No detectable genomic aberrations by BAC array CGH in Kabuki make-up syndrome patients

Identifying novel disease genes and revealing the pathomechanism of monogenic diseases

Diseases are caused by genetic and/or environmental factors. It is important to understand the pathomechanism of monogenic diseases that are caused only by genetic factors, especially prenatal- or childhood-onset diseases for pediatricians. Identifying "novel" disease genes and elucidating how genomic changes lead to human phenotypes would develop new therapeutic approaches for rare diseases for which no fundamental cure has yet been established. Genomic analysis has evolved along with the development of analytical techniques, from Sanger sequencing (first-generation sequencing) to techniques such as comparative genomic hybridization, massive parallel short-read sequencing (using a next-generation sequencer or second-generation sequencer) and long-read sequencing (using a next-next generation sequencer or third-generation sequencer). I have been researching human genetics using conventional and new technologies, together with my mentors and numerous collaborators, and have identified genes responsible for more than 60 diseases. Here, an overview of genomic analyses of monogenic diseases that aims to identify novel disease genes, and several examples using different approaches depending on the disease characteristics are presented.

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.

Zebrafish gene knockdowns imply roles for human YWHAG in infantile spasms and cardiomegaly

Williams-Beuren syndrome (WBS) is a neurodevelopmental disorder presenting with an elfin-like face, supravalvular aortic stenosis, a specific cognitive-behavioral profile, and infantile hypercalcemia. We encountered two WBS patients presenting with infantile spasms, which is extremely rare in WBS. Array comparative genomic hybridization (aCGH) and fluorescent in situ hybridization (FISH) analyses revealed atypical 5.7-Mb and 4.1-Mb deletions at 7q11.23 in the two patients, including the WBS critical region and expanding into the proximal side and the telomeric side, respectively. On the proximal side, AUTS2 and CALN1 may contribute to the phenotype. On the telomeric side, there are two candidate genes HIP1 and YWHAG. Because detailed information of them was unavailable, we investigated their functions using gene knockdowns of zebrafish. When zebrafish ywhag1 was knocked down, reduced brain size and increased diameter of the heart tube were observed, indicating that the infantile spasms and cardiomegaly seen in the patient with the telomeric deletion may be derived from haploinsufficiency of YWHAG.

Intervenção fonoaudiológica na síndrome de kabuki: relato de caso

TEMA: este trabalho teve como objetivo descrever o processo de intervenção fonoaudiológica em um caso de síndrome de Kabuki, com ênfase na terapia de linguagem. PROCEDIMENTOS: trata-se de relato de caso de uma criança de seis anos e seis meses de idade, gênero feminino, com diagnóstico de síndrome de Kabuki, que realizou terapia fonoaudiológica durante três anos em uma clínica-escola. Foi realizada análise documental dos dados do prontuário relativos à anamnese, avaliação e relatórios terapêuticos fonoaudiológicos, exames e avaliações multidisciplinares. Aos três anos e cinco meses, a criança passou por avaliação fonoaudiológica e apresentou, como histórico, características típicas da síndrome de Kabuki: alteração cardíaca, episódios de pneumonia, otite média secretora recorrente, alterações ortopédicas e crises convulsivas. Na avaliação fonoaudiológica, apresentou tempo de atenção auditiva e visual reduzido, dificuldade de compreensão oral, comunicação por meio de poucos gestos e vocalizações e problemas de comportamento. RESULTADOS: o processo terapêutico teve como objetivo principal promover o desenvolvimento da linguagem com ênfase na interação social por meio de atividades lúdicas, orientação familiar e escolar. Foi observada melhora na compreensão e emissão oral, no contato social e manutenção da atenção. CONCLUSÃO: este estudo permitiu divulgar o percurso de atuação fonoaudiológica na síndrome de Kabuki, do processo diagnóstico à terapia de linguagem. Verificou-se que a terapia foi eficaz no que se refere às habilidades comunicativas e de interação social. Esses dados podem contribuir para elucidar lacunas existentes na literatura acerca da terapia fonoaudiológica na síndrome em questão e subsidiar intervenções clínicas nesses casos.

Array CGH in patients with learning disability (mental retardation) and congenital anomalies: updated systematic review and meta-analysis of 19 studies and 13,926 subjects

Array-based comparative genomic hybridization is being increasingly used in patients with learning disability (mental retardation) and congenital anomalies. In this article, we update our previous meta-analysis evaluating the diagnostic and false-positive yields of this technology. An updated systematic review and meta-analysis was conducted investigating patients with learning disability and congenital anomalies in whom conventional cytogenetic analyses have proven negative. Nineteen studies (13,926 patients) were included of which 12 studies (13,464 patients) were published since our previous analysis. The overall diagnostic yield of causal abnormalities was 10% (95% confidence interval: 8-12%). The overall number needed to test to identify an extra causal abnormality was 10 (95% confidence interval: 8-13). The overall false-positive yield of noncausal abnormalities was 7% (95% confidence interval: 5-10%). This updated meta-analysis provides new evidence to support the use of array-based comparative genomic hybridization in investigating patients with learning disability and congenital anomalies in whom conventional cytogenetic tests have proven negative. However, given that this technology also identifies false positives at a similar rate to causal variants, caution in clinical practice should be advised.

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.

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.

Kabuki syndrome with trichrome vitiligo, ectodermal defect and hypogammaglobulinemia A and G

We report a unique combination of symptoms in a case of Kabuki syndrome (KS), a multiple malformation/mental retardation syndrome that has a prevalence of 1:32,000 to 1:86,000. The patient was a mentally delayed 12-year-old male with trichrome vitiligo, ectodermal defect, and hypogammaglobulinemia A and G. This unique combination of signs, described here for the first time, indicates that KS comprises multiple deficits that affect not only the brain, but ectoderm-derived structures and the immune system as well. Our report may provide important clues for understanding the pathogenesis of the KS.

Congenital arhinia: molecular-genetic analysis of five patients

Congenital arhinia, complete absence of the nose, is an extremely rare anomaly with unknown cause. To our knowledge, a total of 36 cases have been reported, but there has been no molecular-genetic study on this anomaly. We encountered a sporadic case of congenital arhinia associated with a de novo chromosomal translocation, t(3;12)(q13.2;p11.2). This led us to analyze the patient by BAC-based FISH for translocation breakpoints and whole-genome array CGH for other possible deletions/duplications in the genome. We found in this patient an approximately 19 Mb deletion spanning from 3q11.2 to 3q13.31 but no disruption of any gene(s) at the other breakpoint, 12p11.2. As the deleted segment at 3q was a strong candidate region containing the putative arhinia gene, we also performed the array CGH in four other arhinia patients with normal karyotypes, as well as mutation analysis of two genes, COL8A1 and CPOX, selected among hundreds of genes located to the deleted region, because they are expressed during early stages of human craniofacial development. However, in the four patients, there were no copy number aberrations in the region examined or no mutations in the two genes. Although our study failed to identify the putative arhinia gene, the data may become a clue to unravel the underlying mechanism of arhinia.

Array-based comparative genomic hybridization for investigating chromosomal abnormalities in patients with learning disability: Systematic review meta-analysis of diagnostic and false-positive yields

PURPOSE

Array-based comparative genomic hybridization is increasingly being used in patients with learning disability, in addition to existing cytogenetic techniques. This paper reports the results of an evaluation of this emerging technology and discusses the challenges faced in conducting the evaluation.

METHODS

Systematic review and meta-analysis of studies investigating patients with learning disability and dysmorphic features in whom conventional cytogenetic analysis has proven negative. Conventional indices of clinical validity could not be calculated, and we use an alternative, based on the extent to which array-based comparative genomic hybridization met its clinical objectives.

RESULTS

Seven studies (462 patients) were included. The overall diagnostic yield of causal abnormalities was 13% (95% confidence interval: 10-17%; heterogeneity test statistic I = 0%), and the overall number needed to test was eight (95% confidence interval: 6-10). The false-positive yield of noncausal abnormalities ranged from 5% to 67%, although this range was only 5% to 10% in six of the studies.

CONCLUSION

Although promising, there is insufficient evidence to recommend introduction of this test into routine clinical practice. A number of important technical questions need answering, such as optimal array resolution, which clones to include, and the most appropriate platforms. A thorough assessment of clinical utility and cost-effectiveness compared with existing tests is also required.

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.

Array comparative genomic hybridization analysis in first-trimester spontaneous abortions with ‘normal’ karyotypes

Array comparative genomic hybridization (array CGH) analysis was conducted in chorionic villous samples from 20 first-trimester spontaneous abortions with G-banding normal chromosomes. A microarray, containing 2,173 BAC clones and covering the whole genome with a 1.5-Mb resolution, was constructed and used in the analysis. Two deletions were identified: a 1.4-Mb deletion at 3p26.2-p26.3 and a 13.7-Mb deletion at 13q32.3-qter. Reexamination of chromosome preparations from the sample with the 13.7-Mb deletion documented a mixture of cells with the 13q- chromosome and those with 46,XX chromosomes, the latter of which are likely to have been derived from contaminating decidual cells. This left the 1.4-Mb 3p deletion as the only instance with submicroscopic imbalance detected, giving a frequency of 1 in 19 (5%) G-banding normal abortions.