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Abedini SS, Akhavantabasi S, Liang Y, Heng JIT, Alizadehsani R, Dehzangi I, Bauer DC, Alinejad-Rokny H. A critical review of the impact of candidate copy number variants on autism spectrum disorder. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 794:108509. [PMID: 38977176 DOI: 10.1016/j.mrrev.2024.108509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/14/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder (NDD) influenced by genetic, epigenetic, and environmental factors. Recent advancements in genomic analysis have shed light on numerous genes associated with ASD, highlighting the significant role of both common and rare genetic mutations, as well as copy number variations (CNVs), single nucleotide polymorphisms (SNPs) and unique de novo variants. These genetic variations disrupt neurodevelopmental pathways, contributing to the disorder's complexity. Notably, CNVs are present in 10 %-20 % of individuals with autism, with 3 %-7 % detectable through cytogenetic methods. While the role of submicroscopic CNVs in ASD has been recently studied, their association with genomic loci and genes has not been thoroughly explored. In this review, we focus on 47 CNV regions linked to ASD, encompassing 1632 genes, including protein-coding genes and long non-coding RNAs (lncRNAs), of which 659 show significant brain expression. Using a list of ASD-associated genes from SFARI, we detect 17 regions harboring at least one known ASD-related protein-coding gene. Of the remaining 30 regions, we identify 24 regions containing at least one protein-coding gene with brain-enriched expression and a nervous system phenotype in mouse mutants, and one lncRNA with both brain-enriched expression and upregulation in iPSC to neuron differentiation. This review not only expands our understanding of the genetic diversity associated with ASD but also underscores the potential of lncRNAs in contributing to its etiology. Additionally, the discovered CNVs will be a valuable resource for future diagnostic, therapeutic, and research endeavors aimed at prioritizing genetic variations in ASD.
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Affiliation(s)
- Seyedeh Sedigheh Abedini
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; School of Biotechnology & Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Shiva Akhavantabasi
- Department of Molecular Biology and Genetics, Yeni Yuzyil University, Istanbul, Turkey; Ghiaseddin Jamshid Kashani University, Andisheh University Town, Danesh Blvd, 3441356611, Abyek, Qazvin, Iran
| | - Yuheng Liang
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Julian Ik-Tsen Heng
- Curtin Health Innovation Research Institute, Curtin University, Bentley 6845, Australia
| | - Roohallah Alizadehsani
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Victoria, Australia
| | - Iman Dehzangi
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; Department of Computer Science, Rutgers University, Camden, NJ 08102, USA
| | - Denis C Bauer
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia; Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, Australia
| | - Hamid Alinejad-Rokny
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; Tyree Institute of Health Engineering (IHealthE), UNSW Sydney, Sydney, NSW 2052, Australia.
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2
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Visibelli E, Vigna G, Nascimben C, Benavides-Varela S. Neurobiology of numerical learning. Neurosci Biobehav Rev 2024; 158:105545. [PMID: 38220032 DOI: 10.1016/j.neubiorev.2024.105545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
Numerical abilities are complex cognitive skills essential for dealing with requirements of the modern world. Although the brain structures and functions underlying numerical cognition in different species have long been appreciated, genetic and molecular techniques have more recently expanded the knowledge about the mechanisms underlying numerical learning. In this review, we discuss the status of the research related to the neurobiological bases of numerical abilities. We consider how genetic factors have been associated with mathematical capacities and how these link to the current knowledge of brain regions underlying these capacities in human and non-human animals. We further discuss the extent to which significant variations in the levels of specific neurotransmitters may be used as potential markers of individual performance and learning difficulties and take into consideration the therapeutic potential of brain stimulation methods to modulate learning and improve interventional outcomes. The implications of this research for formulating a more comprehensive view of the neural basis of mathematical learning are discussed.
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Affiliation(s)
- Emma Visibelli
- Department of Developmental Psychology and Socialization, University of Padova, Padova, Italy; Padova Neuroscience Center, University of Padova, Padova, Italy
| | - Giulia Vigna
- Department of Developmental Psychology and Socialization, University of Padova, Padova, Italy
| | - Chiara Nascimben
- Department of Developmental Psychology and Socialization, University of Padova, Padova, Italy
| | - Silvia Benavides-Varela
- Department of Developmental Psychology and Socialization, University of Padova, Padova, Italy; Padova Neuroscience Center, University of Padova, Padova, Italy.
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3
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Serrano-Juárez CA, Prieto-Corona B, Rodríguez-Camacho M, Sandoval-Lira L, Villalva-Sánchez ÁF, Yáñez-Téllez MG, López MFR. Neuropsychological Genotype-Phenotype in Patients with Williams Syndrome with Atypical Deletions: A Systematic Review. Neuropsychol Rev 2023; 33:891-911. [PMID: 36520254 DOI: 10.1007/s11065-022-09571-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/04/2022] [Indexed: 12/16/2022]
Abstract
Williams syndrome (WS) is a neurodevelopmental disorder caused by a microdeletion in the q11.23 region of chromosome 7. Recent case series reports and clinical case studies have suggested that the cognitive, behavioral, emotional, and social profile in WS could depend on the genes involved in the deletion. The objective of this systematic review was to analyze and synthesize the variability of the cognitive and behavioral profile of WS with atypical deletion and its probable relationship with the affected genes. The medical subject headings searched were "Williams syndrome," "genotype," "phenotype," "cognitive profile," and "atypical deletion." The studies included were in English or Spanish, with children and adults, and published between January 2000 and October 2022. Twenty-three studies are reported. The characteristics of the participants, the genes involved, the neuropsychological domains and instruments, and the prevalence of the WS cognitive profile criteria were used for the genotype-phenotype analysis. The genes with a major impact on the cognitive profile of WS were (a) LIMK1 and those belonging to the GTF2I family, the former with a greater influence on visuospatial abilities; (b) GTF2IRD1 and GTF2I, which have an impact on intellectual capacity as well as on visuospatial and social skills; (c) FZD9, BAZ1B, STX1A, and CLIP2, which influence the cognitive profile if other genes are also effected; and (d) GTF2IRD2, which is related to the severity of the effect on visuospatial and social skills, producing a behavioral phenotype like that of the autism spectrum. The review revealed four neuropsychological phenotypes, depending on the genes involved, and established the need for more comprehensive study of the neuropsychological profile of these patients. Based on the results found, we propose a model for the investigation of and clinical approach to the WS neuropsychological phenotype.
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Affiliation(s)
- Carlos Alberto Serrano-Juárez
- Neuroscience Group. Laboratorio de Neurometría, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios #1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, CP 54090, México
| | - Belén Prieto-Corona
- Neuroscience Group. Laboratorio de Neurometría, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios #1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, CP 54090, México.
| | - Mario Rodríguez-Camacho
- Neuroscience Group. Laboratorio de Neurometría, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios #1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, CP 54090, México
| | - Lucero Sandoval-Lira
- Neuroscience Group. Laboratorio de Neurometría, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios #1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, CP 54090, México
| | - Ángel Fernando Villalva-Sánchez
- Neuroscience Group. Laboratorio de Neurometría, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios #1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, CP 54090, México
| | - Ma Guillermina Yáñez-Téllez
- Neuroscience Group. Laboratorio de Neurometría, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. De los Barrios #1, Col. Los Reyes Iztacala, Tlalnepantla, Estado de México, CP 54090, México
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Moradi A, Shahabinezhad F, Dehshahri A. An in silico study to find potential effective circRNAs in the progression of Huntington's disease. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2023; 26:934-940. [PMID: 37427327 PMCID: PMC10329238 DOI: 10.22038/ijbms.2023.67791.14839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 05/03/2023] [Indexed: 07/11/2023]
Abstract
Objectives Huntington's disease (HD) is identified as a progressive genetic disorder caused by a mutation in the Huntington gene. Although the pathogenesis of this disease has not been fully understood, investigations have demonstrated the role of various genes and non-coding RNAs in the disease progression. In this study, we aimed to discover the potential promising circRNAs which can bind to miRNAs of HD. Materials and Methods We used several bioinformatics tools such as ENCORI, Cytoscape, circBase, Knime, and Enrichr to collect possible circRNAs and then evaluate their connections with target miRNAs to reach this goal. We also found the probable relationship between parental genes of these circRNAs and the disease progress. Results According to the data collected, more than 370 thousand circRNA-miRNA interactions were found for 57 target miRNAs. Several of circRNAs were spliced out of parental genes involved in the etiology of HD. Some of them need to be further investigated to elucidate their role in this neurodegenerative disease. Conclusion This in silico investigation highlights the potential role of circRNAs in the progression of HD and opens up new horizons for drug discovery as well as diagnostic approaches for the disease.
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Affiliation(s)
- Anahita Moradi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farbod Shahabinezhad
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Dehshahri
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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5
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Kozel BA, Barak B, Ae Kim C, Mervis CB, Osborne LR, Porter M, Pober BR. Williams syndrome. Nat Rev Dis Primers 2021; 7:42. [PMID: 34140529 PMCID: PMC9437774 DOI: 10.1038/s41572-021-00276-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 11/09/2022]
Abstract
Williams syndrome (WS) is a relatively rare microdeletion disorder that occurs in as many as 1:7,500 individuals. WS arises due to the mispairing of low-copy DNA repetitive elements at meiosis. The deletion size is similar across most individuals with WS and leads to the loss of one copy of 25-27 genes on chromosome 7q11.23. The resulting unique disorder affects multiple systems, with cardinal features including but not limited to cardiovascular disease (characteristically stenosis of the great arteries and most notably supravalvar aortic stenosis), a distinctive craniofacial appearance, and a specific cognitive and behavioural profile that includes intellectual disability and hypersociability. Genotype-phenotype evidence is strongest for ELN, the gene encoding elastin, which is responsible for the vascular and connective tissue features of WS, and for the transcription factor genes GTF2I and GTF2IRD1, which are known to affect intellectual ability, social functioning and anxiety. Mounting evidence also ascribes phenotypic consequences to the deletion of BAZ1B, LIMK1, STX1A and MLXIPL, but more work is needed to understand the mechanism by which these deletions contribute to clinical outcomes. The age of diagnosis has fallen in regions of the world where technological advances, such as chromosomal microarray, enable clinicians to make the diagnosis of WS without formally suspecting it, allowing earlier intervention by medical and developmental specialists. Phenotypic variability is considerable for all cardinal features of WS but the specific sources of this variability remain unknown. Further investigation to identify the factors responsible for these differences may lead to mechanism-based rather than symptom-based therapies and should therefore be a high research priority.
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Affiliation(s)
- Beth A. Kozel
- Translational Vascular Medicine Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, USA
| | - Boaz Barak
- The Sagol School of Neuroscience and The School of Psychological Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Chong Ae Kim
- Department of Pediatrics, Universidade de São Paulo, São Paulo, Brazil
| | - Carolyn B. Mervis
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, USA
| | - Lucy R. Osborne
- Department of Medicine, University of Toronto, Ontario, Canada
| | - Melanie Porter
- Department of Psychology, Macquarie University, Sydney, Australia
| | - Barbara R. Pober
- Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Boston, USA
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Tabatabai M, Bailey S, Bursac Z, Tabatabai H, Wilus D, Singh KP. An introduction to new robust linear and monotonic correlation coefficients. BMC Bioinformatics 2021; 22:170. [PMID: 33789571 PMCID: PMC8011137 DOI: 10.1186/s12859-021-04098-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/22/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The most common measure of association between two continuous variables is the Pearson correlation (Maronna et al. in Safari an OMC. Robust statistics, 2019. https://login.proxy.bib.uottawa.ca/login?url=https://learning.oreilly.com/library/view/-/9781119214687/?ar&orpq&email=^u). When outliers are present, Pearson does not accurately measure association and robust measures are needed. This article introduces three new robust measures of correlation: Taba (T), TabWil (TW), and TabWil rank (TWR). The correlation estimators T and TW measure a linear association between two continuous or ordinal variables; whereas TWR measures a monotonic association. The robustness of these proposed measures in comparison with Pearson (P), Spearman (S), Quadrant (Q), Median (M), and Minimum Covariance Determinant (MCD) are examined through simulation. Taba distance is used to analyze genes, and statistical tests were used to identify those genes most significantly associated with Williams Syndrome (WS). RESULTS Based on the root mean square error (RMSE) and bias, the three proposed correlation measures are highly competitive when compared to classical measures such as P and S as well as robust measures such as Q, M, and MCD. Our findings indicate TBL2 was the most significant gene among patients diagnosed with WS and had the most significant reduction in gene expression level when compared with control (P value = 6.37E-05). CONCLUSIONS Overall, when the distribution is bivariate Log-Normal or bivariate Weibull, TWR performs best in terms of bias and T performs best with respect to RMSE. Under the Normal distribution, MCD performs well with respect to bias and RMSE; but TW, TWR, T, S, and P correlations were in close proximity. The identification of TBL2 may serve as a diagnostic tool for WS patients. A Taba R package has been developed and is available for use to perform all necessary computations for the proposed methods.
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Affiliation(s)
| | | | - Zoran Bursac
- Department of Biostatistics, Florida International University, Miami, FL 33199 USA
| | - Habib Tabatabai
- Department of Civil and Environmental Engineering, University of Wisconsin Milwaukee, Milwaukee, WI 53211 USA
| | - Derek Wilus
- Meharry Medical College, Nashville, TN 37208 USA
| | - Karan P. Singh
- Department of Epidemiology and Biostatistics, University of Texas Health Sciences Center at Tyler, Tyler, TX 75708 USA
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7
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Riddle MR, Aspiras A, Damen F, Hutchinson JN, Chinnapen D, Tabin J, Tabin CJ. Genetic architecture underlying changes in carotenoid accumulation during the evolution of the blind Mexican cavefish, Astyanax mexicanus. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:405-422. [PMID: 32488995 PMCID: PMC7708440 DOI: 10.1002/jez.b.22954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 03/25/2020] [Accepted: 05/02/2020] [Indexed: 12/16/2022]
Abstract
Carotenoids are lipid-soluble yellow to orange pigments produced by plants, bacteria, and fungi. They are consumed by animals and metabolized to produce molecules essential for gene regulation, vision, and pigmentation. Cave animals represent an interesting opportunity to understand how carotenoid utilization evolves. Caves are devoid of light, eliminating primary production of energy through photosynthesis and, therefore, limiting carotenoid availability. Moreover, the selective pressures that favor carotenoid-based traits, like pigmentation and vision, are relaxed. Astyanax mexicanus is a species of fish with multiple river-adapted (surface) and cave-adapted populations (i.e., Tinaja, Pachón, Molino). Cavefish exhibit regressive features, such as loss of eyes and melanin pigment, and constructive traits, like increased sensory neuromasts and starvation resistance. Here, we show that, unlike surface fish, Tinaja and Pachón cavefish accumulate carotenoids in the visceral adipose tissue. Carotenoid accumulation is not observed in Molino cavefish, indicating that it is not an obligatory consequence of eye loss. We used quantitative trait loci mapping and RNA sequencing to investigate genetic changes associated with carotenoid accumulation. Our findings suggest that multiple stages of carotenoid processing may be altered in cavefish, including absorption and transport of lipids, cleavage of carotenoids into unpigmented molecules, and differential development of intestinal cell types involved in carotenoid assimilation. Our study establishes A. mexicanus as a model to study the genetic basis of natural variation in carotenoid accumulation and how it impacts physiology.
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Affiliation(s)
- Misty R. Riddle
- Genetics Department, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Ariel Aspiras
- Genetics Department, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
- Current affiliation: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138
| | - Fleur Damen
- Genetics Department, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - John N. Hutchinson
- Department of Biostatistics, The Harvard Chan School of Public Health, Boston, MA 02115
| | - Daniel Chinnapen
- Division of Gastroenterology and Nutrition, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Julius Tabin
- Genetics Department, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Clifford J. Tabin
- Genetics Department, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
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8
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Genes dysregulated in the blood of people with Williams syndrome are enriched in protein-coding genes positively selected in humans. Eur J Med Genet 2020; 63:103828. [DOI: 10.1016/j.ejmg.2019.103828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/09/2019] [Accepted: 12/21/2019] [Indexed: 12/29/2022]
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9
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Drozd M, Delhaye S, Maurin T, Castagnola S, Grossi M, Brau F, Jarjat M, Willemsen R, Capovilla M, Hukema RK, Lalli E, Bardoni B. Reduction of Fmr1 mRNA Levels Rescues Pathological Features in Cortical Neurons in a Model of FXTAS. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 18:546-553. [PMID: 31671347 PMCID: PMC6838541 DOI: 10.1016/j.omtn.2019.09.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/02/2019] [Accepted: 09/08/2019] [Indexed: 02/08/2023]
Abstract
Fragile X-associated tremor ataxia syndrome (FXTAS) is a rare disorder associated to the presence of the fragile X premutation, a 55–200 CGG repeat expansion in the 5′ UTR of the FMR1 gene. Two main neurological phenotypes have been described in carriers of the CGG premutation: (1) neurodevelopmental disorders characterized by anxiety, attention deficit hyperactivity disorder (ADHD), social deficits, or autism spectrum disorder (ASD); and (2) after 50 years old, the FXTAS phenotype. This neurodegenerative disorder is characterized by ataxia and a form of parkinsonism. The molecular pathology of this disorder is characterized by the presence of elevated levels of Fragile X Mental Retardation 1 (FMR1) mRNA, presence of a repeat-associated non-AUG (RAN) translated peptide, and FMR1 mRNA-containing nuclear inclusions. Whereas in the past FXTAS was mainly considered as a late-onset disorder, some phenotypes of patients and altered learning and memory behavior of a mouse model of FXTAS suggested that this disorder involves neurodevelopment. To better understand the physiopathological role of the increased levels of Fmr1 mRNA during neuronal differentiation, we used a small interfering RNA (siRNA) approach to reduce the abundance of this mRNA in cultured cortical neurons from the FXTAS mouse model. Morphological alterations of neurons were rescued by this approach. This cellular phenotype is associated to differentially expressed proteins that we identified by mass spectrometry analysis. Interestingly, phenotype rescue is also associated to the rescue of the abundance of 29 proteins that are involved in various pathways, which represent putative targets for early therapeutic approaches.
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Affiliation(s)
- Malgorzata Drozd
- Université Côte d'Azur, CNRS, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia Antipolis, France
| | - Sébastien Delhaye
- Université Côte d'Azur, CNRS, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia Antipolis, France
| | - Thomas Maurin
- Université Côte d'Azur, CNRS, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia Antipolis, France
| | - Sara Castagnola
- Université Côte d'Azur, CNRS, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia Antipolis, France
| | - Mauro Grossi
- Université Côte d'Azur, CNRS, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia Antipolis, France
| | - Frédéric Brau
- Université Côte d'Azur, CNRS, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia Antipolis, France
| | - Marielle Jarjat
- Université Côte d'Azur, CNRS, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia Antipolis, France
| | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Maria Capovilla
- Université Côte d'Azur, CNRS, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia Antipolis, France
| | - Renate K Hukema
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Enzo Lalli
- Université Côte d'Azur, INSERM, CNRS, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia Antipolis, France
| | - Barbara Bardoni
- Université Côte d'Azur, INSERM, CNRS, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne Sophia Antipolis, France.
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10
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Konki M, Malonzo M, Karlsson IK, Lindgren N, Ghimire B, Smolander J, Scheinin NM, Ollikainen M, Laiho A, Elo LL, Lönnberg T, Röyttä M, Pedersen NL, Kaprio J, Lähdesmäki H, Rinne JO, Lund RJ. Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease. Clin Epigenetics 2019; 11:130. [PMID: 31477183 PMCID: PMC6721173 DOI: 10.1186/s13148-019-0729-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Alzheimer's disease results from a neurodegenerative process that starts well before the diagnosis can be made. New prognostic or diagnostic markers enabling early intervention into the disease process would be highly valuable. Environmental and lifestyle factors largely modulate the disease risk and may influence the pathogenesis through epigenetic mechanisms, such as DNA methylation. As environmental and lifestyle factors may affect multiple tissues of the body, we hypothesized that the disease-associated DNA methylation signatures are detectable in the peripheral blood of discordant twin pairs. RESULTS Comparison of 23 disease discordant Finnish twin pairs with reduced representation bisulfite sequencing revealed peripheral blood DNA methylation differences in 11 genomic regions with at least 15.0% median methylation difference and FDR adjusted p value ≤ 0.05. Several of the affected genes are primarily associated with neuronal functions and pathologies and do not display disease-associated differences in gene expression in blood. The DNA methylation mark in ADARB2 gene was found to be differentially methylated also in the anterior hippocampus, including entorhinal cortex, of non-twin cases and controls. Targeted bisulfite pyrosequencing of the DNA methylation mark in ADARB2 gene in 62 Finnish and Swedish twin pairs revealed that, in addition to the disease status, DNA methylation of this region is influenced by gender, age, zygosity, APOE genotype, and smoking. Further analysis of 120 Swedish twin pairs indicated that this specific DNA methylation mark is not predictive for Alzheimer's disease and becomes differentially methylated after disease onset. CONCLUSIONS DNA methylation differences can be detected in the peripheral blood of twin pairs discordant for Alzheimer's disease. These DNA methylation signatures may have value as disease markers and provide insights into the molecular mechanisms of pathogenesis. We found no evidence that the DNA methylation marks would be associated with gene expression in blood. Further studies are needed to elucidate the potential importance of the associated genes in neuronal functions and to validate the prognostic or diagnostic value of the individual marks or marker panels.
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Affiliation(s)
- Mikko Konki
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland.,Turku Doctoral Programme of Molecular Medicine, University of Turku, FI-20014, Turku, Finland
| | - Maia Malonzo
- Department of Computer Science, Aalto University School of Science, FI-00076, Helsinki, Finland
| | - Ida K Karlsson
- Institute of Gerontology and Aging Research Network-Jönköping (ARN-J), School of Health and Welfare, Jönköping University, SE-55111, Jönköping, Sweden.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden
| | - Noora Lindgren
- Drug Research Doctoral Program, University of Turku, FI-20014, Turku, Finland.,Turku PET Centre, University of Turku, FI-20520, Turku, Finland
| | - Bishwa Ghimire
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland.,Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
| | - Johannes Smolander
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Noora M Scheinin
- Turku PET Centre, University of Turku, FI-20520, Turku, Finland.,Turku Brain and Mind Center, FinnBrain Birth Cohort Study, Institute of Clinical Medicine, University of Turku, FI-20014, Turku, Finland.,Department of Psychiatry, University of Turku and Turku University Hospital, FI-20014, Turku, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Matias Röyttä
- Department of Pathology/Neuropathology, Turku University Hospital, University of Turku, FI-20014, Turku, Finland
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden.,Department of Psychology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland.,Department of Public Health, University of Helsinki, FI-00271, Helsinki, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University School of Science, FI-00076, Helsinki, Finland
| | - Juha O Rinne
- Turku PET Centre, University of Turku, FI-20520, Turku, Finland.,Division of Clinical Neurosciences, Turku University Hospital, FI-20014, Turku, Finland
| | - Riikka J Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland.
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11
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Gao Y, Zhang C, Liu Y, Wang M. Circular RNA profiling reveals circRNA1656 as a novel biomarker in high grade serous ovarian cancer. Biosci Trends 2019; 13:204-211. [PMID: 31019161 DOI: 10.5582/bst.2019.01021] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yan Gao
- Department of Gynecology and Obstetrics, Shengjing Hospital Affiliated of China Medical University
- Department of Gynecology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute
| | - Chuanqi Zhang
- Department of Gynecology and Obstetrics, Shengjing Hospital Affiliated of China Medical University
| | - Yisi Liu
- Department of Gynecology and Obstetrics, Shengjing Hospital Affiliated of China Medical University
| | - Min Wang
- Department of Gynecology and Obstetrics, Shengjing Hospital Affiliated of China Medical University
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12
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Niego A, Benítez-Burraco A. Williams Syndrome, Human Self-Domestication, and Language Evolution. Front Psychol 2019; 10:521. [PMID: 30936846 PMCID: PMC6431629 DOI: 10.3389/fpsyg.2019.00521] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/22/2019] [Indexed: 01/06/2023] Open
Abstract
Language evolution resulted from changes in our biology, behavior, and culture. One source of these changes might be human self-domestication. Williams syndrome (WS) is a clinical condition with a clearly defined genetic basis which results in a distinctive behavioral and cognitive profile, including enhanced sociability. In this paper we show evidence that the WS phenotype can be satisfactorily construed as a hyper-domesticated human phenotype, plausibly resulting from the effect of the WS hemideletion on selected candidates for domestication and neural crest (NC) function. Specifically, we show that genes involved in animal domestication and NC development and function are significantly dysregulated in the blood of subjects with WS. We also discuss the consequences of this link between domestication and WS for our current understanding of language evolution.
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Affiliation(s)
- Amy Niego
- Ph.D. Program, Faculty of Humanities, University of Huelva, Huelva, Spain
| | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, Faculty of Philology, University of Seville, Seville, Spain
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13
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Luo E, Liu H, Zhao Q, Shi B, Chen Q. Dental-craniofacial manifestation and treatment of rare diseases. Int J Oral Sci 2019; 11:9. [PMID: 30783081 PMCID: PMC6381182 DOI: 10.1038/s41368-018-0041-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/22/2018] [Accepted: 10/28/2018] [Indexed: 02/05/2023] Open
Abstract
Rare diseases are usually genetic, chronic and incurable disorders with a relatively low incidence. Developments in the diagnosis and management of rare diseases have been relatively slow due to a lack of sufficient profit motivation and market to attract research by companies. However, due to the attention of government and society as well as economic development, rare diseases have been gradually become an increasing concern. As several dental-craniofacial manifestations are associated with rare diseases, we summarize them in this study to help dentists and oral maxillofacial surgeons provide an early diagnosis and subsequent management for patients with these rare diseases.
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Affiliation(s)
- En Luo
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Hanghang Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qiucheng Zhao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
| | - Qianming Chen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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14
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Wu Y, Lin X, Lim IY, Chen L, Teh AL, MacIsaac JL, Tan KH, Kobor MS, Chong YS, Gluckman PD, Karnani N. Analysis of two birth tissues provides new insights into the epigenetic landscape of neonates born preterm. Clin Epigenetics 2019; 11:26. [PMID: 30744680 PMCID: PMC6371604 DOI: 10.1186/s13148-018-0599-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/17/2018] [Indexed: 01/04/2023] Open
Abstract
Background Preterm birth (PTB), defined as child birth before completion of 37 weeks of gestation, is a major challenge in perinatal health care and can bear long-term medical and financial burden. Over a million children die each year due to PTB complications, and those who survive can face developmental delays. Unfortunately, our understanding of the molecular pathways associated with PTB remains limited. There is a growing body of evidence suggesting the role of DNA methylation (DNAm) in mediating the effects of PTB on future health outcomes. Thus, epigenome-wide association studies (EWAS), where DNAm sites are examined for associations with PTB, can help shed light on the biological mechanisms linking the two. Results In an Asian cohort of 1019 infants (68 preterm, 951 full term), we examined and compared the associations between PTB and genome-wide DNAm profiles using both cord tissue (n = 1019) and cord blood (n = 332) samples on Infinium HumanMethylation450 arrays. PTB was significantly associated (P < 5.8e−7) with DNAm at 296 CpGs (209 genes) in the cord blood. Over 95% of these CpGs were replicated in other PTB/gestational age EWAS conducted in (cord) blood. This replication was apparent even across populations of different ethnic origin (Asians, Caucasians, and African Americans). More than a third of these 296 CpGs were replicated in at least 4 independent studies, thereby identifying a robust set of PTB-linked epigenetic signatures in cord blood. Interrogation of cord tissue in addition to cord blood provided novel insights into the epigenetic status of the neonates born preterm. Overall, 994 CpGs (608 genes, P < 3.7e−7) associated with PTB in cord tissue, of which only 10 of these CpGs were identified in the analysis using cord blood. Genes from cord tissue showed enrichment of molecular pathways related to fetal growth and development, while those from cord blood showed enrichment of immune response pathways. A substantial number of PTB-associated CpGs from both the birth tissues were also associated with gestational age. Conclusions Our findings provide insights into the epigenetic landscape of neonates born preterm, and that its status is captured more comprehensively by interrogation of more than one neonatal tissue in tandem. Both these neonatal tissues are clinically relevant in their unique ways and require careful consideration in identification of biomarkers related to PTB and gestational age. Trial registration This birth cohort is a prospective observational study designed to study the developmental origins of health and disease, and was retrospectively registered on 1 July 2010 under the identifier NCT01174875. Electronic supplementary material The online version of this article (10.1186/s13148-018-0599-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yonghui Wu
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Xinyi Lin
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Ives Yubin Lim
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Li Chen
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Ai Ling Teh
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Julia L MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
| | - Kok Hian Tan
- KK Women's and Children's Hospital, Singapore, Singapore
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.,Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Peter D Gluckman
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.,Centre for Human Evolution, Adaptation and Disease, Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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15
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Xie JL, Liu J, Lian ZY, Chen HX, Shi ZY, Zhang Q, Feng HR, Du Q, Miao XH, Zhou HY. Association of GTF2IRD1-GTF2I polymorphisms with neuromyelitis optica spectrum disorders in Han Chinese patients. Neural Regen Res 2018; 14:346-353. [PMID: 30531019 PMCID: PMC6301177 DOI: 10.4103/1673-5374.244800] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Variants at the GTF2I repeat domain containing 1 (GTF2IRD1)–GTF2I locus are associated with primary Sjögren’s syndrome, systemic lupus erythematosus, and rheumatoid arthritis. Numerous studies have indicated that this susceptibility locus is shared by multiple autoimmune diseases. However, until now there were no studies of the correlation between GTF2IRD1–GTF2I polymorphisms and neuromyelitis optica spectrum disorders (NMOSD). This case control study assessed this association by recruiting 305 participants with neuromyelitis optica spectrum disorders and 487 healthy controls at the Department of Neurology, from September 2014 to April 2017. Peripheral blood was collected, DNA extracteds and the genetic association between GTF2IRD1–GTF2I polymorphisms and neuromyelitis optica spectrum disorders in the Chinese Han population was analyzed by genotyping. We found that the T allele of rs117026326 was associated with an increased risk of neuromyelitis optica spectrum disorders (odds ratio (OR) = 1.364, 95% confidence interval (CI) 1.019–1.828; P = 0.037). This association persisted after stratification analysis for aquaporin-4 immunoglobulin G antibodies (AQP4-IgG) positivity (OR = 1.397, 95% CI 1.021–1.912; P = 0.036) and stratification according to coexisting autoimmune diseases (OR = 1.446, 95% CI 1.072–1.952; P = 0.015). Furthermore, the CC genotype of rs73366469 was frequent in AQP4-IgG-seropositive patients (OR = 3.15, 95% CI 1.183–8.393, P = 0.022). In conclusion, the T allele of rs117026326 was associated with susceptibility to neuromyelitis optica spectrum disorders, and the CC genotype of rs73366469 conferred susceptibility to AQP4-IgG-seropositivity in Han Chinese patients. The protocol was approved by the Ethics Committee of West China Hospital of Sichuan University, China (approval number: 2016-31) on March 2, 2016.
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Affiliation(s)
- Jing-Lu Xie
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Ju Liu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Zhi-Yun Lian
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Hong-Xi Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Zi-Yan Shi
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Qin Zhang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Hui-Ru Feng
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Qin Du
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Xiao-Hui Miao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Hong-Yu Zhou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
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16
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Cognitive, Behavioral, and Adaptive Profiles in Williams Syndrome With and Without Loss of GTF2IRD2. J Int Neuropsychol Soc 2018; 24:896-904. [PMID: 30375319 DOI: 10.1017/s1355617718000711] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
UNLABELLED Williams syndrome (WS) is a neurodevelopmental disorder that results from a heterozygous microdeletion on chromosome 7q11.23. Most of the time, the affected region contains ~1.5 Mb of sequence encoding approximately 24 genes. Some 5-8% of patients with WS have a deletion exceeding 1.8 Mb, thereby affecting two additional genes, including GTF2IRD2. Currently, there is no consensus regarding the implications of GTF2IRD2 loss for the neuropsychological phenotype of WS patients. OBJECTIVES The present study aimed to identify the role of GTF2IRD2 in the cognitive, behavioral, and adaptive profile of WS patients. METHODS Twelve patients diagnosed with WS participated, four with GTF2IRD2 deletion (atypical WS group), and eight without this deletion (typical WS group). The age range of both groups was 7-18 years old. Each patient's 7q11.23 deletion scope was determined by chromosomal microarray analysis. Cognitive, behavioral, and adaptive abilities were assessed with a battery of neuropsychological tests. RESULTS Compared with the typical WS group, the atypical WS patients with GTF2IRD2 deletion had more impaired visuospatial abilities and more significant behavioral problems, mainly related to the construct of social cognition. CONCLUSIONS These findings provide new evidence regarding the influence of the GTF2IRD2 gene on the severity of behavioral symptoms of WS related to social cognition and certain visuospatial abilities. (JINS, 2018, 24, 896-904).
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17
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Li L, Huang L, Luo Y, Huang X, Lin S, Fang Q. Differing Microdeletion Sizes and Breakpoints in Chromosome 7q11.23 in Williams-Beuren Syndrome Detected by Chromosomal Microarray Analysis. Mol Syndromol 2016; 6:268-75. [PMID: 27022327 DOI: 10.1159/000443942] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2015] [Indexed: 01/01/2023] Open
Abstract
Williams-Beuren syndrome (WBS) manifests as supravalvular aortic stenosis, intellectual disability, developmental delay and characteristic facial features. The common WBS deletion region ranges from 1.55 to 1.84 Mb and primarily contains the ELN gene. We analyzed 10 patients diagnosed with 7q11.23 microdeletion syndrome by chromosomal microarray analysis. The clinical features of these patients varied from classic WBS to normal phenotype. All 10 patients exhibited different sizes and breakpoints of chromosome microdeletions ranging from 44 kb to 9.88 Mb. The hemizygosity of the ELN gene was detected in 7 patients, while a normal ELN gene was present in 3 other patients with small deletions. We observed that the phenotypic features of WBS varied in fetuses, children and adults, influenced by the genes, deletion size and breakpoint. Our findings provide more information on the genotype-phenotype correlations of WBS. However, further research is needed to explore the size and breakpoint effect and functions of the genes on chromosome 7q11.23.
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Affiliation(s)
- Lin Li
- Department of Gynecology and Obstetrics, Fetal Medicine Center, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Linhuan Huang
- Department of Gynecology and Obstetrics, Fetal Medicine Center, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Yanmin Luo
- Department of Gynecology and Obstetrics, Fetal Medicine Center, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Xuan Huang
- Department of Gynecology and Obstetrics, Fetal Medicine Center, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Shaobin Lin
- Department of Gynecology and Obstetrics, Fetal Medicine Center, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Qun Fang
- Department of Gynecology and Obstetrics, Fetal Medicine Center, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
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18
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High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry. Nat Genet 2016; 48:323-30. [PMID: 26808113 PMCID: PMC4767573 DOI: 10.1038/ng.3496] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/23/2015] [Indexed: 01/04/2023]
Abstract
Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,478 SLE cases and 12,656 controls from six East Asian cohorts to identify new SLE susceptibility loci and better localize known loci. We identified ten new loci and confirmed 20 known loci with genome-wide significance. Among the new loci, the most significant locus was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta = 3.75 × 10(-117), odds ratio (OR) = 2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We identified the most likely functional variants at each locus by analyzing epigenetic marks and gene expression data. Ten candidate variants are known to alter gene expression in cis or in trans. Enrichment analysis highlights the importance of these loci in B cell and T cell biology. The new loci, together with previously known loci, increase the explained heritability of SLE to 24%. The new loci share functional and ontological characteristics with previously reported loci and are possible drug targets for SLE therapeutics.
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19
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Al-Qattan SM, Wakil SM, Anazi S, Alazami AM, Patel N, Shaheen R, Shamseldin HE, Hagos ST, AlDossari HM, Salih MA, El Khashab HY, Kentab AY, AlNasser MN, Bashiri FA, Kaya N, Hashem MO, Alkuraya FS. The clinical utility of molecular karyotyping for neurocognitive phenotypes in a consanguineous population. Genet Med 2014; 17:719-25. [PMID: 25503496 DOI: 10.1038/gim.2014.184] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 11/11/2014] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Molecular karyotyping has rapidly become the test of choice in patients with neurocognitive phenotypes, but studies of its clinical utility have largely been limited to outbred populations. In consanguineous populations, single-gene recessive causes of neurocognitive phenotypes are expected to account for a relatively high percentage of cases, thus diminishing the yield of molecular karyotyping. The aim of this study was to test the clinical yield of molecular karyotyping in the highly consanguineous population of Saudi Arabia. METHODS We have reviewed the data of 584 patients with neurocognitive phenotypes (mainly referred from pediatric neurology clinics), all evaluated by a single clinical geneticist. RESULTS At least 21% of tested cases had chromosomal aberrations that are likely disease-causing. These changes include both known and novel deletion syndromes. The higher yield of molecular karyotyping in this study as compared with the commonly cited 11% can be explained by our ability to efficiently identify single-gene disorders, thus enriching the samples that underwent molecular karyotyping for de novo chromosomal aberrations. We show that we were able to identify a causal mutation in 37% of cases on a clinical basis with the help of autozygome analysis, thus bypassing the need for molecular karyotyping. CONCLUSION Our study confirms the clinical utility of molecular karyotyping even in highly consanguineous populations.
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Affiliation(s)
- Sarah M Al-Qattan
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Salma M Wakil
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shamsa Anazi
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Anas M Alazami
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ranad Shaheen
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Samya T Hagos
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Haya M AlDossari
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Heba Y El Khashab
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Pediatrics, Children Hospital, Ain Shams University, Cairo, Egypt
| | - Amal Y Kentab
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed N AlNasser
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Fahad A Bashiri
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Namik Kaya
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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20
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Broadbent H, Farran EK, Chin E, Metcalfe K, Tassabehji M, Turnpenny P, Sansbury F, Meaburn E, Karmiloff-Smith A. Genetic contributions to visuospatial cognition in Williams syndrome: insights from two contrasting partial deletion patients. J Neurodev Disord 2014; 6:18. [PMID: 25057328 PMCID: PMC4107613 DOI: 10.1186/1866-1955-6-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/23/2014] [Indexed: 11/10/2022] Open
Abstract
Background Williams syndrome (WS) is a rare neurodevelopmental disorder arising from a hemizygotic deletion of approximately 27 genes on chromosome 7, at locus 7q11.23. WS is characterised by an uneven cognitive profile, with serious deficits in visuospatial tasks in comparison to relatively proficient performance in some other cognitive domains such as language and face processing. Individuals with partial genetic deletions within the WS critical region (WSCR) have provided insights into the contribution of specific genes to this complex phenotype. However, the combinatorial effects of different genes remain elusive. Methods We report on visuospatial cognition in two individuals with contrasting partial deletions in the WSCR: one female (HR), aged 11 years 9 months, with haploinsufficiency for 24 of the WS genes (up to GTF2IRD1), and one male (JB), aged 14 years 2 months, with the three most telomeric genes within the WSCR deleted, or partially deleted. Results Our in-depth phenotyping of the visuospatial domain from table-top psychometric, and small- and large-scale experimental tasks reveal a profile in HR in line with typically developing controls, albeit with some atypical features. These data are contrasted with patient JB’s atypical profile of strengths and weaknesses across the visuospatial domain, as well as with more substantial visuospatial deficits in individuals with the full WS deletion. Conclusions Our findings point to the contribution of specific genes to spatial processing difficulties associated with WS, highlighting the multifaceted nature of spatial cognition and the divergent effects of genetic deletions within the WSCR on different components of visuospatial ability. The importance of general transcription factors at the telomeric end of the WSCR, and their combinatorial effects on the WS visuospatial phenotype are also discussed.
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Affiliation(s)
| | - Emily K Farran
- Institute of Education, University of London, London, UK
| | - Esther Chin
- Birkbeck Centre for Brain and Cognitive Development, University of London, London, UK
| | - Kay Metcalfe
- Genetic Medicine, St. Mary's Hospital, Manchester, UK
| | | | - Peter Turnpenny
- Royal Devon and Exeter Foundation Trust, Exeter, UK ; Penninsula College of Medicine and Dentistry, Universities of Exeter and Plymouth, Exeter, UK
| | - Francis Sansbury
- Royal Devon and Exeter Foundation Trust, Exeter, UK ; Penninsula College of Medicine and Dentistry, Universities of Exeter and Plymouth, Exeter, UK
| | - Emma Meaburn
- Birkbeck Centre for Brain and Cognitive Development, University of London, London, UK
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21
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Helsmoortel C, Vulto-van Silfhout AT, Coe BP, Vandeweyer G, Rooms L, van den Ende J, Schuurs-Hoeijmakers JHM, Marcelis CL, Willemsen MH, Vissers LELM, Yntema HG, Bakshi M, Wilson M, Witherspoon KT, Malmgren H, Nordgren A, Annerén G, Fichera M, Bosco P, Romano C, de Vries BBA, Kleefstra T, Kooy RF, Eichler EE, Van der Aa N. A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP. Nat Genet 2014; 46:380-4. [PMID: 24531329 PMCID: PMC3990853 DOI: 10.1038/ng.2899] [Citation(s) in RCA: 233] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/23/2014] [Indexed: 12/11/2022]
Abstract
Despite a high heritability, a genetic diagnosis can only be established in a minority of patients with autism spectrum disorder (ASD), characterized by persistent deficits in social communication and interaction and restricted, repetitive patterns of behavior, interests or activities1. Known genetic causes include chromosomal aberrations, such as the duplication of the 15q11-13 region, and monogenic causes, such as the Rett and Fragile X syndromes. The genetic heterogeneity within ASD is striking, with even the most frequent causes responsible for only 1% of cases at the most. Even with the recent developments in next generation sequencing, for the large majority of cases no molecular diagnosis can be established 2-7. Here, we report 10 patients with ASD and other shared clinical characteristics, including intellectual disability and facial dysmorphisms caused by a mutation in ADNP, a transcription factor involved in the SWI/SNF remodeling complex. We estimate this gene to be mutated in at least 0.17% of ASD cases, making it one of the most frequent ASD genes known to date.
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Affiliation(s)
| | - Anneke T Vulto-van Silfhout
- 1] Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands. [2]
| | - Bradley P Coe
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA. [3]
| | - Geert Vandeweyer
- 1] Department of Medical Genetics, University of Antwerp, Antwerp, Belgium. [2] Biomedical informatics research center Antwerpen (Biomina), Department of Mathematics and Computer Science, University of Antwerp, Edegem, Belgium
| | - Liesbeth Rooms
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | | | - Janneke H M Schuurs-Hoeijmakers
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carlo L Marcelis
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Madhura Bakshi
- Department of Genetic Medicine, Westmead Hospital, Sydney, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Westmead, Australia
| | - Kali T Witherspoon
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Helena Malmgren
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Göran Annerén
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Marco Fichera
- 1] Unit of Neurology, I.R.C.C.S. Associazione Oasi Maria Santissima, Troina, Italy. [2] Medical Genetics, University of Catania, Catania, Italy
| | - Paolo Bosco
- Laboratory of Cytogenetics, I.R.C.C.S. Associazione Oasi Maria Santissima, Troina, Italy
| | - Corrado Romano
- Unit of Pediatrics and Medical Genetics, I.R.C.C.S. Associazione Oasi Maria Santissima, Troina, Italy
| | - Bert B A de Vries
- 1] Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands. [2] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- 1] Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands. [2] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Evan E Eichler
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Nathalie Van der Aa
- 1] Department of Medical Genetics, University of Antwerp, Antwerp, Belgium. [2] University Hospital Antwerp, Antwerp, Belgium
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Nijmeijer JS, Arias-Vásquez A, Rommelse NNJ, Altink ME, Buschgens CJM, Fliers EA, Franke B, Minderaa RB, Sergeant JA, Buitelaar JK, Hoekstra PJ, Hartman CA. Quantitative Linkage for Autism Spectrum Disorders Symptoms in Attention-Deficit/Hyperactivity Disorder: Significant Locus on Chromosome 7q11. J Autism Dev Disord 2014; 44:1671-80. [DOI: 10.1007/s10803-014-2039-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Vandeweyer G, Kooy RF. Detection and interpretation of genomic structural variation in health and disease. Expert Rev Mol Diagn 2014; 13:61-82. [DOI: 10.1586/erm.12.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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24
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Euteneuer J, Carvalho CMB, Kulkarni S, Vineyard M, Grady RM, Lupski JR, Shinawi M. Molecular and phenotypic characterization of atypical Williams-Beuren syndrome. Clin Genet 2013; 86:487-91. [PMID: 24246242 DOI: 10.1111/cge.12305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 10/08/2013] [Accepted: 10/16/2013] [Indexed: 11/29/2022]
Abstract
Williams-Beuren syndrome (WBS) is a multisystemic genomic disorder typically caused by a recurrent ˜1.5-1.8 Mb deletion on 7q11.23. Atypical deletions can provide important insight into the genotype-phenotype correlations. Here, we report the phenotypic and molecular characterization of a girl with a de novo 81.8 kb deletion in the WBS critical region, which involves the ELN and LIMK1 genes only. The patient presented at 2 months of age with extensive vascular abnormalities, mild facial dysmorphism and delays in her fine motor skills. We discuss potential molecular mechanisms and the role of ELN and LIMK1 in the different phenotypic features. We compare the findings in our patient with previously reported overlapping deletions. The phenotypic variability among these patients suggests that other factors are important in the phenotype and possibly include: position effects related to copy number variation size, variations in the non-deleted alleles, genetic modifiers elsewhere in the genome, or reduced penetrance for specific phenotypes.
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Affiliation(s)
- J Euteneuer
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
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25
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Li Y, Zhang K, Chen H, Sun F, Xu J, Wu Z, Li P, Zhang L, Du Y, Luan H, Li X, Wu L, Li H, Wu H, Li X, Li X, Zhang X, Gong L, Dai L, Sun L, Zuo X, Xu J, Gong H, Li Z, Tong S, Wu M, Li X, Xiao W, Wang G, Zhu P, Shen M, Liu S, Zhao D, Liu W, Wang Y, Huang C, Jiang Q, Liu G, Liu B, Hu S, Zhang W, Zhang Z, You X, Li M, Hao W, Zhao C, Leng X, Bi L, Wang Y, Zhang F, Shi Q, Qi W, Zhang X, Jia Y, Su J, Li Q, Hou Y, Wu Q, Xu D, Zheng W, Zhang M, Wang Q, Fei Y, Zhang X, Li J, Jiang Y, Tian X, Zhao L, Wang L, Zhou B, Li Y, Zhao Y, Zeng X, Ott J, Wang J, Zhang F. A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren's syndrome at 7q11.23. Nat Genet 2013; 45:1361-5. [PMID: 24097066 DOI: 10.1038/ng.2779] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/06/2013] [Indexed: 12/15/2022]
Abstract
Primary Sjögren's syndrome is one of the most common autoimmune diseases. So far, genetic studies of Sjögren's syndrome have relied mostly on candidate gene approaches. To identify new genetic susceptibility loci for primary Sjögren's syndrome, we performed a three-stage genome-wide association study in Han Chinese. In the discovery stage, we analyzed 556,134 autosomal SNPs in 542 cases and 1,050 controls. We then validated promising associations in 2 replication stages comprising 1,303 cases and 2,727 controls. The combined analysis identified GTF2I at 7q11.23 (rs117026326: Pcombined = 1.31 × 10(-53), combined odds ratio (ORcombined) = 2.20) as a new susceptibility locus for primary Sjögren's syndrome. Our analysis also confirmed previously reported associations in Europeans in the regions of STAT4, TNFAIP3 and the major histocompatibility complex (MHC). Fine mapping of the region around GTF2I showed that rs117026326 in GTF2I had the most significant association, with associated SNPs extending from GTF2I to GTF2IRD1-GTF2I.
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Affiliation(s)
- Yongzhe Li
- 1] Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China. [2]
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26
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Genetic insights into the functional elements of language. Hum Genet 2013; 132:959-86. [PMID: 23749164 DOI: 10.1007/s00439-013-1317-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 05/22/2013] [Indexed: 12/11/2022]
Abstract
Language disorders cover a wide range of conditions with heterologous and overlapping phenotypes and complex etiologies harboring both genetic and environmental influences. Genetic approaches including the identification of genes linked to speech and language phenotypes and the characterization of normal and aberrant functions of these genes have, in recent years, unraveled complex details of molecular and cognitive mechanisms and provided valuable insight into the biological foundations of language. Consistent with this approach, we have reviewed the functional aspects of allelic variants of genes which are currently known to be either causally associated with disorders of speech and language or impact upon the spectrum of normal language ability. We have also reviewed candidate genes associated with heritable speech and language disorders. In addition, we have evaluated language phenotypes and associated genetic components in developmental syndromes that, together with a spectrum of altered language abilities, manifest various phenotypes and offer details of multifactorial determinants of language function. Data from this review have revealed a predominance of regulatory networks involved in the control of differentiation and functioning of neurons, neuronal tracks and connections among brain structures associated with both cognitive and language faculties. Our findings, furthermore, have highlighted several multifactorial determinants in overlapping speech and language phenotypes. Collectively this analysis has revealed an interconnected developmental network and a close association of the language faculty with cognitive functions, a finding that has the potential to provide insight into linguistic hypotheses defining in particular, the contribution of genetic elements to and the modular nature of the language faculty.
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27
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Delgado LM, Gutierrez M, Augello B, Fusco C, Micale L, Merla G, Pastene EA. A 1.3-mb 7q11.23 atypical deletion identified in a cohort of patients with williams-beuren syndrome. Mol Syndromol 2013; 4:143-7. [PMID: 23653586 DOI: 10.1159/000347167] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2013] [Indexed: 11/19/2022] Open
Abstract
Williams-Beuren syndrome is a rare multisystem neurodevelopmental disorder caused by a 1.55-1.84-Mb hemizygous deletion on chromosome 7q11.23. The classical phenotype consists of characteristic facial features, supravalvular aortic stenosis, intellectual disability, overfriendliness, and visuospatial impairment. So far, 26-28 genes have been shown to contribute to the multisystem phenotype associated with Williams-Beuren syndrome. Among them, haploinsufficiency of the ELN gene has been shown to cause the cardiovascular anomalies. Identification of patients with atypical deletions has provided valuable information for genotype-phenotype correlation, in which other genes such as LIMK1,CLIP2, GTF2IRD1, or GTF2I have been correlated with specific cognitive profiles or craniofacial features. Here, we report the clinical and molecular characteristics of a patient with an atypical deletion that does not include the GTF2I gene and only partially includes the GTF2IRD1 gene.
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Affiliation(s)
- L M Delgado
- Department of Experimental Genetics, Centro Nacional de Genética Médica (CENAGEM), ANLIS Dr. Carlos G. Malbrán, Buenos Aires, Argentina
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28
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Helsmoortel C, Vandeweyer G, Kooy RF. On the spot: very local chromosomal rearrangements. F1000 BIOLOGY REPORTS 2012. [PMID: 23189093 PMCID: PMC3505860 DOI: 10.3410/b4-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the last decade, the detection of chromosomal abnormalities has shifted from conventional karyotyping under a light microscope to molecular detection using microarrays. The latter technology identified copy number variation as a major source of variation in the human genome; moreover, copy number variants were found responsible for 10-20% of cases of intellectual disability. Recent technological advances in microarray technology have also enabled the detection of very small local chromosomal rearrangements, sometimes affecting the function of only a single gene. Here, we illustrate how high resolution microarray analysis has led to increased insights into the contribution of specific genes in disease.
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Affiliation(s)
- Céline Helsmoortel
- Cognitive Genetics, Department of Medical Genetics, University of Antwerp Prins Boudewijnlaan 43, B-2650 Edegem, Belgium
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