List of Publications
There are numbers of autism related research can be found in Malaysia that generally focus on the ASD, learning disorder, communication aids, therapy and many more. The list of publications is provided below:
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2019 |
Mohamad, F H; Has, A T C The α5-Containing GABA A Receptors—a Brief Summary Journal Article Journal of Molecular Neuroscience, 67 (2), pp. 343-351, 2019, ISSN: 08958696, (cited By 1). Abstract | Links | BibTeX | Tags: 4 Aminobutyric Acid, 4 Aminobutyric Acid A Receptor, Alpha5 Containing 4 Aminobutyric Acid A Receptor, Animals, Autism, Brain, Cognitive Defect, Cognitive Dysfunction, Drug Effect, GABA Agents, GABA-A, GABAergic Receptor Affecting Agent, Genetics, Human, Metabolism, Nonhuman, Protein Subunit, Protein Subunits, Receptors, Review, Schizophrenia, Unclassified Drug @article{Mohamad2019343, title = {The α5-Containing GABA A Receptors—a Brief Summary}, author = {F H Mohamad and A T C Has}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85059596842&doi=10.1007%2fs12031-018-1246-4&partnerID=40&md5=7b2ba0dc86c6c3f890f226cad8195ee5}, doi = {10.1007/s12031-018-1246-4}, issn = {08958696}, year = {2019}, date = {2019-01-01}, journal = {Journal of Molecular Neuroscience}, volume = {67}, number = {2}, pages = {343-351}, publisher = {Springer New York LLC}, abstract = {GABA A receptors are the major inhibitory neurotransmitter receptor in the human brain. The receptors are assembled from combination of protein subunits in pentameric complex which may consist of α1–6, β1–3, γ1–3, ρ1–3, δ, ε, θ, or π subunits. There are a theoretical > 150,000 possible assemblies and arrangements of GABA A subunits, although only a few combinations have been found in human with the most dominant consists of 2α1, 2β2, and 1γ2 in a counterclockwise arrangement as seen from the synaptic cleft. The receptors also possess binding sites for various unrelated substances including benzodiazepines, barbiturates, and anesthetics. The α5-containing GABA A Rs only make up ≤ 5% of the entire receptor population, but up to 25% of the receptor subtype is located in the crucial learning and memory-associated area of the brain—the hippocampus, which has ignited myriads of hypotheses and theories in regard to its role. As well as exhibiting synaptic phasic inhibition, the α5-containing receptors are also extrasynaptic and mediate tonic inhibition with continuously occurring smaller amplitude. Studies on negative-allosteric modulators for reducing this tonic inhibition have been shown to enhance learning and memory in neurological disorders such as schizophrenia, Down syndrome, and autism with a possible alternative benzodiazepine binding site. Therefore, a few α5 subunit-specific compounds have been developed to address these pharmacological needs. With its small population, the α5-containing receptors could be the key and also the answer for many untreated cognitive dysfunctions and disorders. © 2019, Springer Science+Business Media, LLC, part of Springer Nature.}, note = {cited By 1}, keywords = {4 Aminobutyric Acid, 4 Aminobutyric Acid A Receptor, Alpha5 Containing 4 Aminobutyric Acid A Receptor, Animals, Autism, Brain, Cognitive Defect, Cognitive Dysfunction, Drug Effect, GABA Agents, GABA-A, GABAergic Receptor Affecting Agent, Genetics, Human, Metabolism, Nonhuman, Protein Subunit, Protein Subunits, Receptors, Review, Schizophrenia, Unclassified Drug}, pubstate = {published}, tppubtype = {article} } GABA A receptors are the major inhibitory neurotransmitter receptor in the human brain. The receptors are assembled from combination of protein subunits in pentameric complex which may consist of α1–6, β1–3, γ1–3, ρ1–3, δ, ε, θ, or π subunits. There are a theoretical > 150,000 possible assemblies and arrangements of GABA A subunits, although only a few combinations have been found in human with the most dominant consists of 2α1, 2β2, and 1γ2 in a counterclockwise arrangement as seen from the synaptic cleft. The receptors also possess binding sites for various unrelated substances including benzodiazepines, barbiturates, and anesthetics. The α5-containing GABA A Rs only make up ≤ 5% of the entire receptor population, but up to 25% of the receptor subtype is located in the crucial learning and memory-associated area of the brain—the hippocampus, which has ignited myriads of hypotheses and theories in regard to its role. As well as exhibiting synaptic phasic inhibition, the α5-containing receptors are also extrasynaptic and mediate tonic inhibition with continuously occurring smaller amplitude. Studies on negative-allosteric modulators for reducing this tonic inhibition have been shown to enhance learning and memory in neurological disorders such as schizophrenia, Down syndrome, and autism with a possible alternative benzodiazepine binding site. Therefore, a few α5 subunit-specific compounds have been developed to address these pharmacological needs. With its small population, the α5-containing receptors could be the key and also the answer for many untreated cognitive dysfunctions and disorders. © 2019, Springer Science+Business Media, LLC, part of Springer Nature. |
2018 |
Tsuchida, N; Hamada, K; Shiina, M; Kato, M; Kobayashi, Y; Tohyama, J; Kimura, K; Hoshino, K; Ganesan, V; Teik, K W; Nakashima, M; Mitsuhashi, S; Mizuguchi, T; Takata, A; Miyake, N; Saitsu, H; Ogata, K; Miyatake, S; Matsumoto, N GRIN2D variants in three cases of developmental and epileptic encephalopathy Journal Article Clinical Genetics, 94 (6), pp. 538-547, 2018, ISSN: 00099163, (cited By 4). Abstract | Links | BibTeX | Tags: Adolescent, Allele, Amino Acid Sequence, Amino Acid Substitution, Amino Terminal Sequence, Anemia, Antibiotic Agent, Antibiotic Therapy, Article, Atonic Seizure, Attention Deficit Disorder, Autism, Binding Affinity, Brain, Brain Atrophy, Carbamazepine, Case Report, Channel Gating, Chemistry, Children, Clinical Article, Clinical Feature, Clobazam, Clonazepam, Conformational Transition, Continuous Infusion, Contracture, Crystal Structure, Cysteine Ethyl Ester Tc 99m, Developmental Delay, Developmental Disorders, Electroencephalogram, Electroencephalography, Epilepsy, Epileptic Discharge, Ethosuximide, Eye Tracking, Febrile Convulsion, Female, Frontal Lobe Epilepsy, Gene, Gene Frequency, Genetic Variation, Genetics, Genotype, GRIN2D Protein, Heterozygosity, Home Oxygen Therapy, Human, Human Cell, Hydrogen Bond, Intellectual Impairment, Intelligence Quotient, Intractable Epilepsy, Ketamine, Lacosamide, Lamotrigine, Lennox Gastaut Syndrome, Levetiracetam, Magnetoencephalography, Male, Maternal Hypertension, Melatonin, Migraine, Missense Mutation, Molecular Dynamics, Molecular Dynamics Simulation, Mutation, Myoclonus Seizure, N Methyl Dextro Aspartic Acid Receptor, N Methyl Dextro Aspartic Acid Receptor 2D, N-Methyl-D-Aspartate, Neonatal Pneumonia, Neonatal Respiratory Distress Syndrome, Neuroimaging, Nuclear Magnetic Resonance Imaging, Phenobarbital, Premature Labor, Preschool, Preschool Child, Priority Journal, Protein Conformation, Proximal Interphalangeal Joint, Pyridoxine, Receptors, Respiratory Arrest, Sanger Sequencing, School Child, Single Photon Emission Computed Tomography, Sleep Disordered Breathing, Static Electricity, Stridor, Structure-Activity Relationship, Subglottic Stenosis, Superior Temporal Gyrus, Supramarginal Gyrus, Thiopental, Tonic Seizure, Valproic Acid, Wakefulness, Wechsler Intelligence Scale for Children, Whole Exome Sequencing @article{Tsuchida2018538, title = {GRIN2D variants in three cases of developmental and epileptic encephalopathy}, author = {N Tsuchida and K Hamada and M Shiina and M Kato and Y Kobayashi and J Tohyama and K Kimura and K Hoshino and V Ganesan and K W Teik and M Nakashima and S Mitsuhashi and T Mizuguchi and A Takata and N Miyake and H Saitsu and K Ogata and S Miyatake and N Matsumoto}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85056487337&doi=10.1111%2fcge.13454&partnerID=40&md5=f0d32670db57261820bc244943cffd62}, doi = {10.1111/cge.13454}, issn = {00099163}, year = {2018}, date = {2018-01-01}, journal = {Clinical Genetics}, volume = {94}, number = {6}, pages = {538-547}, publisher = {Blackwell Publishing Ltd}, abstract = {N-methyl-d-aspartate (NMDA) receptors are glutamate-activated ion channels that are widely distributed in the central nervous system and essential for brain development and function. Dysfunction of NMDA receptors has been associated with various neurodevelopmental disorders. Recently, a de novo recurrent GRIN2D missense variant was found in two unrelated patients with developmental and epileptic encephalopathy. In this study, we identified by whole exome sequencing novel heterozygous GRIN2D missense variants in three unrelated patients with severe developmental delay and intractable epilepsy. All altered residues were highly conserved across vertebrates and among the four GluN2 subunits. Structural consideration indicated that all three variants are probably to impair GluN2D function, either by affecting intersubunit interaction or altering channel gating activity. We assessed the clinical features of our three cases and compared them to those of the two previously reported GRIN2D variant cases, and found that they all show similar clinical features. This study provides further evidence of GRIN2D variants being causal for epilepsy. Genetic diagnosis for GluN2-related disorders may be clinically useful when considering drug therapy targeting NMDA receptors. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd}, note = {cited By 4}, keywords = {Adolescent, Allele, Amino Acid Sequence, Amino Acid Substitution, Amino Terminal Sequence, Anemia, Antibiotic Agent, Antibiotic Therapy, Article, Atonic Seizure, Attention Deficit Disorder, Autism, Binding Affinity, Brain, Brain Atrophy, Carbamazepine, Case Report, Channel Gating, Chemistry, Children, Clinical Article, Clinical Feature, Clobazam, Clonazepam, Conformational Transition, Continuous Infusion, Contracture, Crystal Structure, Cysteine Ethyl Ester Tc 99m, Developmental Delay, Developmental Disorders, Electroencephalogram, Electroencephalography, Epilepsy, Epileptic Discharge, Ethosuximide, Eye Tracking, Febrile Convulsion, Female, Frontal Lobe Epilepsy, Gene, Gene Frequency, Genetic Variation, Genetics, Genotype, GRIN2D Protein, Heterozygosity, Home Oxygen Therapy, Human, Human Cell, Hydrogen Bond, Intellectual Impairment, Intelligence Quotient, Intractable Epilepsy, Ketamine, Lacosamide, Lamotrigine, Lennox Gastaut Syndrome, Levetiracetam, Magnetoencephalography, Male, Maternal Hypertension, Melatonin, Migraine, Missense Mutation, Molecular Dynamics, Molecular Dynamics Simulation, Mutation, Myoclonus Seizure, N Methyl Dextro Aspartic Acid Receptor, N Methyl Dextro Aspartic Acid Receptor 2D, N-Methyl-D-Aspartate, Neonatal Pneumonia, Neonatal Respiratory Distress Syndrome, Neuroimaging, Nuclear Magnetic Resonance Imaging, Phenobarbital, Premature Labor, Preschool, Preschool Child, Priority Journal, Protein Conformation, Proximal Interphalangeal Joint, Pyridoxine, Receptors, Respiratory Arrest, Sanger Sequencing, School Child, Single Photon Emission Computed Tomography, Sleep Disordered Breathing, Static Electricity, Stridor, Structure-Activity Relationship, Subglottic Stenosis, Superior Temporal Gyrus, Supramarginal Gyrus, Thiopental, Tonic Seizure, Valproic Acid, Wakefulness, Wechsler Intelligence Scale for Children, Whole Exome Sequencing}, pubstate = {published}, tppubtype = {article} } N-methyl-d-aspartate (NMDA) receptors are glutamate-activated ion channels that are widely distributed in the central nervous system and essential for brain development and function. Dysfunction of NMDA receptors has been associated with various neurodevelopmental disorders. Recently, a de novo recurrent GRIN2D missense variant was found in two unrelated patients with developmental and epileptic encephalopathy. In this study, we identified by whole exome sequencing novel heterozygous GRIN2D missense variants in three unrelated patients with severe developmental delay and intractable epilepsy. All altered residues were highly conserved across vertebrates and among the four GluN2 subunits. Structural consideration indicated that all three variants are probably to impair GluN2D function, either by affecting intersubunit interaction or altering channel gating activity. We assessed the clinical features of our three cases and compared them to those of the two previously reported GRIN2D variant cases, and found that they all show similar clinical features. This study provides further evidence of GRIN2D variants being causal for epilepsy. Genetic diagnosis for GluN2-related disorders may be clinically useful when considering drug therapy targeting NMDA receptors. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd |
2017 |
Hnoonual, A; Thammachote, W; Tim-Aroon, T; Rojnueangnit, K; Hansakunachai, T; Sombuntham, T; Roongpraiwan, R; Worachotekamjorn, J; Chuthapisith, J; Fucharoen, S; Wattanasirichaigoon, D; Ruangdaraganon, N; Limprasert, P; Jinawath, N Scientific Reports, 7 (1), 2017, ISSN: 20452322, (cited By 6). Abstract | Links | BibTeX | Tags: Adolescent, Autism, Autism Spectrum Disorders, Children, Chromosomal Mapping, Chromosome Mapping, Cohort Analysis, Cohort Studies, Copy Number Variation, DNA Copy Number Variations, Female, Genetic Predisposition, Genetic Predisposition to Disease, Genetics, Human, Infant, Male, Membrane Protein, Membrane Proteins, Microarray Analysis, Polymorphism, Preschool, Preschool Child, Procedures, SERINC2 Protein, Single Nucleotide, Single Nucleotide Polymorphism @article{Hnoonual2017, title = {Chromosomal microarray analysis in a cohort of underrepresented population identifies SERINC2 as a novel candidate gene for autism spectrum disorder}, author = {A Hnoonual and W Thammachote and T Tim-Aroon and K Rojnueangnit and T Hansakunachai and T Sombuntham and R Roongpraiwan and J Worachotekamjorn and J Chuthapisith and S Fucharoen and D Wattanasirichaigoon and N Ruangdaraganon and P Limprasert and N Jinawath}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85029864969&doi=10.1038%2fs41598-017-12317-3&partnerID=40&md5=3c1b6a0c064665aab8ace8e8f58c2b01}, doi = {10.1038/s41598-017-12317-3}, issn = {20452322}, year = {2017}, date = {2017-01-01}, journal = {Scientific Reports}, volume = {7}, number = {1}, publisher = {Nature Publishing Group}, abstract = {Chromosomal microarray (CMA) is now recognized as the first-tier genetic test for detection of copy number variations (CNVs) in patients with autism spectrum disorder (ASD). The aims of this study were to identify known and novel ASD associated-CNVs and to evaluate the diagnostic yield of CMA in Thai patients with ASD. The Infinium CytoSNP-850K BeadChip was used to detect CNVs in 114 Thai patients comprised of 68 retrospective ASD patients (group 1) with the use of CMA as a second line test and 46 prospective ASD and developmental delay patients (group 2) with the use of CMA as the first-tier test. We identified 7 (6.1%) pathogenic CNVs and 22 (19.3%) variants of uncertain clinical significance (VOUS). A total of 29 patients with pathogenic CNVs and VOUS were found in 22% (15/68) and 30.4% (14/46) of the patients in groups 1 and 2, respectively. The difference in detected CNV frequencies between the 2 groups was not statistically significant (Chi square = 1.02}, note = {cited By 6}, keywords = {Adolescent, Autism, Autism Spectrum Disorders, Children, Chromosomal Mapping, Chromosome Mapping, Cohort Analysis, Cohort Studies, Copy Number Variation, DNA Copy Number Variations, Female, Genetic Predisposition, Genetic Predisposition to Disease, Genetics, Human, Infant, Male, Membrane Protein, Membrane Proteins, Microarray Analysis, Polymorphism, Preschool, Preschool Child, Procedures, SERINC2 Protein, Single Nucleotide, Single Nucleotide Polymorphism}, pubstate = {published}, tppubtype = {article} } Chromosomal microarray (CMA) is now recognized as the first-tier genetic test for detection of copy number variations (CNVs) in patients with autism spectrum disorder (ASD). The aims of this study were to identify known and novel ASD associated-CNVs and to evaluate the diagnostic yield of CMA in Thai patients with ASD. The Infinium CytoSNP-850K BeadChip was used to detect CNVs in 114 Thai patients comprised of 68 retrospective ASD patients (group 1) with the use of CMA as a second line test and 46 prospective ASD and developmental delay patients (group 2) with the use of CMA as the first-tier test. We identified 7 (6.1%) pathogenic CNVs and 22 (19.3%) variants of uncertain clinical significance (VOUS). A total of 29 patients with pathogenic CNVs and VOUS were found in 22% (15/68) and 30.4% (14/46) of the patients in groups 1 and 2, respectively. The difference in detected CNV frequencies between the 2 groups was not statistically significant (Chi square = 1.02 |
Hameed, S S; Hassan, R; Muhammad, F F Selection and classification of gene expression in autism disorder: Use of a combination of statistical filters and a GBPSO-SVM algorithm Journal Article PLoS ONE, 12 (11), 2017, ISSN: 19326203, (cited By 11). Abstract | Links | BibTeX | Tags: Accuracy, Algorithms, Article, Autism, Autism Spectrum Disorders, CAPS2 Gene, Classification (of information), Classifier, Experimental Study, Gene, Gene Expression, Gene Identification, Genetic Association, Genetic Procedures, Genetic Risk, Genetics, Geometric Binary Particle Swarm Optimization Support Vector Machine Algorithm, Human, RIsk Assessment, Standardization, Statistical Filter, Statistical Parameters, Statistics, Support Vector Machines @article{Hameed2017, title = {Selection and classification of gene expression in autism disorder: Use of a combination of statistical filters and a GBPSO-SVM algorithm}, author = {S S Hameed and R Hassan and F F Muhammad}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85033361187&doi=10.1371%2fjournal.pone.0187371&partnerID=40&md5=f9260d41165145f229a3cf157699635e}, doi = {10.1371/journal.pone.0187371}, issn = {19326203}, year = {2017}, date = {2017-01-01}, journal = {PLoS ONE}, volume = {12}, number = {11}, publisher = {Public Library of Science}, abstract = {In this work, gene expression in autism spectrum disorder (ASD) is analyzed with the goal of selecting the most attributed genes and performing classification. The objective was achieved by utilizing a combination of various statistical filters and a wrapper-based geometric binary particle swarm optimization-support vector machine (GBPSO-SVM) algorithm. The utilization of different filters was accentuated by incorporating a mean and median ratio criterion to remove very similar genes. The results showed that the most discriminative genes that were identified in the first and last selection steps included the presence of a repetitive gene (CAPS2), which was assigned as the gene most highly related to ASD risk. The merged gene subset that was selected by the GBPSO-SVM algorithm was able to enhance the classification accuracy. © 2017 Hameed et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.}, note = {cited By 11}, keywords = {Accuracy, Algorithms, Article, Autism, Autism Spectrum Disorders, CAPS2 Gene, Classification (of information), Classifier, Experimental Study, Gene, Gene Expression, Gene Identification, Genetic Association, Genetic Procedures, Genetic Risk, Genetics, Geometric Binary Particle Swarm Optimization Support Vector Machine Algorithm, Human, RIsk Assessment, Standardization, Statistical Filter, Statistical Parameters, Statistics, Support Vector Machines}, pubstate = {published}, tppubtype = {article} } In this work, gene expression in autism spectrum disorder (ASD) is analyzed with the goal of selecting the most attributed genes and performing classification. The objective was achieved by utilizing a combination of various statistical filters and a wrapper-based geometric binary particle swarm optimization-support vector machine (GBPSO-SVM) algorithm. The utilization of different filters was accentuated by incorporating a mean and median ratio criterion to remove very similar genes. The results showed that the most discriminative genes that were identified in the first and last selection steps included the presence of a repetitive gene (CAPS2), which was assigned as the gene most highly related to ASD risk. The merged gene subset that was selected by the GBPSO-SVM algorithm was able to enhance the classification accuracy. © 2017 Hameed et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
Shuib, S; Saaid, N N; Zakaria, Z; Ismail, J; Latiff, Abdul Z Duplication 17p11.2 (Potocki-Lupski syndrome) in a child with developmental delay Journal Article Malaysian Journal of Pathology, 39 (1), pp. 77-81, 2017, ISSN: 01268635, (cited By 0). Abstract | Links | BibTeX | Tags: Abnormalities, Agarose, Article, Autism, Autism Spectrum Disorders, Blood Culture, Case Report, Children, Chromosome 17, Chromosome Analysis, Chromosome Disorder, Chromosome Duplication, Chromosomes, Clinical Article, Comparative Genomic Hybridization, Developmental Delay, Electrophoresis, Female, Fluorescence, Fluorescence in Situ Hybridization, Gene, Gene Identification, Genetics, Genomic DNA, Human, In Situ Hybridization, Lymphocyte Culture, Microarray Analysis, Multiple, Multiple Malformation Syndrome, Pair 17, Phenotype, Potocki Lupski Syndrome, Preschool, Preschool Child, Procedures, RAI1 Gene, Ultraviolet Spectrophotometry @article{Shuib201777, title = {Duplication 17p11.2 (Potocki-Lupski syndrome) in a child with developmental delay}, author = {S Shuib and N N Saaid and Z Zakaria and J Ismail and Z Abdul Latiff}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85037028880&partnerID=40&md5=624b87d1e9ebac2d1bf66b4d30c0f6e9}, issn = {01268635}, year = {2017}, date = {2017-01-01}, journal = {Malaysian Journal of Pathology}, volume = {39}, number = {1}, pages = {77-81}, publisher = {Malaysian Society of Pathologists}, abstract = {Potocki-Lupski syndrome (PTLS), also known as duplication 17p11.2 syndrome, trisomy 17p11.2 or dup(17)(p11.2p11.2) syndrome, is a developmental disorder and a rare contiguous gene syndrome affecting 1 in 20,000 live births. Among the key features of such patients are autism spectrum disorder, learning disabilities, developmental delay, attention-deficit disorder, infantile hypotonia and cardiovascular abnormalities. Previous studies using microarray identified variations in the size and extent of the duplicated region of chromosome 17p11.2. However, there are a few genes which are considered as candidates for PTLS which include RAI1, SREBF1, DRG2, LLGL1, SHMT1 and ZFP179. In this report, we investigated a case of a 3-year-old girl who has developmental delay. Her chromosome analysis showed a normal karyotype (46,XX). Analysis using array CGH (4X44 K, Agilent USA) identified an ~4.2 Mb de novo duplication in chromosome 17p11.2. The result was confirmed by fluorescence in situ hybridization (FISH) using probes in the critical PTLS region. This report demonstrates the importance of microarray and FISH in the diagnosis of PTLS. © 2017, Malaysian Society of Pathologists. All rights reserved.}, note = {cited By 0}, keywords = {Abnormalities, Agarose, Article, Autism, Autism Spectrum Disorders, Blood Culture, Case Report, Children, Chromosome 17, Chromosome Analysis, Chromosome Disorder, Chromosome Duplication, Chromosomes, Clinical Article, Comparative Genomic Hybridization, Developmental Delay, Electrophoresis, Female, Fluorescence, Fluorescence in Situ Hybridization, Gene, Gene Identification, Genetics, Genomic DNA, Human, In Situ Hybridization, Lymphocyte Culture, Microarray Analysis, Multiple, Multiple Malformation Syndrome, Pair 17, Phenotype, Potocki Lupski Syndrome, Preschool, Preschool Child, Procedures, RAI1 Gene, Ultraviolet Spectrophotometry}, pubstate = {published}, tppubtype = {article} } Potocki-Lupski syndrome (PTLS), also known as duplication 17p11.2 syndrome, trisomy 17p11.2 or dup(17)(p11.2p11.2) syndrome, is a developmental disorder and a rare contiguous gene syndrome affecting 1 in 20,000 live births. Among the key features of such patients are autism spectrum disorder, learning disabilities, developmental delay, attention-deficit disorder, infantile hypotonia and cardiovascular abnormalities. Previous studies using microarray identified variations in the size and extent of the duplicated region of chromosome 17p11.2. However, there are a few genes which are considered as candidates for PTLS which include RAI1, SREBF1, DRG2, LLGL1, SHMT1 and ZFP179. In this report, we investigated a case of a 3-year-old girl who has developmental delay. Her chromosome analysis showed a normal karyotype (46,XX). Analysis using array CGH (4X44 K, Agilent USA) identified an ~4.2 Mb de novo duplication in chromosome 17p11.2. The result was confirmed by fluorescence in situ hybridization (FISH) using probes in the critical PTLS region. This report demonstrates the importance of microarray and FISH in the diagnosis of PTLS. © 2017, Malaysian Society of Pathologists. All rights reserved. |
Hakim, N H A; Majlis, B Y; Suzuki, H; Tsukahara, T Neuron-specific splicing Journal Article BioScience Trends, 11 (1), pp. 16-22, 2017, ISSN: 18817815, (cited By 0). Abstract | Links | BibTeX | Tags: Alternative RNA Splicing, Alternative Splicing, Animals, Antibody Specificity, Biological, Biological Model, Diseases, Genetics, Human, Metabolism, Models, Nerve Cell, Neurons, Organ Specificity, RNA Splicing @article{Hakim201716, title = {Neuron-specific splicing}, author = {N H A Hakim and B Y Majlis and H Suzuki and T Tsukahara}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85014435502&doi=10.5582%2fbst.2016.01169&partnerID=40&md5=8a5044dbf3b905fc2553520a048bcd59}, doi = {10.5582/bst.2016.01169}, issn = {18817815}, year = {2017}, date = {2017-01-01}, journal = {BioScience Trends}, volume = {11}, number = {1}, pages = {16-22}, publisher = {International Advancement Center for Medicine and Health Research Co., Ltd.}, abstract = {During pre-mRNA splicing events, introns are removed from the pre-mRNA, and the remaining exons are connected together to form a single continuous molecule. Alternative splicing is a common mechanism for the regulation of gene expression in eukaryotes. More than 90% of human genes are known to undergo alternative splicing. The most common type of alternative splicing is exon skipping, which is also known as cassette exon. Other known alternative splicing events include alternative 5' splice sites, alternative 3' splice sites, intron retention, and mutually exclusive exons. Alternative splicing events are controlled by regulatory proteins responsible for both positive and negative regulation. In this review, we focus on neuronal splicing regulators and discuss several notable regulators in depth. In addition, we have also included an example of splicing regulation mediated by the RBFox protein family. Lastly, as previous studies have shown that a number of splicing factors are associated with neuronal diseases such as Alzheime's disease (AD) and Autism spectrum disorder (ASD), here we consider their importance in neuronal diseases wherein the underlying mechanisms have yet to be elucidated.}, note = {cited By 0}, keywords = {Alternative RNA Splicing, Alternative Splicing, Animals, Antibody Specificity, Biological, Biological Model, Diseases, Genetics, Human, Metabolism, Models, Nerve Cell, Neurons, Organ Specificity, RNA Splicing}, pubstate = {published}, tppubtype = {article} } During pre-mRNA splicing events, introns are removed from the pre-mRNA, and the remaining exons are connected together to form a single continuous molecule. Alternative splicing is a common mechanism for the regulation of gene expression in eukaryotes. More than 90% of human genes are known to undergo alternative splicing. The most common type of alternative splicing is exon skipping, which is also known as cassette exon. Other known alternative splicing events include alternative 5' splice sites, alternative 3' splice sites, intron retention, and mutually exclusive exons. Alternative splicing events are controlled by regulatory proteins responsible for both positive and negative regulation. In this review, we focus on neuronal splicing regulators and discuss several notable regulators in depth. In addition, we have also included an example of splicing regulation mediated by the RBFox protein family. Lastly, as previous studies have shown that a number of splicing factors are associated with neuronal diseases such as Alzheime's disease (AD) and Autism spectrum disorder (ASD), here we consider their importance in neuronal diseases wherein the underlying mechanisms have yet to be elucidated. |
2015 |
Haerian, B S; Shaári, H M; Tan, H J; Fong, C Y; Wong, S W; Ong, L C; Raymond, A A; Tan, C T; Mohamed, Z Genomics, 105 (4), pp. 229-236, 2015, ISSN: 08887543, (cited By 5). Abstract | Links | BibTeX | Tags: Adolescent, Adult, Article, Case-Control Studies, Controlled Study, DNA, Epilepsy, Epistasis, Female, Gene, Gene Interaction, Genetic Polymorphism, Genetic Predisposition, Genetic Predisposition to Disease, Genetic Risk, Genetic Variability, Genetics, Genotype, Group F, Human, Major Clinical Study, Malaysia, Male, Member 1, Member 2, Middle Aged, Nav1.1 Voltage-Gated Sodium Channel, Nuclear Receptor Subfamily 1, Polymorphism, Priority Journal, Retinoid Related Orphan Receptor Alpha, Retinoid Related Orphan Receptor Beta, Risk, RORA Gene, RORA Protein, RORB Protein, SCN1A Gene, SCN1A Protein, Single Nucleotide, Single Nucleotide Polymorphism, Sodium Channel Nav1.1, Young Adult @article{Haerian2015229, title = {RORA gene rs12912233 and rs880626 polymorphisms and their interaction with SCN1A rs3812718 in the risk of epilepsy: A case-control study in Malaysia}, author = {B S Haerian and H M Shaári and H J Tan and C Y Fong and S W Wong and L C Ong and A A Raymond and C T Tan and Z Mohamed}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84924135981&doi=10.1016%2fj.ygeno.2015.02.001&partnerID=40&md5=209a1720cddfd76bfa515ee8940749d5}, doi = {10.1016/j.ygeno.2015.02.001}, issn = {08887543}, year = {2015}, date = {2015-01-01}, journal = {Genomics}, volume = {105}, number = {4}, pages = {229-236}, publisher = {Academic Press Inc.}, abstract = {RAR-related orphan receptors A (RORA) and B (RORB) and voltage-gated sodium channel type 1 (SCN1A) genes play critical roles in the regulation of the circadian clock. Evidence has shown an association of RORA and RORB polymorphisms with susceptibility to autism and depression. Hence, we tested the association of RORA rs12912233, rs16943429, rs880626, rs2290430, and rs12900948; RORB rs1157358, rs7022435, rs3750420, and rs3903529; and SCN1A rs3812718 with epilepsy risk in the Malaysians. DNA was genotyped in 1789 subjects (39% epilepsy patients) by using MassARRAY (Sequenom). Significant association was obtained for rs12912233 in Malaysian Chinese (p= 0.003). Interaction between rs12912233-rs880626 and rs3812718 was associated with the epilepsy risk in the subjects overall (p= 0.001). Results show that RORA rs12912233 alone might be a possible risk variant for epilepsy in Malaysian Chinese, but that, together with RORA rs880626 and SCN1A rs3812718, this polymorphism may have a synergistic effect in the epilepsy risk in Malaysians. © 2015 Elsevier Inc.}, note = {cited By 5}, keywords = {Adolescent, Adult, Article, Case-Control Studies, Controlled Study, DNA, Epilepsy, Epistasis, Female, Gene, Gene Interaction, Genetic Polymorphism, Genetic Predisposition, Genetic Predisposition to Disease, Genetic Risk, Genetic Variability, Genetics, Genotype, Group F, Human, Major Clinical Study, Malaysia, Male, Member 1, Member 2, Middle Aged, Nav1.1 Voltage-Gated Sodium Channel, Nuclear Receptor Subfamily 1, Polymorphism, Priority Journal, Retinoid Related Orphan Receptor Alpha, Retinoid Related Orphan Receptor Beta, Risk, RORA Gene, RORA Protein, RORB Protein, SCN1A Gene, SCN1A Protein, Single Nucleotide, Single Nucleotide Polymorphism, Sodium Channel Nav1.1, Young Adult}, pubstate = {published}, tppubtype = {article} } RAR-related orphan receptors A (RORA) and B (RORB) and voltage-gated sodium channel type 1 (SCN1A) genes play critical roles in the regulation of the circadian clock. Evidence has shown an association of RORA and RORB polymorphisms with susceptibility to autism and depression. Hence, we tested the association of RORA rs12912233, rs16943429, rs880626, rs2290430, and rs12900948; RORB rs1157358, rs7022435, rs3750420, and rs3903529; and SCN1A rs3812718 with epilepsy risk in the Malaysians. DNA was genotyped in 1789 subjects (39% epilepsy patients) by using MassARRAY (Sequenom). Significant association was obtained for rs12912233 in Malaysian Chinese (p= 0.003). Interaction between rs12912233-rs880626 and rs3812718 was associated with the epilepsy risk in the subjects overall (p= 0.001). Results show that RORA rs12912233 alone might be a possible risk variant for epilepsy in Malaysian Chinese, but that, together with RORA rs880626 and SCN1A rs3812718, this polymorphism may have a synergistic effect in the epilepsy risk in Malaysians. © 2015 Elsevier Inc. |
Gallagher, D; Voronova, A; Zander, M A; Cancino, G I; Bramall, A; Krause, M P; Abad, C; Tekin, M; Neilsen, P M; Callen, D F; Scherer, S W; Keller, G M; Kaplan, D R; Walz, K; Miller, F D Ankrd11 is a chromatin regulator involved in autism that is essential for neural development Journal Article Developmental Cell, 32 (1), pp. 31-42, 2015, ISSN: 15345807, (cited By 52). Abstract | Links | BibTeX | Tags: Acetylation, Animal Behavior, Animal Cell, Animals, Ankrd11 Protein, Ankyrin, Ankyrin Repeat Domain Containing Protein 11, Article, Autism, Autism Spectrum Disorders, Behaviour, Biological Marker, Blotting, Brain Cell Culture, Cell Culture, Cell Differentiation, Cell Proliferation, Cells, Chemistry, Chromatin, Chromatin Immunoprecipitation, Cultured, DNA Binding Protein, DNA Microarray, DNA-Binding Proteins, Enzyme Activity, Female, Gene, Gene Expression Profiling, Gene Targeting, Genetics, Histone, Histone Acetylation, Histone Acetyltransferase, Histone Deacetylase, Histone Deacetylase 3, Histone Deacetylases, Histones, Human, Human Cell, Immunoprecipitation, Messenger, Messenger RNA, Metabolism, Mice, Mouse, Murinae, Mus, Nerve Cell Differentiation, Nervous System Development, Neurogenesis, Nonhuman, Oligonucleotide Array Sequence Analysis, Pathology, Phenotype, Physiology, Point Mutation, Post-Translational, Priority Journal, Protein Expression, Protein Processing, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, RNA, Small Interfering, Small Interfering RNA, Unclassified Drug, Western, Western Blotting @article{Gallagher201531, title = {Ankrd11 is a chromatin regulator involved in autism that is essential for neural development}, author = {D Gallagher and A Voronova and M A Zander and G I Cancino and A Bramall and M P Krause and C Abad and M Tekin and P M Neilsen and D F Callen and S W Scherer and G M Keller and D R Kaplan and K Walz and F D Miller}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84922343890&doi=10.1016%2fj.devcel.2014.11.031&partnerID=40&md5=ad7b8bd3ead790f092e1d8a276d4f25c}, doi = {10.1016/j.devcel.2014.11.031}, issn = {15345807}, year = {2015}, date = {2015-01-01}, journal = {Developmental Cell}, volume = {32}, number = {1}, pages = {31-42}, publisher = {Cell Press}, abstract = {Ankrd11 is a potential chromatin regulator implicated in neural development and autism spectrum disorder (ASD) with no known function in the brain. Here, we show that knockdown of Ankrd11 in developing murine or human cortical neural precursors caused decreased proliferation, reduced neurogenesis, andaberrant neuronal positioning. Similar cellular phenotypes and aberrant ASD-like behaviors were observed in Yoda mice carrying a point mutation inthe Ankrd11 HDAC-binding domain. Consistent with a role for Ankrd11 in histone acetylation, Ankrd11 was associated with chromatin and colocalized with HDAC3, and expression and histone acetylation of Ankrd11 target genes were altered in Yoda neural precursors. Moreover, the Ankrd11 knockdown-mediated decrease in precursor proliferation was rescued by inhibiting histone acetyltransferase activity or expressing HDAC3. Thus, Ankrd11 is a crucial chromatin regulator that controls histone acetylation and gene expression during neural development, thereby providing a likely explanation for its association with cognitive dysfunction and ASD. © 2015 Elsevier Inc.}, note = {cited By 52}, keywords = {Acetylation, Animal Behavior, Animal Cell, Animals, Ankrd11 Protein, Ankyrin, Ankyrin Repeat Domain Containing Protein 11, Article, Autism, Autism Spectrum Disorders, Behaviour, Biological Marker, Blotting, Brain Cell Culture, Cell Culture, Cell Differentiation, Cell Proliferation, Cells, Chemistry, Chromatin, Chromatin Immunoprecipitation, Cultured, DNA Binding Protein, DNA Microarray, DNA-Binding Proteins, Enzyme Activity, Female, Gene, Gene Expression Profiling, Gene Targeting, Genetics, Histone, Histone Acetylation, Histone Acetyltransferase, Histone Deacetylase, Histone Deacetylase 3, Histone Deacetylases, Histones, Human, Human Cell, Immunoprecipitation, Messenger, Messenger RNA, Metabolism, Mice, Mouse, Murinae, Mus, Nerve Cell Differentiation, Nervous System Development, Neurogenesis, Nonhuman, Oligonucleotide Array Sequence Analysis, Pathology, Phenotype, Physiology, Point Mutation, Post-Translational, Priority Journal, Protein Expression, Protein Processing, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, RNA, Small Interfering, Small Interfering RNA, Unclassified Drug, Western, Western Blotting}, pubstate = {published}, tppubtype = {article} } Ankrd11 is a potential chromatin regulator implicated in neural development and autism spectrum disorder (ASD) with no known function in the brain. Here, we show that knockdown of Ankrd11 in developing murine or human cortical neural precursors caused decreased proliferation, reduced neurogenesis, andaberrant neuronal positioning. Similar cellular phenotypes and aberrant ASD-like behaviors were observed in Yoda mice carrying a point mutation inthe Ankrd11 HDAC-binding domain. Consistent with a role for Ankrd11 in histone acetylation, Ankrd11 was associated with chromatin and colocalized with HDAC3, and expression and histone acetylation of Ankrd11 target genes were altered in Yoda neural precursors. Moreover, the Ankrd11 knockdown-mediated decrease in precursor proliferation was rescued by inhibiting histone acetyltransferase activity or expressing HDAC3. Thus, Ankrd11 is a crucial chromatin regulator that controls histone acetylation and gene expression during neural development, thereby providing a likely explanation for its association with cognitive dysfunction and ASD. © 2015 Elsevier Inc. |
2014 |
Brett, M; McPherson, J; Zang, Z J; Lai, A; Tan, E -S; Ng, I; Ong, L -C; Cham, B; Tan, P; Rozen, S; Tan, E -C PLoS ONE, 9 (4), 2014, ISSN: 19326203, (cited By 20). Abstract | Links | BibTeX | Tags: Article, ATRX Gene, Autism, Autism Spectrum Disorders, Children, Clinical Article, Congenital Abnormalities, Congenital Malformation, Controlled Study, Diagnostic Test, DNA Mutational Analysis, Female, Gene, Gene Expression Profiling, Gene Mutation, Gene Targeting, Genetic Association, Genetic Association Studies, Genetic Disorder, Genetic Variability, Genetic Variation, Genetics, Genome-Wide Association Study, High Throughput Sequencing, High-Throughput Nucleotide Sequencing, Human, Intellectual Disability, Intellectual Impairment, Karyotype, L1CAM Gene, Male, Mutation, Nonsense Mutation, Nucleotide Sequence, Phenotype, Polymorphism, RNA Splice Sites, RNA Splicing, Single Nucleotide, Single Nucleotide Polymorphism @article{Brett2014, title = {Massively parallel sequencing of patients with intellectual disability, congenital anomalies and/or autism spectrum disorders with a targeted gene panel}, author = {M Brett and J McPherson and Z J Zang and A Lai and E -S Tan and I Ng and L -C Ong and B Cham and P Tan and S Rozen and E -C Tan}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84898625023&doi=10.1371%2fjournal.pone.0093409&partnerID=40&md5=f673e204a009bf84de81ea69dcd026db}, doi = {10.1371/journal.pone.0093409}, issn = {19326203}, year = {2014}, date = {2014-01-01}, journal = {PLoS ONE}, volume = {9}, number = {4}, publisher = {Public Library of Science}, abstract = {Developmental delay and/or intellectual disability (DD/ID) affects 1-3% of all children. At least half of these are thought to have a genetic etiology. Recent studies have shown that massively parallel sequencing (MPS) using a targeted gene panel is particularly suited for diagnostic testing for genetically heterogeneous conditions. We report on our experiences with using massively parallel sequencing of a targeted gene panel of 355 genes for investigating the genetic etiology of eight patients with a wide range of phenotypes including DD/ID, congenital anomalies and/or autism spectrum disorder. Targeted sequence enrichment was performed using the Agilent SureSelect Target Enrichment Kit and sequenced on the Illumina HiSeq2000 using paired-end reads. For all eight patients, 81-84% of the targeted regions achieved read depths of at least 20×, with average read depths overlapping targets ranging from 322 × to 798 ×. Causative variants were successfully identified in two of the eight patients: a nonsense mutation in the ATRX gene and a canonical splice site mutation in the L1CAM gene. In a third patient, a canonical splice site variant in the USP9X gene could likely explain all or some of her clinical phenotypes. These results confirm the value of targeted MPS for investigating DD/ID in children for diagnostic purposes. However, targeted gene MPS was less likely to provide a genetic diagnosis for children whose phenotype includes autism. © 2014 Brett et al.}, note = {cited By 20}, keywords = {Article, ATRX Gene, Autism, Autism Spectrum Disorders, Children, Clinical Article, Congenital Abnormalities, Congenital Malformation, Controlled Study, Diagnostic Test, DNA Mutational Analysis, Female, Gene, Gene Expression Profiling, Gene Mutation, Gene Targeting, Genetic Association, Genetic Association Studies, Genetic Disorder, Genetic Variability, Genetic Variation, Genetics, Genome-Wide Association Study, High Throughput Sequencing, High-Throughput Nucleotide Sequencing, Human, Intellectual Disability, Intellectual Impairment, Karyotype, L1CAM Gene, Male, Mutation, Nonsense Mutation, Nucleotide Sequence, Phenotype, Polymorphism, RNA Splice Sites, RNA Splicing, Single Nucleotide, Single Nucleotide Polymorphism}, pubstate = {published}, tppubtype = {article} } Developmental delay and/or intellectual disability (DD/ID) affects 1-3% of all children. At least half of these are thought to have a genetic etiology. Recent studies have shown that massively parallel sequencing (MPS) using a targeted gene panel is particularly suited for diagnostic testing for genetically heterogeneous conditions. We report on our experiences with using massively parallel sequencing of a targeted gene panel of 355 genes for investigating the genetic etiology of eight patients with a wide range of phenotypes including DD/ID, congenital anomalies and/or autism spectrum disorder. Targeted sequence enrichment was performed using the Agilent SureSelect Target Enrichment Kit and sequenced on the Illumina HiSeq2000 using paired-end reads. For all eight patients, 81-84% of the targeted regions achieved read depths of at least 20×, with average read depths overlapping targets ranging from 322 × to 798 ×. Causative variants were successfully identified in two of the eight patients: a nonsense mutation in the ATRX gene and a canonical splice site mutation in the L1CAM gene. In a third patient, a canonical splice site variant in the USP9X gene could likely explain all or some of her clinical phenotypes. These results confirm the value of targeted MPS for investigating DD/ID in children for diagnostic purposes. However, targeted gene MPS was less likely to provide a genetic diagnosis for children whose phenotype includes autism. © 2014 Brett et al. |