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Labonne JDJ, Shen Y, Kong IK, Diamond MP, Layman LC, Kim HG. Comparative deletion mapping at 1p31.3-p32.2 implies NFIA responsible for intellectual disability coupled with macrocephaly and the presence of several other genes for syndromic intellectual disability. Mol Cytogenet 2016; 9:24. [PMID: 26997977 PMCID: PMC4797196 DOI: 10.1186/s13039-016-0234-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 03/09/2016] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND While chromosome 1 is the largest chromosome in the human genome, less than two dozen cases of interstitial microdeletions in the short arm have been documented. More than half of the 1p microdeletion cases were reported in the pre-microarray era and as a result, the proximal and distal boundaries containing the exact number of genes involved in the microdeletions have not been clearly defined. RESULTS We revisited a previous case of a 10-year old female patient with a 1p32.1p32.3 microdeletion displaying syndromic intellectual disability. We performed microarray analysis as well as qPCR to define the proximal and distal deletion breakpoints and revised the karyotype from 1p32.1p32.3 to 1p31.3p32.2. The deleted chromosomal region contains at least 35 genes including NFIA. Comparative deletion mapping shows that this region can be dissected into five chromosomal segments containing at least six candidate genes (DAB1, HOOK1, NFIA, DOCK7, DNAJC6, and PDE4B) most likely responsible for syndromic intellectual disability, which was corroborated by their reduced transcript levels in RT-qPCR. Importantly, one patient with an intragenic microdeletion within NFIA and an additional patient with a balanced translocation disrupting NFIA display intellectual disability coupled with macrocephaly. CONCLUSION We propose NFIA is responsible for intellectual disability coupled with macrocephaly, and microdeletions at 1p31.3p32.2 constitute a contiguous gene syndrome with several genes contributing to syndromic intellectual disability.
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Affiliation(s)
- Jonathan D. J. Labonne
- />Department of Obstetrics & Gynecology, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
- />Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
| | - Yiping Shen
- />Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - Il-Keun Kong
- />Department of Animal Science, Division of Applied Life Science (BK21plus), Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Gyeongsangnam-do Korea
| | - Michael P. Diamond
- />Department of Obstetrics & Gynecology, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
| | - Lawrence C. Layman
- />Department of Obstetrics & Gynecology, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
- />Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
- />Neuroscience Program, Medical College of Georgia, Augusta University, Augusta, GA 30912 USA
| | - Hyung-Goo Kim
- />Department of Obstetrics & Gynecology, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
- />Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA 30912 USA
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Vincent-Chong VK, Anwar A, Karen-Ng LP, Cheong SC, Yang YH, Pradeep PJ, Rahman ZAA, Ismail SM, Zaini ZM, Prepageran N, Kallarakkal TG, Ramanathan A, Mohayadi NABM, Rosli NSBM, Mustafa WMW, Abraham MT, Tay KK, Zain RB. Genome wide analysis of chromosomal alterations in oral squamous cell carcinomas revealed over expression of MGAM and ADAM9. PLoS One 2013; 8:e54705. [PMID: 23405089 PMCID: PMC3566089 DOI: 10.1371/journal.pone.0054705] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 12/14/2012] [Indexed: 12/26/2022] Open
Abstract
Despite the advances in diagnosis and treatment of oral squamous cell carcinoma (OSCC), mortality and morbidity rates have not improved over the past decade. A major drawback in diagnosis and treatment of OSCC is the lack of knowledge relating to how genetic instability in oral cancer genomes affects oral carcinogenesis. Hence, the key aim of this study was to identify copy number alterations (CNAs) that may be cancer associated in OSCC using high-resolution array comparative genomic hybridization (aCGH). To our knowledge this is the first study to use ultra-high density aCGH microarrays to profile a large number of OSCC genomes (n = 46). The most frequently amplified CNAs were located on chromosome 11q11(52%), 2p22.3(52%), 1q21.3-q22(54%), 6p21.32(59%), 20p13(61%), 7q34(52% and 72%),8p11.23-p11.22(80%), 8q11.1-q24.4(54%), 9q13-q34.3(54%), 11q23.3-q25(57%); 14q21.3-q31.1(54%); 14q31.3-q32.33(57%), 20p13-p12.3(54%) and 20q11.21-q13.33(52%). The most frequently deleted chromosome region was located on 3q26.1 (54%). In order to verify the CNAs from aCGH using quantitative polymerase chain reaction (qPCR), the three top most amplified regions and their associated genes, namely ADAM5P (8p11.23-p11.22), MGAM (7q34) and SIRPB1 (20p13.1), were selected in this study. The ADAM5P locus was found to be amplified in 39 samples and deleted in one; MGAM (24 amplifications and 3 deletions); and SIRPB1 (12 amplifications, others undetermined). On the basis of putative cancer-related annotations, two genes, namely ADAM metallopeptidase domain 9 (ADAM9) and maltase-glucoamylase alpha-glucosidase (MGAM), that mapped to CNA regions were selected for further evaluation of their mRNA expression using reverse transcriptase qPCR. The over-expression of MGAM was confirmed with a 6.6 fold increase in expression at the mRNA level whereas the fold change in ADAM9 demonstrated a 1.6 fold increase. This study has identified significant regions in the OSCC genome that were amplified and resulted in consequent over-expression of the MGAM and ADAM9 genes that may be utilized as biological markers for OSCC.
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Affiliation(s)
- Vui King Vincent-Chong
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Arif Anwar
- Sengenics Sdn Bhd, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Lee Peng Karen-Ng
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Sok Ching Cheong
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Oral Cancer Research Team, Cancer Research Initiatives Foundation, Selangor Darul Ehsan, Malaysia
| | - Yi-Hsin Yang
- Department of Dental Hygiene, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Padmaja Jayaprasad Pradeep
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Zainal Ariff Abdul Rahman
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Siti Mazlipah Ismail
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Zuraiza Mohamad Zaini
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral Pathology, Oral Medicine and Periodontology, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Narayanan Prepageran
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Otorhinolaringology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Thomas George Kallarakkal
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral Pathology, Oral Medicine and Periodontology, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Anand Ramanathan
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral Pathology, Oral Medicine and Periodontology, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | | | | | - Keng Kiong Tay
- Oral Health Division, Ministry of Health, Putrajaya, Malaysia
| | - Rosnah Binti Zain
- Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Department of Oral Pathology, Oral Medicine and Periodontology, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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Freitag CM, Asherson P, Hebebrand J. Behavioural genetics of childhood disorders. Curr Top Behav Neurosci 2012; 12:395-428. [PMID: 22382729 DOI: 10.1007/7854_2011_178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
After a general introduction into genetic risk factors for child psychiatric disorders, four specific child psychiatric disorders with a strong genetic component, namely, Autism Spectrum Disorders, Attention Deficit / Hyperactivity Disorder, Nocturnal Enuresis, and obesity, are discussed in detail. Recent evidence of linkage, candidate gene, and genome-wide association studies are presented. This chapter ends with a prospectus on further research needs.
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Affiliation(s)
- Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe-Universität Frankfurt am Main, Deutschordenstraße 50, 60528, Frankfurt am Main, Germany,
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Abstract
Autism spectrum disorder (ASD) is a behaviourally defined syndrome where the etiology and pathophysiology is only partially understood. In a small proportion of children with the condition, a specific medical disorder is identified, but the causal significance in many instances is unclear. Currently, the medical conditions that are best established as probable causes of ASD include Fragile X syndrome, Tuberous Sclerosis and abnormalities of chromosome 15 involving the 15q11-13 region. Various other single gene mutations, genetic syndromes, chromosomal abnormalities and rare de novo copy number variants have been reported as being possibly implicated in etiology, as have several ante and post natal exposures and complications. However, in most instances the evidence base for an association with ASD is very limited and largely derives from case reports or findings from small, highly selected and uncontrolled case series. Not only therefore, is there uncertainty over whether the condition is associated, but the potential basis for the association is very poorly understood. In some cases the medical condition may be a consequence of autism or simply represent an associated feature deriving from an underlying shared etiology. Nevertheless, it is clear that in a growing proportion of individuals potentially causal medical conditions are being identified and clarification of their role in etio-pathogenesis is necessary. Indeed, investigations into the causal mechanisms underlying the association between conditions such as tuberous sclerosis, Fragile X and chromosome 15 abnormalities are beginning to cast light on the molecular and neurobiological pathways involved in the pathophysiology of ASD. It is evident therefore, that much can be learnt from the study of probably causal medical disorders as they represent simpler and more tractable model systems in which to investigate causal mechanisms. Recent advances in genetics, molecular and systems biology and neuroscience now mean that there are unparalleled opportunities to test causal hypotheses and gain fundamental insights into the nature of autism and its development.
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Affiliation(s)
- Patrick F Bolton
- The Social Genetic & Developmental Psychiatry Centre and The Department of Child and Adolescent Psychiatry, The Institute of Psychiatry, King's College London, London, England,
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