Genetic profile and clinical application of chromosomal microarray in children with intellectual disability in Hong Kong.

INTRODUCTION: Chromosomal microarray (CMA) is recommended as a first-tier genetic investigation for intellectual disability (ID), developmental delay, or autism spectrum disorder due to its higher diagnostic yield with respect to conventional karyotyping. The aim of the present study was to investigate the genetic profile and diagnostic yield of CMA in children with moderate, severe and profound ID. METHODS: A pilot cross-sectional study was performed by the Child Assessment Service and the Clinical Genetic Service in Hong Kong from July 2016 to June 2017. Children with unexplained ID were recruited for CMA testing by an expedited referral pathway. Children who were existing clients of the Clinical Genetic Service were also recruited. RESULTS: Of 225 children included in this study, 68 (30.2%) had genetic diagnoses. Among the 138 children who underwent CMA testing, 53 (38%) children were referred to the Clinical Genetic Service by the expedited referral pathway. The respective diagnostic yields of CMA in moderate, severe, and profound ID were 8.7%, 17.6%, and 23.5% (P<0.05). Children with dysmorphic features demonstrated a much higher yield from CMA (45.8% vs 4.4%, P<0.05). CONCLUSTION. The overall diagnostic yield (11.6%) of CMA in this cohort is comparable with that of other international cohorts. This further supports the use of CMA as a first-tier genetic investigation for children with ID, developmental delay, or autism spectrum disorder, particularly for those with severe disease.

Mechanisms for the Generation of Two Quadruplications Associated with Split-Hand Malformation.

Germline copy-number variants (CNVs) involving quadruplications are rare and the mechanisms generating them are largely unknown. Previously, we reported a 20-week gestation fetus with split-hand malformation; clinical microarray detected two maternally inherited triplications separated by a copy-number neutral region at 17p13.3, involving BHLHA9 and part of YWHAE. Here, we describe an 18-month-old male sibling of the previously described fetus with split-hand malformation. Custom high-density microarray and digital droplet PCR revealed the copy-number gains were actually quadruplications in the mother, the fetus, and her later born son. This quadruplication-normal-quadruplication pattern was shown to be expanded from the triplication-normal-triplication CNV at the same loci in the maternal grandmother. We mapped two breakpoint junctions and demonstrated that both are mediated by Alu repetitive elements and identical in these four individuals. We propose a three-step process combining Alu-mediated replicative-repair-based mechanism(s) and intergenerational, intrachromosomal nonallelic homologous recombination to generate the quadruplications in this family.

Silver-Russell syndrome in Hong Kong.

OBJECTIVES: To examine the molecular pathogenetic mechanisms, (epi)genotype-phenotype correlation, and the performance of the three clinical scoring systems-namely Netchine et al, Bartholdi et al, and Birmingham scores-for patients with Silver-Russell syndrome in Hong Kong. METHODS: This retrospective case series was conducted at two tertiary genetic clinics, the Clinical Genetic Service, Department of Health, and clinical genetic clinic in Queen Mary Hospital in Hong Kong. All records of patients with suspected Silver-Russell syndrome under the care of the two genetic clinics between January 2010 and September 2015 were retrieved from the computer database. RESULTS: Of the 28 live-birth patients with Silver-Russell syndrome, 35.7% had H19 loss of DNA methylation, 21.4% had maternal uniparental disomy of chromosome 7, 3.6% had mosaic maternal uniparental disomy of chromosome 11, and the remaining 39.3% were Silver-Russell syndrome of unexplained molecular origin. No significant correlation between (epi)genotype and phenotype could be identified between H19 loss of DNA methylation and maternal uniparental disomy of chromosome 7. Comparison of molecularly confirmed patients and patients with Silver-Russell syndrome of unexplained origin revealed that postnatal microcephaly and café-au-lait spots were more common in the latter group, and body and limb asymmetry was more common in the former group. Performance analysis showed the Netchine et al and Birmingham scoring systems had similar sensitivity in identifying Hong Kong Chinese subjects with Silver-Russell syndrome. CONCLUSION: This is the first territory-wide study of Silver-Russell syndrome in Hong Kong. The clinical features and the spectrum of underlying epigenetic defects were comparable to those reported in western populations.

Spread of X inactivation on chromosome 15 is associated with a more severe phenotype in a girl with an unbalanced t(X; 15) translocation.

We report on a baby girl with multiple congenital abnormalities, including cleft palate, intrauterine growth restriction, and double outlet right ventricle (DORV) with ventricular septal defect. She had an unbalanced chromosome translocation t (X;15) resulting in monosomy 15pter → p10 and trisomy Xq13.1 → q28. All three copies of Xq encompass the XIST gene. It is known that X chromosome inactivation could spread to the autosome part of an unbalanced translocation involving chromosome X and an autosome. To confirm the spread of X chromosome inactivation on chromosome 15, we evaluate the methylation change by the HumanMethylation450 BeadChip, a whole genome DNA methylation micorarray that includes 15,259 probes spanning 717 genes on chromosome 15. Results showed there was gain in DNA methylation of more than 20% in 586 CpG sites spanning the long arm of chromosome 15. We further examined the hypermethylated CpG sites located in CpG-island promoter, because genes subjected to X chromosome inactivation will have an increase in DNA methylation level in this region. A total of 75 sites representing 24 genes were hypermethylated. Nearly all of these probes are located in region proximal to the breakpoint, from 15q11.2 to 15q21.3 (35Mb) suggesting that X inactivation was spread to the proximal region of 15q. Gain of DNA methylation, especially in the CpG-island promoter, can result in functional inactivation of genes, and therefore could potentially worsen the phenotype of our patient.

Congenital fibrosis of extraocular muscle type 1A due to KIF21A mutation: first case report from Hong Kong.

With the advancement of ophthalmological genetics, the molecular basis for more and more eye diseases can be elucidated. Congenital fibrosis of extraocular muscle (CFEOM) is an example. It is characterised by a congenital non-progressive restrictive ophthalmoplegia and ptosis. It is an autosomal dominant disease, caused by mutations of the KIF21A gene. With positive family history and typical ophthalmological findings, mutational analysis of KIF21A gene should be performed, not only to confirming the diagnosis, but also to offer a prognosis, for genetic counselling, and the possibility of prenatal diagnosis. Here we report the first KIF21A mutation associated with CFEOM1A in Hong Kong.

Oculopharyngeal muscular dystrophy: underdiagnosed disease in Hong Kong.

Despite the advances in the understanding of the molecular basis for oculopharyngeal muscular dystrophy in the last decade, it remains an underdiagnosed disease, especially among the Chinese. In the presence of a positive family history and late-onset ptosis, dysphagia, and proximal muscle weakness (its cardinal features), we suggest that PABPN1 gene analysis should be the first-line investigation to rule out this condition. Muscle biopsy can be reserved for atypical cases. Non-specific mitochondrial changes in the muscle specimens of these patients should be appreciated, so as to avoid diagnostic confusion. It is hoped that greater awareness among medical professionals and judicious use of PABPN1 gene analysis will lead to earlier diagnosis, better management, and avoidance of unnecessary invasive investigations of affected patients.

Collagen VI-related myopathies: clinical variability, phenotype-genotype correlation and exploratory transcriptome study.

Collagen VI-related myopathies are a group of disorders that cause muscle weakness and joint contractures with significant variability in disease severity among patients. Here we report the clinical and genetic characteristics of 13 Chinese patients. Detailed histological, radiological and muscle transcriptomic evaluations were also conducted for selected representative patients. Across the cohort, fifteen putative disease causal variants were identified in three genes encoding collagen VI subunits, COL6A1 (n=6), COL6A2 (n=5), and COL6A3 (n=4). Most of these variants (12/15, 80%) were dominant negative and occurred at the triple helical domain. The rest (3/15, 20%) were located at the C-terminus. Two previously unreported variants, an in-frame mutation (COL6A1:c.1084_1092del) and a missense mutation (COL6A2:c.811G>C), were also noted. The transcriptome data from the muscle biopsies of two patients in the study with dominant negative mutations [COL6A2:c.811G>C and COL6A1:c.930+189C>T] supports the accepted aetiology of Collagen VI myopathy as dysfunction of the extracellular matrix. It also suggests there are perturbations to skeletal muscle differentiation and skeletal system development. It should be noted that although the phenotypes of patients can be mostly explained by the position and dominant-negative effect of the variants, exceptions and variability still exist and have to be reckoned with. This study provides valuable data explaining the varying severity of phenotypes among ethnically Chinese patients.

Familial patellar dislocation associated with t(15;20) (q24;q13.1).

Patellar instability is a common debilitating injury affecting young active individuals. It accounts for approximately 3% of all knee injuries. We report a family, of which five members across three generations, who suffered from autosomal dominant familial recurrent patellar dislocation as well as short stature. All of them have recurrent patellar dislocations before the age of 15. The affected patients in all three generations have been genetically screened. Genotypical evaluation revealed a balanced translocation of chromosomes 15 and 20.

Integrating Functional Analysis in the Next-Generation Sequencing Diagnostic Pipeline of RASopathies.

RASopathies are a group of heterogeneous conditions caused by germline mutations in RAS/MAPK signalling pathway genes. With next-generation sequencing (NGS), sequencing capacity is no longer a limitation to molecular diagnosis. Instead, the rising number of variants of unknown significance (VUSs) poses challenges to clinical interpretation and genetic counselling. We investigated the potential of an integrated pipeline combining NGS and the functional assessment of variants for the diagnosis of RASopathies. We included 63 Chinese patients with RASopathies that had previously tested negative for PTPN11 and HRAS mutations. In these patients, we performed a genetic analysis of genes associated with RASopathies using a multigene NGS panel and Sanger sequencing. For the VUSs, we evaluated evidence from genetic, bioinformatic and functional data. Twenty disease-causing mutations were identified in the 63 patients, providing a primary diagnostic yield of 31.7%. Four VUSs were identified in five patients. The functional assessment supported the pathogenicity of the RAF1 and RIT1 VUSs, while the significance of two VUSs in A2ML1 remained unclear. In summary, functional analysis improved the diagnostic yield from 31.7% to 36.5%. Although technically demanding and time-consuming, a functional genetic diagnostic analysis can ease the clinical translation of these findings to aid bedside interpretation.

An Investigation of Sound-Symbolism in the Context of Tactile Feeling.

Sound symbolism suggests a non-arbitrary relationship between speech sounds and the concepts to which those sounds refer (Hinton, Nichols, & Ohala, 2006 ). Supporting evidence comes primarily from studies investigating how speech sounds relate to semantically compatible visual concepts. The present study therefore attempted to examine sound symbolism in the context of tactile perception. Contrary to the propositions of sound symbolism, participants in Experiment 1 did not consistently assign names with plosive consonant to objects with curved frames. Experiment 2, however, found that names with fricative consonants were more likely to be applied to materials with rough surfaces. The results suggested the existence of a direct relationship between speech sounds and their referent concepts that could be crucial in revealing the phenomenon of sound symbolism. A future study was also proposed to study the contributions of mouth shape and airflow to associations between speech sounds and tactile feelings. (161 words).

Angelman syndrome in Hong Kong Chinese: A 20 years' experience.

AS(OMIM #105830) is a neurodevelopmental disease that characterized by severe intellectual disability, lack of speech, happy disposition, ataxia, epilepsy and distinct behavioural profile. A tertiary wide study was performed in Hong Kong with aim to examine the clinical and molecular features, genotype-phenotype correlation of the Angelman syndrome (AS) patients. There were total 55 molecularly confirmed AS between January 1995 to September 2015 for review. 65.5% of them were caused by maternal microdeletion, 10.9% by paternal uniparental disomy, 3.6% by imprinting center defect and 14.5% by UBE3A gene mutation. Genotype-phenotype correlation showed epilepsy and microcephaly is more common in microdeletion type as compared with non-microdeletional type. We have concluded that the incidence rate, clinical features and underlying genetic mechanisms in Hong Kong Chinese were comparable with other western populations. The overall average age of diagnosis in this cohort was 6.2 years old (95% C.I was 5.0-7.5 years old). It is hope that by increasing awareness and early referral could result in early diagnosis and better management for AS patient.

NSD1 mutations generate a genome-wide DNA methylation signature.

Sotos syndrome (SS) represents an important human model system for the study of epigenetic regulation; it is an overgrowth/intellectual disability syndrome caused by mutations in a histone methyltransferase, NSD1. As layered epigenetic modifications are often interdependent, we propose that pathogenic NSD1 mutations have a genome-wide impact on the most stable epigenetic mark, DNA methylation (DNAm). By interrogating DNAm in SS patients, we identify a genome-wide, highly significant NSD1(+/-)-specific signature that differentiates pathogenic NSD1 mutations from controls, benign NSD1 variants and the clinically overlapping Weaver syndrome. Validation studies of independent cohorts of SS and controls assigned 100% of these samples correctly. This highly specific and sensitive NSD1(+/-) signature encompasses genes that function in cellular morphogenesis and neuronal differentiation, reflecting cardinal features of the SS phenotype. The identification of SS-specific genome-wide DNAm alterations will facilitate both the elucidation of the molecular pathophysiology of SS and the development of improved diagnostic testing.

A prenatal case of split-hand malformation associated with 17p13.3 triplication - a dilemma in genetic counseling.

Copy number gain of 17p13.3 has been shown to be associated with developmental delay/autism and Split-Hand-Foot malformation. We report a case of fetus with bilateral split-hand malformation detected on prenatal ultrasound. Array comparative genomic hybridization detected 2 maternally inherited copy number gains in the 17p13.3 region with one of them involving the BHLHA9 gene and part of the YWHAE gene. The mother is normal in intelligence with mild right foot anomaly only. Although the BHLHA9 copy gain is known to be associated with split-hand-foot malformation, the penetrance and expressivity is highly variable. More challenging is the effect of partial YWHAE copy number gain on neurodevelopment is inconclusive based on current literature. This case highlights the difficulties of prenatal genetic counseling in array comparative genomic hybridization findings in clinical situation with incomplete understanding of genotype-phenotype correlation.