombination event at the level of the OR-REPs leads to the formation of the dup trp(8p) chromosome. This rearrangement can only arise during meiosis in heterozygous carriers of the polymorphic 8p23.1 inversion, whereas in subjects with noninverted chromosomes 8 or homozygous for the inversion only the dicentric chromosome can be formed. Our study demonstrates that nonallelic homologous recombination involving multiple LCRs can generate more complex rearrangements and cause a greater variety of genomic diseases.

Golli-MBP copy number analysis by FISH, QMPSF and MAPH in 195 patients with hypomyelinating leukodystrophies

The inherited disorders of CNS myelin formation represent a heterogeneous group of leukodystrophies. The proteolipoprotein (PLP1) gene has been implicated in two X-linked forms, Pelizaeus-Merzbacher disease (PMD) and spastic paraplegia type 2, and the gap junction protein alpha12 (GJA12) gene in a recessive form of PMD. The myelin basic protein (MBP) gene, which encodes the second most abundant CNS myelin protein after PLP1, presents rearrangements in hypomyelinating murine mutants and is always included in the minimal region deleted in 18q- patients with an abnormal hypomyelination pattern on cerebral MRI. In this study, we looked at the genomic copy number at the Golli-MBP locus in 195 patients with cerebral MRI suggesting a myelin defect, who do not have PLP1 mutation. Although preliminary results obtained by FISH suggested the duplication of Golli-MBP in 3 out of 10 patients, no abnormal gene quantification was found using Quantitative Multiplex PCR of Short Fluorescent fragments (QMPSF), Multiplex Amplifiable Probe Hybridization (MAPH), or another FISH protocol using directly-labelled probes. Pitfalls and interest in these different techniques to detect duplication events are emphasised. Finally, the study of this large cohort of patients suggests that Golli-MBP deletion or duplication is rarely involved in inherited defects of myelin formation.

BAC-FISH refutes report of an 8p22-8p23.1 inversion or duplication in 8 patients with Kabuki syndrome

Background

Kabuki syndrome is a multiple congenital anomaly/mental retardation syndrome. The syndrome is characterized by varying degrees of mental retardation, postnatal growth retardation, distinct facial characteristics resembling the Kabuki actor's make-up, cleft or high-arched palate, brachydactyly, scoliosis, and persistence of finger pads. The multiple organ involvement suggests that this is a contiguous gene syndrome but no chromosomal anomalies have been isolated as an etiology. Recent studies have focused on possible duplications in the 8p22–8p23.1 region but no consensus has been reached.

Methods

We used bacterial artificial chromosome-fluorescent in-situ hybridization (BAC-FISH) and G-band analysis to study eight patients with Kabuki syndrome.

Results

Metaphase analysis revealed no deletions or duplications with any of the BAC probes. Interphase studies of the Kabuki patients yielded no evidence of inversions when using three-color FISH across the region. These results agree with other research groups' findings but disagree with the findings of Milunsky and Huang.

Conclusion

It seems likely that Kabuki syndrome is not a contiguous gene syndrome of the 8p region studied.

The spectrum of congenital cardiac malformations encountered in six children with Kabuki syndrome

We investigated the prevalence and forms of congenital cardiac malformations in six children with Kabuki syndrome. There were three girls and three boys, diagnosed at a median age of 1.7 years, with a range from 0.7 to 11.1 years. Cardiac lesions were present in five children (83%), specifically complete transposition, tetralogy of Fallot, coarctation of the aorta, ventricular septal defect, and patency of the arterial duct. Characteristic dysmorphic findings were noted in all patients, as well as a strong predisposition to severe problems with feeding in the neonatal period, and developmental delay. Cardiologists should be alert to this syndrome in children who present with the aforementioned constellation of findings, as patients with mild expression of Kabuki syndrome may go unrecognized for a considerable time.

Triplication of 8p22-8p23 in a patient with features similar to Kabuki syndrome

Kabuki syndrome (KS) comprises multiple congenital anomalies and distinctive facial appearance. Although a number of chromosome abnormalities have been described in patients with KS-like phenotypes, no consensus has been reached regarding the genetic basis underlying the classic Kabuki phenotype. A recent study reported on 8p22-8p23.1 duplication in patients diagnosed with KS; however, a number of other studies have not found this duplication in patients with classic KS. We report on a girl with triplication of 8p22-8p23 who has mental retardation and some features suggestive of KS, including growth retardation, left-sided obstructive heart lesion, long-appearing palpebral fissures, hypertelorism, sparse lateral eyebrows, prominent ears, and persistent fetal fingertip pads. She does not have the typical facial gestalt of KS, nor does she have other more specific findings of KS. We propose that abnormal copy number of genes in the 8p22-8p23 region results in a syndrome of multiple congenital anomalies with many features that overlap with classic KS. However, data from this patient and others with similar duplications in the literature suggest that duplication or triplication of 8p22-8p23 represents a recognizable pattern of malformation distinct from classic KS. The exact genetic abnormality underlying KS currently remains unknown.

Molecular karyotyping in human constitutional cytogenetics

Using array CGH it is possible to detect very small genetic imbalances anywhere in the genome. Its usefulness has been well documented in cancer and more recently in constitutional disorders. In particular it has been used to detect interstitial and subtelomeric submicroscopic imbalances, to characterize their size at the molecular level and to define the breakpoints of chromosomal translocation. Here, we review the various applications of array CGH in constitutional cytogenetics. This technology remains expensive and the existence of numerous sequence polymorphisms makes its interpretation difficult. The challenge today is to transfer this technology in the clinical setting.

Kabuki syndrome: new ocular findings but no evidence of 8p22-p23.1 duplications in a clinically defined cohort

The underlying cause of the multiple congenital anomalies/mental retardation syndrome Kabuki syndrome (KS, OMIM 147920) has not yet been established. We identified seven patients who fulfilled the classical clinical criteria for this syndrome and undertook a detailed clinical, ophthalomological and molecular cytogenetic review. Three of the seven patients had previously undetected ocular anomalies including myopia, ptosis, strabismus and tilted discs. The identification of preventable causes of loss of vision underlines the value of detailed ophthalmologic examination of KS patients. Using BAC fluorescence in situ hybridisation, there was no evidence of the duplication of 8p recently reported by Milunsky and Huang. We conclude that the cause of KS has yet to be established.