Gene expression analysis in recurrent benign paroxysmal positional vertigo: a preliminary study.

Objectives: This study aimed to determine the pathophysiology of recurrent benign paroxysmal positional vertigo (BPPV) in young patients using gene expression profiling combined with bioinformatics analysis. Methods: Total RNA was extracted from the whole blood of four young patients with recurrent BPPV and four controls. The differentially expressed genes (DEGs) between the groups were screened using a microarray analysis based on the cutoff criteria of |log2 fold change| > 1 and an adjusted p-value of < 0.05. Functional enrichment analysis of DEGs was performed using Gene Ontology analysis, and the protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of the Interacting Genes database. Results: A total of 39 DEGs were detected between the BPPV and control samples, comprising 33 upregulated DEGs and six downregulated DEGs in the BPPV group. Functional enrichment analysis indicated that the upregulated DEGs were significantly enriched in terms related to metabolic processes and the immune system. Two main pathways were extracted from the PPI network: one was associated with oxidative phosphorylation and stress and the other with the adaptive immune system and extracellular matrix degradation. Conclusion: The findings of our bioinformatics analysis indicated that oxidative stress or extracellular matrix degradation due to immune-mediated inflammatory responses may contribute to the development of recurrent BPPV in young patients.

Otoconial Degeneration After Transient Ischemia Induced by Four-Vessel Occlusion in Rats.

BACKGROUND AND PURPOSE: Ischemia of the inner ear may damage the otoconia. However, no study has explored any changes in the configuration of otoconia after transient ischemia of the labyrinth. METHODS: Nineteen 7-week-old Sprague-Dawley rats were randomly assigned to either the sham (n=5) or the experimental group (n=14). The rats in the experimental group were subjected to global ischemia for 20 minutes using a four-vessel occlusion model, and were sacrificed seven days after the procedure. The rats in the sham group were sacrificed without any procedure. The otolithic organs (utricle and saccule) were dissected out for scanning electron microscope. RESULTS: The otolithic organs in the sham group showed their normal gross configuration with a dense clumping of otoconia with a normal hexagonal morphology and a smooth surface. The otolithic organs in the experimental group also maintained a grossly normal configuration, but each otoconia showed irregular surfaces with numerous cracks or furrows, especially in the periphery of the otoconial bed. CONCLUSIONS: The current study showed that otoconial degeneration may occur even after transient ischemia of the labyrinth. This finding supports an association between cerebral ischemia and benign paroxysmal positional vertigo.

AS-CMC: a pan-cancer database of alternative splicing for molecular classification of cancer.

Alternative splicing (AS) is a post-transcriptional regulation that leads to the complexity of the transcriptome. Despite the growing importance of AS in cancer research, the role of AS has not been systematically studied, especially in understanding cancer molecular classification. Herein, we analyzed the molecular subtype-specific regulation of AS using The Cancer Genome Atlas data and constructed a web-based database, named Alternative Splicing for Cancer Molecular Classification (AS-CMC). Our system harbors three analysis modules for exploring subtype-specific AS events, evaluating their phenotype association, and performing pan-cancer comparison. The number of subtype-specific AS events was found to be diverse across cancer types, and some differentially regulated AS events were recurrently found in multiple cancer types. We analyzed a subtype-specific AS in exon 11 of mitogen-activated protein kinase kinase 7 (MAP3K7) as an example of a pan-cancer AS biomarker. This AS marker showed significant association with the survival of patients with stomach adenocarcinoma. Our analysis revealed AS as an important determinant for cancer molecular classification. AS-CMC is the first web-based resource that provides a comprehensive tool to explore the biological implications of AS events, facilitating the discovery of novel AS biomarkers.

tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data.

BACKGROUND: Recent deep sequencing technologies have proven to be valuable resources to gain insights into the expression profiles of diverse tRNAs. However, despite these technologies, the association of tRNAs with diverse diseases has not been explored in depth because analytical tools are lacking. RESULTS: We developed a user-friendly tool, tRNA Expression Analysis Software Utilizing R for Easy use (tReasure), to analyze differentially expressed tRNAs (DEtRNAs) from deep sequencing data of small RNAs using R packages. tReasure can quantify individual mature tRNAs, isodecoders, and isoacceptors. By adopting stringent mapping strategies, tReasure supports the precise measurement of mature tRNA read counts. The whole analysis workflow for determining DEtRNAs (uploading FASTQ files, removing adapter sequences and poor-quality reads, mapping and quantifying tRNAs, filtering out low count tRNAs, determining DEtRNAs, and visualizing statistical analysis) can be performed with the tReasure package. CONCLUSIONS: tReasure is an open-source software available for download at https://treasure.pmrc.re.kr and will be indispensable for users who have little experience with command-line software to explore the biological implication of tRNA expression.

Dissection of molecular and histological subtypes of papillary thyroid cancer using alternative splicing profiles.

Despite growing evidence of the relevance of alternative splicing (AS) to cancer development and progression, the biological implications of AS for tumor behaviors, including papillary thyroid cancer (PTC), remain elusive. With the aim of further understanding the molecular and histological subtypes of PTC, we in this study explored whether AS events might act as new molecular determinants. For this purpose, AS profiles were analyzed in RNA-sequencing data from The Cancer Genome Atlas (TCGA) and from a Korean patient dataset. A total of 23 distinct exon-skipping (ES) events that correlated significantly with PTC oncogenic activity and differentiation scores were identified. The two top-ranked ES events, NUMA1_17515 in exon 18 of NUMA1 and TUBB3_38175 in exon 6 of TUBB3, showed high correlations with oncogenic activities and discriminated histological and molecular subtypes of PTC. Furthermore, two novel intron-retention (IR) events for TUBB3 were uncovered. All ES and IR events for the TUBB3 gene were predicted to induce nonsense-mediated mRNA decay. The relative abundances of intron reads in the PTC dataset from TCGA showed IR levels to differ significantly among PTC subtypes, possibly reflecting their different tumor behaviors. This study provides a landscape of AS changes among PTC subtypes and identified two significant AS events, NUMA1_17515 and TUBB3_38175, as potential AS biomarkers for PTC subclassification and characterization. The AS events identified in this study may be involved in the development of phenotypic differences underlying the functional characteristics and histological differentiation of PTCs.

Whole Exome Sequencing in Patients with Phenotypically Associated Familial Intracranial Aneurysm.

OBJECTIVE: Familial intracranial aneurysms (FIAs) are found in approximately 6%-20% of patients with intracranial aneurysms (IAs), suggesting that genetic predisposition likely plays a role in its pathogenesis. The aim of this study was to identify possible IA-associated variants using whole exome sequencing (WES) in selected Korean families with FIA. MATERIALS AND METHODS: Among the 26 families in our institutional database with two or more IA-affected first-degree relatives, three families that were genetically enriched (multiple, early onset, or common site involvement within the families) for IA were selected for WES. Filtering strategies, including a family-based approach and knowledge-based prioritization, were applied to derive possible IA-associated variants from the families. A chromosomal microarray was performed to detect relatively large chromosomal abnormalities. RESULTS: Thirteen individuals from the three families were sequenced, of whom seven had IAs. We noted three rare, potentially deleterious variants (PLOD3 c.1315G>A, NTM c.968C>T, and CHST14 c.58C>T), which are the most promising candidates among the 11 potential IA-associated variants considering gene-phenotype relationships, gene function, co-segregation, and variant pathogenicity. Microarray analysis did not reveal any significant copy number variants in the families. CONCLUSION: Using WES, we found that rare, potentially deleterious variants in PLOD3, NTM, and CHST14 genes are likely responsible for the subsets of FIAs in a cohort of Korean families.

DBtRend: A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans.

Transfer RNA (tRNA), a key component of the translation machinery, plays critical roles in stress conditions and various diseases. While knowledge regarding the importance of tRNA function is increasing, its biological roles are still not well understood. There is currently no comprehensive database or web server providing the expression landscape of tRNAs across a variety of human tissues and diseases. Here, we constructed a user-friendly and interactive database, DBtRend, which provides a profile of mature tRNA expression across various biological conditions by reanalyzing the small RNA or microRNA sequencing data from the Cancer Genome Atlas (TCGA) and NCBI's Gene Expression Omnibus (GEO) in humans. Users can explore not only the expression values of mature individual tRNAs in the human genome, but also those of isodecoders and isoacceptors based on our specific pipelines. DBtRend provides the expressed patterns of tRNAs, the differentially expressed tRNAs in different biological conditions, and the information of samples or patients, tissue types, and molecular subtype of cancers. The database is expected to help researchers interested in functional discoveries of tRNAs.

Protective Effects of Deferoxamine on Vestibulotoxicity in Gentamicin-Induced Bilateral Vestibulopathy Rat Model.

Introduction: Administration of aminoglycoside (AG) antibiotics is one of the most common causes of ototoxicity. This study aimed to determine the protective effects of deferoxamine, an iron-chelating agent, on vestibulotoxicity using an intratympanic gentamicin injection (ITGM)-induced bilateral vestibulopathy rat model. Methods: Fifteen Sprague-Dawley rats were randomly assigned to the ITGM only (n = 5), the ITGM combined with intramuscular deferoxamine (DFO) injection (ITGM+DFO, n = 5), or the intratympanic normal saline (control, n = 5) group. The rats in the ITGM+DFO group received intramuscular injection of 150 mg/kg of deferoxamine at 30, 90, and 150 min after the ITGM. The vestibular function was evaluated using the rotarod and open field test every 3 days after the injection until Day 16 when the rats were subjected to histological changes. Results: The rats in the ITGM only group began to show significantly impaired vestibular function 2 days after ITGM into both ears. In contrast, the vestibular function was maintained in the control and ITGM+DFO groups without a difference throughout the experiments. The rats in the ITGM only group showed a near-complete loss of the type I and II hair cells and a collapse of the sensory epithelium in both the saccule and utricle. In contrast, the rats in the ITGM+DFO and control groups showed a relatively well-preserved sensory epithelium including the hair cells, cilia, and otolith layer. Conclusion: This study provides experimental evidence for preventive effects of iron-chelating agents on AG-induced vestibulotoxicity. Simultaneous administration of iron-chelating agents may be considered when using ototoxic agents, especially in those considered to be vulnerable to toxic damage of the inner ear.

Altered brain function in persistent postural perceptual dizziness: A study on resting state functional connectivity.

This study used resting state functional magnetic resonance imaging (rsfMRI) to investigate whole brain networks in patients with persistent postural perceptual dizziness (PPPD). We compared rsfMRI data from 38 patients with PPPD and 38 healthy controls using whole brain and region of interest analyses. We examined correlations among connectivity and clinical variables and tested the ability of a machine learning algorithm to classify subjects using rsfMRI results. Patients with PPPD showed: (a) increased connectivity of subcallosal cortex with left superior lateral occipital cortex and left middle frontal gyrus, (b) decreased connectivity of left hippocampus with bilateral central opercular cortices, left posterior opercular cortex, right insular cortex and cerebellum, and (c) decreased connectivity between right nucleus accumbens and anterior left temporal fusiform cortex. After controlling for anxiety and depression as covariates, patients with PPPD still showed decreased connectivity between left hippocampus and right inferior frontal gyrus, bilateral temporal lobes, bilateral insular cortices, bilateral central opercular cortex, left parietal opercular cortex, bilateral occipital lobes and cerebellum (bilateral lobules VI and V, and left I-IV). Dizziness handicap, anxiety, and depression correlated with connectivity in clinically meaningful brain regions. The machine learning algorithm correctly classified patients and controls with a sensitivity of 78.4%, specificity of 76.9%, and area under the curve = 0.88 using 11 connectivity parameters. Patients with PPPD showed reduced connectivity among the areas involved in multisensory vestibular processing and spatial cognition, but increased connectivity in networks linking visual and emotional processing. Connectivity patterns may become an imaging biomarker of PPPD.

Diverse genetic aetiologies and clinical outcomes of paediatric hypoparathyroidism.

CONTEXT: Hypoparathyroidism is characterized by hypocalcaemia, hyperphosphataemia, and low or inappropriately normal parathyroid hormone (PTH) levels. Idiopathic or genetic drivers are the predominant causes of hypoparathyroidism in paediatric-age patients. OBJECTIVE: This study investigated the aetiology and clinical course of primary hypoparathyroidism in infancy and childhood. SUBJECTS AND MEASUREMENTS: This study included 37 patients (23 males, 14 females) with primary hypoparathyroidism diagnosed prior to 18 years of age. We analysed aetiologies, initial presentation, age at diagnosis, endocrine and radiological findings, and outcomes. RESULTS: The median age at presentation was 1·7 months (range 1 day-17 years), and the mean follow-up duration was 7·0 ± 5·3 years (range 0·5-16·8 years). Our cohort included 22 cases (59·5%) of 22q11·2 microdeletion syndrome. Other aetiologies included hypoparathyroidism-deafness-renal dysplasia syndrome (5/37, 13·5%) and one patient each with autoimmune polyglandular syndrome type 1, Kearns-Sayre syndrome and Kenny-Caffey syndrome. The remaining 7 (18·9%) patients were classified as idiopathic hypoparathyroidism cases. Among the 15 patients who underwent brain imaging, 5 (33·3%) had basal ganglia calcification. Among the 26 patients examined by renal imaging, 5 (19·2%) had either nephrocalcinosis or a renal stone. After 11 months of calcium or calcitriol supplementation, 16 patients (43·2%) discontinued medication. The final PTH levels were significantly higher in patients with transient hypoparathyroidism than those with permanent hypoparathyroidism. CONCLUSIONS: Identification of the genetic aetiologies of hypoparathyroidism makes it possible to predict patient outcomes and provide appropriate genetic counselling. Long-term treatment with calcium and calcitriol necessitates monitoring for renal complications.

Clinical and molecular characterisation of Holt-Oram syndrome focusing on cardiac manifestations.

BACKGROUND: Holt-Oram syndrome is characterised by CHD and limb anomalies. Mutations in TBX5 gene, encoding the T-box transcription factor, are responsible for the development of Holt-Oram syndrome, but such mutations are variably detected in 30-75% of patients. METHODS: Clinically diagnosed eight Holt-Oram syndrome patients from six families were evaluated the clinical characteristics, focusing on the cardiac manifestations, in particular, and molecular aetiologies. In addition to the investigation of the mutation of TBX5, SALL4, NKX2.5, and GATA4 genes, which are known to regulate cardiac development by physically and functionally interacting with TBX5, were also analyzed. Multiple ligation-dependent probe amplification analysis was performed to detect exonic deletion and duplication mutations in these genes. RESULTS: All included patients showed cardiac septal defects and upper-limb anomalies. Of the eight patients, seven underwent cardiac surgery, and four suffered from conduction abnormalities such as severe sinus bradycardia and complete atrioventricular block. Although our patients showed typical clinical findings of Holt-Oram syndrome, only three distinct TBX5 mutations were detected in three families: one nonsense, one splicing, and one missense mutation. No new mutations were identified by testing SALL4, NKX2.5, and GATA4 genes. CONCLUSIONS: All Holt-Oram syndrome patients in this study showed cardiac septal anomalies. Half of them showed TBX5 gene mutations. To understand the genetic causes for inherited CHD such as Holt-Oram syndrome is helpful to take care of the patients and their families. Further efforts with large-scale genomic research are required to identify genes responsible for cardiac manifestations or genotype-phenotype relation in Holt-Oram syndrome.

A de novo microdeletion of ANKRD11 gene in a Korean patient with KBG syndrome.

KBG syndrome is a very rare genetic disorder characterized by macrodontia of upper central incisors, global developmental delay, distinctive craniofacial features, short stature, and skeletal anomalies. Ankyrin repeat domain 11 gene (ANKRD11) has recently been identified as a causal factor of this syndrome. We describe a 6-yr-old Korean boy with features of KBG syndrome. The patient had a short stature, macrodontia, dysmorphic facial features, speech and motor delay with intellectual disability, and partial seizures as indicated by the electroencephalogram, but he was neither autistic nor had autism spectrum disorders. Using high-resolution oligonucleotide array comparative genomic hybridization, we identified a heterozygous 240-kb deletion at 16q24.3 corresponding to ANKRD11. This patient provided additional evidence on the influence of ANKRD11 in KBG syndrome and suggested that deletion limited to ANKRD11 is unlikely to cause autism.

Clinical significance of previously cryptic copy number alterations and loss of heterozygosity in pediatric acute myeloid leukemia and myelodysplastic syndrome determined using combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray analyses.

The combined array comparative genomic hybridization plus single-nucleotide polymorphism microarray (CGH+SNP microarray) platform can simultaneously detect copy number alterations (CNA) and copy-neutral loss of heterozygosity (LOH). Eighteen children with acute myeloid leukemia (AML) (n=15) or myelodysplastic syndrome (MDS) (n=3) were studied using CGH+SNP microarray to evaluate the clinical significance of submicroscopic chromosomal aberrations. CGH+SNP microarray revealed CNAs at 14 regions in 9 patients, while metaphase cytogenetic (MC) analysis detected CNAs in 11 regions in 8 patients. Using CGH+SNP microarray, LOHs>10 Mb involving terminal regions or the whole chromosome were detected in 3 of 18 patients (17%). CGH+SNP microarray revealed cryptic LOHs with or without CNAs in 3 of 5 patients with normal karyotypes. CGH+SNP microarray detected additional cryptic CNAs (n=2) and LOHs (n=5) in 6 of 13 patients with abnormal MC. In total, 9 patients demonstrated additional aberrations, including CNAs (n=3) and/or LOHs (n=8). Three of 15 patients with AML and terminal LOH>10 Mb demonstrated a significantly inferior relapse-free survival rate (P=0.041). This study demonstrates that CGH+SNP microarray can simultaneously detect previously cryptic CNAs and LOH, which may demonstrate prognostic implications.

RANBP2-ALK fusion combined with monosomy 7 in acute myelomonocytic leukemia.

Anaplastic lymphoma receptor tyrosine kinase (ALK) is located on chromosome 2p23; the chromosomal rearrangements of this gene are common genetic alterations, resulting in the creation of multiple fusion genes involved in tumorigenesis. However, the presence of an ALK fusion in myeloid malignancies is extremely rare. We report a case of acute myelomonocytic leukemia in a 31-year-old woman with an unusual rearrangement between RAN-binding protein 2 (RANBP2) and ALK and a karyotype of 45,XX,inv(2)(p23q21),-7[20]. We detected an ALK rearrangement using fluorescence in situ hybridization, identified the ALK fusion partner by using RNA transcriptome sequencing, and demonstrated the RANBP2-ALK fusion transcript by reverse transcriptase--PCR and Sanger sequencing. Immunohistochemistry for ALK showed strong staining of the nuclear membrane in leukemic cells. The patient had an unfavorable clinical course. Our results, together with a literature review, suggest the RANBP2-ALK fusion combined with monosomy 7 may be related to a unique clonal hematologic disorder of childhood and adolescence, characterized by myelomonocytic leukemia and a poor prognosis.

Vulnerability of the vestibular organs to transient ischemia: implications for isolated vascular vertigo.

The aim of this study was to elucidate the mechanism of isolated vascular vertigo by determining selective and relative ischemic vulnerability of the vestibular structures using a global hypoperfusion model in rats. Sprague-Dawley male rats weighing 330-350 g were subjected to transient global ischemia of the brain using a 4-vessel-occlusion (4VO) model. After permanent occlusion of both vertebral arteries (VA) using electrocauterization, both common carotid arteries (CCAs) were occluded for 5-20 min with ligation. One hour after reperfusion of the CCAs, the animals were sacrificed and subjected to c-Fos staining of the entire cerebellum, brainstem, and vestibular ganglion. The rats in the sham group received the same surgical procedures except the vessel ligation. With 4VO for 5-15 min, both the sham and experimental groups showed a weak and scarce c-Fos expression in the medial vestibular nucleus (MVN), neuron Y, and cochlear nucleus. After 4VO for 20 min, only the MVN began to show a significant difference in the number of c-Fos positive neurons between the experimental and sham groups (33.7±17.7 vs.7.1±5.1, Wilcoxon rank test, p=0.005). With 4VO for up to 20 min, c-Fos positive neurons were not found in other areas of the brainstem and cerebellum, including the superior, lateral, and spinal vestibular nuclei, the vestibular ganglion, the cerebellar cortex, and the deep cerebellar nuclei. The vestibular structures appear to be vulnerable to ischemia more than any other structures in the brainstem and cerebellum. Of the vestibular structures, the MVN is most vulnerable to ischemic insults in rats. These findings are consistent with the common findings of vertigo as an initial and isolated symptom of posterior circulation ischemia in human.

Gentamicin-induced bilateral vestibulopathy in rabbits: vestibular dysfunction and histopathology.

OBJECTIVES/HYPOTHESIS: Bilateral vestibulopathy (BV) is a mostly persistent and disabling disorder causing dizziness, oscillopsia, and imbalance during locomotion. The animal model is a prerequisite for experimental investigation on prevention and treatment of this disorder. The aim of this study was to determine the vestibular dysfunction and histopathology in rabbits with gentamicin-induced BV. STUDY DESIGN: Prospective animal study in rabbits. METHODS: We performed intratympanic gentamicin (ITGM) injections in 12 Lionhead rabbits. The injection was applied to each ear with a 3-day interval. The control group received injections of 0.9% normal saline. The animals were subjected to sinusoidal harmonic accelerations and open field tests for evaluation of the vestibular function before and after the procedures. We also determined histologic changes in the vestibular labyrinth 30 days after the first injection. RESULTS: One day after unilateral ITGM injection, the rabbits mostly showed ipsiversive head tilt, contralesional spontaneous nystagmus, ipsiversive circling behavior, and decreased gain of the vestibulo-ocular reflex (VOR) during ipsiversive rotation. The second injection to the contralateral ear improved the head tilt but induced marked reduction in the activities and the VOR gains in both directions. These changes persisted until the histologic study confirmed the loss of the hair and supporting cells, diminished nerve fibers, and thinning of the sensory epithelium of the cristae ampullaris and otolith organs in the ITGM group 1 month later. CONCLUSIONS: ITGM injection securely induced BV in rabbits without side effects such as nephrotoxicity. This rabbit model may be utilized for experiments on the prevention and treatment of BV.

OBFC2A/RARA: a novel fusion gene in variant acute promyelocytic leukemia.

Acute promyelocytic leukemia is characterized by the rearrangement of the retinoic acid receptor α (RARA) gene and its fusion with other genes. We report a novel case of variant acute promyelocytic leukemia with the karyotype der (2)t(2;17)(q32;q21). Array comparative genomic hybridization revealed distinct chromosome breakpoints within the RARA and oligonucleotide/oligosaccharide-binding fold containing 2A (OBFC2A) genes. Sequence analysis of the OBFC2A/RARA transcript showed that exon 5 of OBFC2A was fused with exon 3 of RARA through the same breakpoint as in previously described fusions of RARA. The single-stranded DNA binding protein encoded by OBFC2A is critical for genomic stability. Retention of the OB fold domain of OBFC2A in the fusion protein suggests the possibility of homodimerization. The leukemic cells from the patient showed neutrophilic differentiation in the in vitro all-trans retinoic acid assay. Mutation or rearrangement of the OBFC2A gene has not been previously reported in congenital or acquired disorders.

Molecular cytogenetic and clinical characterization of a patient with a 5.6-Mb deletion in 7p15 including HOXA cluster.

Here, we describe the clinical features of a boy with a 5.6-Mb deletion at chromosome 7p15.1-p15.3. He has mild facial anomalies, hand-foot abnormalities, hypospadias, congenital heart defects, and supernumerary nipples. This deletion was detected by array comparative genomic hybridization and verified by fluorescence in situ hybridization using BACs selected from the USCS genome browser. This deletion was not found in subsequent FISH analysis of the parental chromosomes. The deleted region contains several genes, including contiguous developmental genes on the HOXA cluster, which play a role in regulating aspects of morphogenesis during normal embryonic development. The patient's limb and urogenital features were similar to those observed in hand-foot-genital syndrome, which is caused by haploinsufficiency of HOXA13, whereas the congenital heart defect may reflect the deletion of HOXA3. We hypothesized that many clinical features of the patient were due to combined haploinsufficiency of the HOXA cluster. Our study also demonstrates the clinical usefulness of a molecular cytogenetic tool that is capable of detecting imbalances in the genome.

[Identification of a novel deletion region in 3q29 microdeletion syndrome by oligonucleotide array comparative genomic hybridization].

BACKGROUND: The 3q29 microdeletion syndrome is a genomic disorder characterized by mental retardation, developmental delay, microcephaly, and slight facial dysmorphism. In most cases, the microdeletion spans a 1.6-Mb region between low-copy repeats (LCRs). We identified a novel 4.0- Mb deletion using oligonucleotide array comparative genomic hybridization (array CGH) in monozygotic twin sisters. METHODS: G-banded chromosome analysis was performed in the twins and their parents. Highresolution oligonucleotide array CGH was performed using the human whole genome 244K CGH microarray (Agilent Technologies, USA) followed by validation using FISH, and the obtained results were analyzed using the genome database resources. RESULTS: G-banding revealed that the twins had de novo 46,XX,del(3)(q29) karyotype. Array CGH showed a 4.0-Mb interstitial deletion on 3q29, which contained 39 genes and no breakpoints flanked by LCRs. In addition to the typical characteristics of the 3q29 microdeletion syndrome, the twins had attention deficit-hyperactivity disorder, strabismus, congenital heart defect, and gray hair. Besides the p21-activated protein kinase (PAK2) and discs large homolog 1 (DLG1) genes, which are known to play a critical role in mental retardation, the hairy and enhancer of split 1 (HES1) and antigen p97 (melanoma associated; MFI2) genes might be possible candidate genes associated with strabismus, congenital heart defect, and gray hair. CONCLUSIONS: The novel 4.0-Mb 3q29 microdeletion found in the twins suggested the occurrence of genomic rearrangement mediated by mechanisms other than nonallelic homologous recombination. Molecular genetic and functional studies are required to elucidate the contribution of each gene to a specific phenotype.