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Singh R. A Gene-Based Algorithm for Identifying Factors That May Affect a Speaker's Voice. ENTROPY (BASEL, SWITZERLAND) 2023; 25:897. [PMID: 37372241 DOI: 10.3390/e25060897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023]
Abstract
Over the past decades, many machine-learning- and artificial-intelligence-based technologies have been created to deduce biometric or bio-relevant parameters of speakers from their voice. These voice profiling technologies have targeted a wide range of parameters, from diseases to environmental factors, based largely on the fact that they are known to influence voice. Recently, some have also explored the prediction of parameters whose influence on voice is not easily observable through data-opportunistic biomarker discovery techniques. However, given the enormous range of factors that can possibly influence voice, more informed methods for selecting those that may be potentially deducible from voice are needed. To this end, this paper proposes a simple path-finding algorithm that attempts to find links between vocal characteristics and perturbing factors using cytogenetic and genomic data. The links represent reasonable selection criteria for use by computational by profiling technologies only, and are not intended to establish any unknown biological facts. The proposed algorithm is validated using a simple example from medical literature-that of the clinically observed effects of specific chromosomal microdeletion syndromes on the vocal characteristics of affected people. In this example, the algorithm attempts to link the genes involved in these syndromes to a single example gene (FOXP2) that is known to play a broad role in voice production. We show that in cases where strong links are exposed, vocal characteristics of the patients are indeed reported to be correspondingly affected. Validation experiments and subsequent analyses confirm that the methodology could be potentially useful in predicting the existence of vocal signatures in naïve cases where their existence has not been otherwise observed.
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Affiliation(s)
- Rita Singh
- Center for Voice Intelligence and Security, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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2
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Evaluation of Individuals with Non-Syndromic Global Developmental Delay and Intellectual Disability. CHILDREN 2023; 10:children10030414. [PMID: 36979972 PMCID: PMC10047567 DOI: 10.3390/children10030414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/11/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
Global Developmental Delay (GDD) and Intellectual Disability (ID) are two of the most common presentations encountered by physicians taking care of children. GDD/ID is classified into non-syndromic GDD/ID, where GDD/ID is the sole evident clinical feature, or syndromic GDD/ID, where there are additional clinical features or co-morbidities present. Careful evaluation of children with GDD and ID, starting with detailed history followed by a thorough examination, remain the cornerstone for etiologic diagnosis. However, when initial history and examination fail to identify a probable underlying etiology, further genetic testing is warranted. In recent years, genetic testing has been shown to be the single most important diagnostic modality for clinicians evaluating children with non-syndromic GDD/ID. In this review, we discuss different genetic testing currently available, review common underlying copy-number variants and molecular pathways, explore the recent evidence and recommendations for genetic evaluation and discuss an approach to the diagnosis and management of children with non-syndromic GDD and ID.
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Mahadevan J, Sud R, Nadella RK, Vani P, Subramaniam AG, Paul P, Ganapathy A, Mannan AU, Chandru V, Viswanath B, Purushottam M, Jain S. Targeted Sequencing Detects Variants That May Contribute to the Risk of Neuropsychiatric Disorders. Indian J Psychol Med 2022; 44:516-522. [PMID: 36157006 PMCID: PMC9460021 DOI: 10.1177/0253717621993672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Jayant Mahadevan
- Dept. of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Reeteka Sud
- Molecular Genetics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Ravi Kumar Nadella
- Dept. of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Pulaparambil Vani
- Dept. of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Anand G Subramaniam
- Molecular Genetics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Pradip Paul
- Molecular Genetics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Aparna Ganapathy
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bengaluru, Karnataka, India
| | - Ashraf U Mannan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bengaluru, Karnataka, India
| | - Vijay Chandru
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bengaluru, Karnataka, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Biju Viswanath
- Dept. of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India.,Molecular Genetics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Meera Purushottam
- Molecular Genetics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Sanjeev Jain
- Dept. of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India.,Molecular Genetics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
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4
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A Review of Prader–Willi Syndrome. ENDOCRINES 2022. [DOI: 10.3390/endocrines3020027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Prader–Willi Syndrome (PWS, OMIM #176270) is a rare complex genetic disorder due to the loss of expression of paternally derived genes in the PWS critical region on chromosome 15q11-q13. It affects multiple neuroendocrine systems and may present failure to thrive in infancy, but then, hyperphagia and morbid obesity starting in early childhood became the hallmark of this condition. Short stature, hypogonadism, sleep abnormalities, intellectual disability, and behavioral disturbances highlight the main features of this syndrome. There have been a significant number of advances in our understanding of the genetic mechanisms underlying the disease, especially discoveries of MAGEL2, NDN, MKRN3, and SNORD116 genes in the pathophysiology of PWS. However, early diagnosis and difficulty in treating some of the disease’s most disabling features remain challenging. As our understanding of PWS continues to grow, so does the availability of new therapies and management strategies available to clinicians and families.
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Kang J, Lee CN, Su YN, Lin MW, Tai YY, Hsu WW, Huang KY, Chen CL, Hung CH, Lin SY. The Prenatal Diagnosis and Clinical Outcomes of Fetuses With 15q11.2 Copy Number Variants: A Case Series of 36 Patients. Front Med (Lausanne) 2021; 8:754521. [PMID: 34888324 PMCID: PMC8649837 DOI: 10.3389/fmed.2021.754521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/25/2021] [Indexed: 11/26/2022] Open
Abstract
Prenatal genetic counseling of fetuses diagnosed with 15q11.2 copy number variants (CNVs) involving the BP1–BP2 region is difficult due to limited information and controversial opinion on prognosis. In total, we collected the data of 36 pregnant women who underwent prenatal microarray analysis from 2010 to 2017 and were assessed at National Taiwan University Hospital. Comparison of the maternal characteristics, prenatal ultrasound findings, and postnatal outcomes among the different cases involving the 15q11.2 BP1–BP2 region were presented. Out of the 36 fetuses diagnosed with CNVs involving the BP1–BP2 region, five were diagnosed with microduplications and 31 with microdeletions. Among the participants, 10 pregnant women received termination of pregnancy and 26 gave birth to healthy individuals (27 babies in total). The prognoses of 15q11.2 CNVs were controversial and recent studies have revealed its low pathogenicity. In our study, the prenatal abnormal ultrasound findings were recorded in 12 participants and were associated with 15q11.2 deletions. No obvious developmental delay or neurological disorders were detected in early childhood.
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Affiliation(s)
- Jessica Kang
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Nan Lee
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan.,Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Ning Su
- Sofiva Genomics Co. Ltd., Taipei, Taiwan
| | - Ming-Wei Lin
- Department of Obstetrics and Gynecology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | - Yi-Yun Tai
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Wei Hsu
- Department of Obstetrics and Gynecology, National Taiwan University Hospital Hospital Yun-Lin Branch, Yunlin, Taiwan
| | - Kuan-Ying Huang
- Department of Obstetrics and Gynecology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | - Chi-Ling Chen
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Hui Hung
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Shin-Yu Lin
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
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Chen CP, Ko TM, Huang JP, Chern SR, Wu PS, Chen SW, Wu FT, Chen WL, Lee MS, Wang W. Prenatal diagnosis of a familial normal euchromatic variant of dup(15)(q11.2q11.2) in a pregnancy with a favorable outcome. Taiwan J Obstet Gynecol 2021; 59:770-772. [PMID: 32917335 DOI: 10.1016/j.tjog.2020.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis of a familial normal euchromatic variant of dup(15)(q11.2q11.2) in a pregnancy with a favorable outcome. CASE REPORT A 32-year-old woman underwent elective amniocentesis at 17 weeks of gestation because of anxiety. Amniocentesis revealed a karyotype of 46,XX,dup(15)(q11.2q11.2). Simultaneous array comparative genomic hybridization (aCGH) analysis on the DNA extracted from uncultured amniocytes revealed the result of arr (1-22, X) × 2 with no genomic imbalance. Cytogenetic analysis of the parental bloods showed that the mother had a karyotype of 46,XX,dup(15)(q11.2q11.2), and the father had a karyotype of 46,XY. Prenatal ultrasound findings were unremarkable. A healthy 2948 g female baby was delivered at 39 weeks of gestation without any phenotypic abnormality. Cytogenetic analysis of the cord blood revealed a karyotype of 46,XX,dup(15)(q11.2q11.2). CONCLUSION Prenatal diagnosis of dup(15)(q11.2q11.2) should include a differential diagnosis of a 15q11.2 (BP1-BP2) microduplication encompassing TUBGCP5, CYFIP1, NIPA2 and NIPA1, and aCGH analysis is useful for the differential diagnosis under such a circumstance.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Tsang-Ming Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics and Gynecology, Taipei, Taiwan
| | - Jian-Pei Huang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; MacKay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Fang-Tzu Wu
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wen-Lin Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Meng-Shan Lee
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
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Chen CP, Ko TM, Chern SR, Wu PS, Chen SW, Wu FT, Chen YY, Town DD, Chen LF, Wang W. Prenatal diagnosis of maternal uniparental disomy 16 associated with mosaic trisomy 16 at amniocentesis, and pericardial effusion and intrauterine growth restriction in the fetus. Taiwan J Obstet Gynecol 2021; 60:534-539. [PMID: 33966743 DOI: 10.1016/j.tjog.2021.03.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2021] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis of maternal uniparental disomy (UPD) 16 associated with mosaic trisomy 16 at amniocentesis, and pericardial effusion and intrauterine growth restriction (IUGR) in the fetus. CASE REPORT A 38-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age, and the result was 47,XX,+16[2]/46,XX[54]. Simultaneous array comparative genomic hybridization (aCGH) analysis on the DNA extracted from uncultured amniocytes revealed 14% mosaicism for trisomy 16 and a paternally inherited 319-kb microdeletion of 15q11.2 encompassing the genes of TUBGCP5, CYFIP1, NIPA2 and NIPA1. Prenatal ultrasound revealed persistent left superior vena cava, pericardial effusion and severe IUGR. Cordocentesis at 23 weeks of gestation revealed a karyotype of 46,XX, but polymorphic DNA marker analysis revealed maternal UPD 16. Repeat amniocentesis was performed at 27 weeks of gestation and revealed a karyotype of 46, XX in 21/21 colonies. Molecular cytogenetic analysis on uncultured amniocytes revealed 22.4% mosaicism (26/116 cells) for trisomy 16 on interphase fluorescence in situ hybridization (FISH) analysis, and 20% mosaicism for trisomy 16 on aCGH. Polymorphic DNA marker analysis on the DNAs extracted from uncultured amniocytes and parental bloods revealed maternal UPD 16. The pregnancy was subsequently terminated, and a fetus was delivered with facial dysmorphism and severe IUGR. The umbilical cord had a karyotype of 47,XX,+16[28]/46,XX[16]. Polymorphic DNA marker analysis on placenta confirmed a maternal origin of trisomy 16. CONCLUSION Cytogenetic discrepancy between cultured amniocytes and uncultured amniocytes may present in mosaic trisomy 16 at amniocentesis. Prenatal diagnosis of mosaic trisomy 16 should alert the association of maternal UPD 16 which may be associated with congenital heart defects and severe IUGR on prenatal ultrasound.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan.
| | - Tsang-Ming Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics and Gynecology, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Fang-Tzu Wu
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yun-Yi Chen
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Dai-Dyi Town
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Li-Feng Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
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Phenotypic Diversity of 15q11.2 BP1-BP2 Deletion in Three Korean Families with Development Delay and/or Intellectual Disability: A Case Series and Literature Review. Diagnostics (Basel) 2021; 11:diagnostics11040722. [PMID: 33921555 PMCID: PMC8072617 DOI: 10.3390/diagnostics11040722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 11/30/2022] Open
Abstract
The 15q11.2 breakpoint (BP) 1–BP2 deletion syndrome is emerging as the most frequent pathogenic copy number variation in humans related to neurodevelopmental diseases, with changes in cognition, behavior, and brain morphology. Previous publications have reported that patients with 15q11.2 BP1–BP2 deletion showed intellectual disability (ID), speech impairment, developmental delay (DD), and/or behavioral problems. We describe three new cases, aged 3 or 6 years old and belonging to three unrelated Korean families, with a 350-kb 15q11.2 BP1–BP2 deletion of four highly conserved genes, namely, the TUBGCP5, CYFIP1, NIPA2, and NIPA1 genes. All of our cases presented with global DD and/or ID, and the severity ranged from mild to severe, but common facial dysmorphism and congenital malformations in previous reports were not characteristic. The 15q11.2 BP1–BP2 deletion was inherited from an unaffected parent in all cases. Our three cases, together with previous findings from the literature review, confirm some of the features earlier reported to be associated with 15q11.2 BP1–BP2 deletion and help to further delineate the phenotype associated with 15q11.2 deletion. Identification of more cases with 15q11.2 BP1–BP2 deletion will allow us to obtain a better understanding of the clinical phenotypes. Further explanation of the functions of the genes within the 15q11.2 BP1–BP2 region is required to resolve the pathogenic effects on neurodevelopment.
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Maya I, Perlman S, Shohat M, Kahana S, Yacobson S, Tenne T, Agmon-Fishman I, Tomashov Matar R, Basel-Salmon L, Sukenik-Halevy R. Should We Report 15q11.2 BP1-BP2 Deletions and Duplications in the Prenatal Setting? J Clin Med 2020; 9:jcm9082602. [PMID: 32796639 PMCID: PMC7463673 DOI: 10.3390/jcm9082602] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/22/2020] [Accepted: 08/05/2020] [Indexed: 12/26/2022] Open
Abstract
Copy number variations of the 15q11.2 region at breakpoints 1-2 (BP1-BP2) have been associated with variable phenotypes and low penetrance. Detection of such variations in the prenatal setting can result in significant parental anxiety. The clinical significance of pre- and postnatally detected 15q11.2 BP1-BP2 deletions and duplications was assessed. Of 11,004 chromosomal microarray tests performed in a single referral lab (7596 prenatal, 3408 postnatal), deletions were detected in 66 cases: 39 in prenatal tests (0.51%) and 27 in postnatal tests (0.79%). Duplications were detected in 94 cases: 62 prenatal tests (0.82%) and 32 postnatal tests (0.94%). The prevalence of deletions and duplications among clinically indicated prenatal tests (0.57% and 0.9%, respectively) did not differ significantly in comparison to unindicated tests (0.49% and 0.78%, respectively). The prevalence of deletions and duplications among postnatal tests performed for clinical indications was similar to the prevalence in healthy individuals (0.73% and 1% vs. 0.98% and 0.74%, respectively). The calculated penetrance of deletions and duplications over the background risk was 2.18% and 1.16%, respectively. We conclude that the pathogenicity of 15q11.2 BP1-BP2 deletions and duplications is low. Opting out the report of these copy number variations to both clinicians and couples should be considered.
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Affiliation(s)
- Idit Maya
- Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel; (I.M.); (S.K.); (S.Y.); (I.A.-F.); (R.T.M.); (L.B.-S.)
| | - Sharon Perlman
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (S.P.); (M.S.)
- Ultrasound Unit, Helen Schneider Women’s Hospital, Rabin Medical Center, Petach Tikva 49100, Israel
| | - Mordechai Shohat
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (S.P.); (M.S.)
- Genetic Institute, Maccabi Health medicinal organization, Rehovot, and Bioinformatics Unit, Cancer Research center, Chaim Sheba Medical Center, Tel-Hashome 52621, Israel
| | - Sarit Kahana
- Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel; (I.M.); (S.K.); (S.Y.); (I.A.-F.); (R.T.M.); (L.B.-S.)
| | - Shiri Yacobson
- Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel; (I.M.); (S.K.); (S.Y.); (I.A.-F.); (R.T.M.); (L.B.-S.)
| | - Tamar Tenne
- Genetic Institute, Meir Medical Center, Kfar Saba 28164, Israel;
| | - Ifaat Agmon-Fishman
- Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel; (I.M.); (S.K.); (S.Y.); (I.A.-F.); (R.T.M.); (L.B.-S.)
| | - Reut Tomashov Matar
- Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel; (I.M.); (S.K.); (S.Y.); (I.A.-F.); (R.T.M.); (L.B.-S.)
| | - Lina Basel-Salmon
- Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel; (I.M.); (S.K.); (S.Y.); (I.A.-F.); (R.T.M.); (L.B.-S.)
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (S.P.); (M.S.)
- Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva 49100, Israel
- Pediatric Genetics Unit, Schneider Children’s Medical Center, Petah Tikva 49100, Israel
| | - Rivka Sukenik-Halevy
- Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel; (I.M.); (S.K.); (S.Y.); (I.A.-F.); (R.T.M.); (L.B.-S.)
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; (S.P.); (M.S.)
- Correspondence: ; Tel.: +972-52-6007249
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10
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Woo YJ, Kanellopoulos AK, Hemati P, Kirschen J, Nebel RA, Wang T, Bagni C, Abrahams BS. Domain-Specific Cognitive Impairments in Humans and Flies With Reduced CYFIP1 Dosage. Biol Psychiatry 2019; 86:306-314. [PMID: 31202490 PMCID: PMC6679746 DOI: 10.1016/j.biopsych.2019.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/19/2019] [Accepted: 04/03/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Deletions encompassing a four-gene region on chromosome 15 (BP1-BP2 at 15q11.2), seen at a population frequency of 1 in 500, are associated with increased risk for schizophrenia, epilepsy, and other common neurodevelopmental disorders. However, little is known in terms of how these common deletions impact cognition. METHODS We used a Web-based tool to characterize cognitive function in a novel cohort of adult carriers and their noncarrier family members. Results from 31 carrier and 38 noncarrier parents from 40 families were compared with control data from 6530 individuals who self-registered on the Lumosity platform and opted in to participate in research. We then examined aspects of sensory and cognitive function in flies harboring a mutation in Cyfip, the homologue of one of the genes within the deletion. For the fly studies, 10 or more groups of 50 individuals per genotype were included. RESULTS Our human studies revealed profound deficits in grammatical reasoning, arithmetic reasoning, and working memory in BP1-BP2 deletion carriers. No such deficits were observed in noncarrier spouses. Our fly studies revealed deficits in associative and nonassociative learning despite intact sensory perception. CONCLUSIONS Our results provide new insights into outcomes associated with BP1-BP2 deletions and call for a discussion on how to appropriately communicate these findings to unaffected carriers. Findings also highlight the utility of an online tool in characterizing cognitive function in a geographically distributed population.
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Affiliation(s)
- Young Jae Woo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Parisa Hemati
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York; Human Genetics Program, Sarah Lawrence College, Yonkers, New York
| | - Jill Kirschen
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Rebecca A Nebel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Claudia Bagni
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland; Department of Biomedicine and Prevention, Tor Vergata University, Rome, Italy
| | - Brett S Abrahams
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York.
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11
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Davis KW, Serrano M, Loddo S, Robinson C, Alesi V, Dallapiccola B, Novelli A, Butler MG. Parent-of-Origin Effects in 15q11.2 BP1-BP2 Microdeletion (Burnside-Butler) Syndrome. Int J Mol Sci 2019; 20:E1459. [PMID: 30909440 PMCID: PMC6470921 DOI: 10.3390/ijms20061459] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 01/01/2023] Open
Abstract
To identify whether parent-of-origin effects (POE) of the 15q11.2 BP1-BP2 microdeletion are associated with differences in clinical features in individuals inheriting the deletion, we collected 71 individuals reported with phenotypic data and known inheritance from a clinical cohort, a research cohort, the DECIPHER database, and the primary literature. Chi-squared and Mann-Whitney U tests were used to test for differences in specific and grouped clinical symptoms based on parental inheritance and proband gender. Analyses controlled for sibling sets and individuals with additional variants of uncertain significance (VOUS). Among all probands, maternal deletions were associated with macrocephaly (p = 0.016) and autism spectrum disorder (ASD; p = 0.02), while paternal deletions were associated with congenital heart disease (CHD; p = 0.004). Excluding sibling sets, maternal deletions were associated with epilepsy as well as macrocephaly (p < 0.05), while paternal deletions were associated with CHD and abnormal muscular phenotypes (p < 0.05). Excluding sibling sets and probands with an additional VOUS, maternal deletions were associated with epilepsy (p = 0.019) and paternal deletions associated with muscular phenotypes (p = 0.008). Significant gender-based differences were also observed. Our results supported POEs of this deletion and included macrocephaly, epilepsy and ASD in maternal deletions with CHD and abnormal muscular phenotypes seen in paternal deletions.
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Affiliation(s)
| | | | - Sara Loddo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome 00165, Italy.
| | | | - Viola Alesi
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome 00165, Italy.
| | - Bruno Dallapiccola
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome 00165, Italy.
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome 00165, Italy.
| | - Merlin G Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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Chen CP, Chang SY, Wang LK, Chang TY, Chern SR, Wu PS, Chen SW, Lai ST, Chuang TY, Yang CW, Town DD, Chen LF, Wang W. Prenatal diagnosis of a familial 15q11.2 (BP1-BP2) microdeletion encompassing TUBGCP5, CYFIP1, NIPA2 and NIPA1 in a fetus with ventriculomegaly, microcephaly and intrauterine growth restriction on prenatal ultrasound. Taiwan J Obstet Gynecol 2019; 57:730-733. [PMID: 30342661 DOI: 10.1016/j.tjog.2018.08.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2018] [Indexed: 10/28/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis of a 15q11.2 (BP1-BP2) microdeletion encompassing TUBGCP5, CYFIP1, NIPA2 and NIPA1 in a fetus with ventriculomegaly, microcephaly and intrauterine growth restriction (IUGR) on prenatal ultrasound. CASE REPORT A 30-year-old, gravida 3, para 2, woman was referred to the hospital for amniocentesis because of fetal ventriculomegaly on prenatal ultrasound. Her husband was 31 years old. The couple had two healthy daughters, and there was no family history of mental disorders and congenital malformations. Amniocentesis revealed a karyotype of 46,XX. Array comparative genomic hybridization (aCGH) analysis on the DNA extracted from uncultured amniocytes revealed a 451.89-kb 15q11.2 microdeletion or arr 15q11.2 (22,765,628-23,217,514) × 1.0 [GRCh37 (hg19)] encompassing TUBGCP5, CYFIP1, NIPA2 and NIPA1. The parental karyotypes were normal. aCGH analysis on the DNAs extracted from parental bloods revealed a 402-kb 15q11.2 microdeletion or arr 15q11.2 (22,815,577-23,217,514) × 1.0 (hg19) encompassing TUBGCP5, CYFIP1, NIPA2 and NIPA1 in the phenotypically normal father. The mother did not have any genomic imbalance. Level II ultrasound at 21 weeks of gestation revealed microcephaly and IUGR. The parents elected to terminate the pregnancy at 22 weeks of gestation, and a female fetus was delivered with a body weight of 448 g (10th centile) and a body length of 26 cm (3rd-10th centile) but no gross abnormalities. CONCLUSION Fetuses with a 15q11.2 (BP1-BP2) microdeletion may present ventriculomegaly, microcephaly and IUGR on prenatal ultrasound, and aCGH is helpful for prenatal diagnosis under such a circumstance.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Shu-Yuan Chang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Liang-Kai Wang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Shih-Ting Lai
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Tzu-Yun Chuang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chien-Wen Yang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Dai-Dyi Town
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Li-Feng Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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Butler MG. Clinical and genetic aspects of the 15q11.2 BP1-BP2 microdeletion disorder. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2017; 61:568-579. [PMID: 28387067 PMCID: PMC5464369 DOI: 10.1111/jir.12382] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/09/2017] [Accepted: 03/09/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND The 15q11.2 BP1-BP2 microdeletion (Burnside-Butler susceptibility locus) is an emerging condition with over 200 individuals reported in the literature. TUBGCP5, CFYIP1, NIPA1 and NIPA2 genes are located in this chromosome 15 region and when disturbed individually are known to cause neurological, cognitive or behavioural problems as well as playing a role in both Prader-Willi and Angelman syndromes. These syndromes were the first examples in humans of genomic imprinting and typically caused by a deletion but involving the distal chromosome 15q11-q13 breakpoint BP3 and proximally placed breakpoints BP1 or BP2 of different parental origin. The typical 15q11-q13 deletion involves BP1 and BP3 and the typical type II deletion at BP2 and BP3. Several studies have shown that individuals with the larger type I deletion found in both Prader-Willi and Angelman syndromes are reported with more severe neurodevelopmental symptoms compared to those individuals with the smaller type II deletion. METHODS The literature was reviewed and clinical and cytogenetic findings summarised in 200 individuals with this microdeletion along with the role of deleted genes in diagnosis, medical care and counseling of those affected and their family members. RESULTS Reported findings in this condition include developmental delays (73% of cases) and language impairment (67%) followed by motor delay (42%), attention deficit disorder/attention deficit hyperactivity disorder (35%) and autism spectrum disorder (27%). The de novo deletion frequency has been estimated at 5 to 22% with low penetrance possibly related to subclinical manifestation or incomplete clinical information on family members. A prevalence of 0.6 to 1.3% has been identified in one study for patients with neurological or behavioural problems presenting for genetic services and chromosomal microarray analysis. CONCLUSIONS The summarised results indicate that chromosome 15q11.2 BP1-BP2 microdeletion is emerging as one of the most common cytogenetic abnormalities seen in individuals with intellectual impairment, autism spectrum disorder and other related behavioural or clinical findings, but more research is needed.
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Affiliation(s)
- Merlin G. Butler
- University of Kansas Medical Center, Departments of Psychiatry & Behavioral Sciences and Pediatrics, Kansas City, KS USA
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Chen CP, Lin SP, Lee CL, Chern SR, Wu PS, Chen YN, Chen SW, Wang W. Familial transmission of recurrent 15q11.2 (BP1-BP2) microdeletion encompassing NIPA1 , NIPA2 , CYFIP1 , and TUBGCP5 associated with phenotypic variability in developmental, speech, and motor delay. Taiwan J Obstet Gynecol 2017; 56:93-97. [DOI: 10.1016/j.tjog.2016.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2016] [Indexed: 02/08/2023] Open
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Picinelli C, Lintas C, Piras IS, Gabriele S, Sacco R, Brogna C, Persico AM. Recurrent 15q11.2 BP1-BP2 microdeletions and microduplications in the etiology of neurodevelopmental disorders. Am J Med Genet B Neuropsychiatr Genet 2016; 171:1088-1098. [PMID: 27566550 DOI: 10.1002/ajmg.b.32480] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/22/2016] [Indexed: 01/04/2023]
Abstract
Rare and common CNVs can contribute to the etiology of neurodevelopmental disorders. One of the recurrent genomic aberrations associated with these phenotypes and proposed as a susceptibility locus is the 15q11.2 BP1-BP2 CNV encompassing TUBGCP5, CYFIP1, NIPA2, and NIPA1. Characterizing by array-CGH a cohort of 243 families with various neurodevelopmental disorders, we identified five patients carrying the 15q11.2 duplication and one carrying the deletion. All CNVs were confirmed by qPCR and were inherited, except for one duplication where parents were not available. The phenotypic spectrum of CNV carriers was broad but mainly neurodevelopmental, in line with all four genes being implicated in axonal growth and neural connectivity. Phenotypically normal and mildly affected carriers complicate the interpretation of this aberration. This variability may be due to reduced penetrance or altered gene dosage on a particular genetic background. We evaluated the expression levels of the four genes in peripheral blood RNA and found the expected reduction in the deleted case, while duplicated carriers displayed high interindividual variability. These data suggest that differential expression of these genes could partially account for differences in clinical phenotypes, especially among duplication carriers. Furthermore, urinary Mg2+ levels appear negatively correlated with NIPA2 gene copy number, suggesting they could potentially represent a useful biomarker, whose reliability will need replication in larger samples. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Chiara Picinelli
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy.,Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Carla Lintas
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Ignazio Stefano Piras
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy.,Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Stefano Gabriele
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Roberto Sacco
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Claudia Brogna
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Antonio Maria Persico
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy.,Unit of Child and Adolescent Neuropsychiatry, "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
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Abstract
UNLABELLED Copy number variations encompassing the gene encoding Cyfip1 have been associated with a variety of human diseases, including autism and schizophrenia. Here we show that juvenile mice hemizygous for Cyfip1 have altered presynaptic function, enhanced protein translation, and increased levels of F-actin. In developing hippocampus, reduced Cyfip1 levels serve to decrease paired pulse facilitation and increase miniature EPSC frequency without a change in amplitude. Higher-resolution examination shows these changes to be caused primarily by an increase in presynaptic terminal size and enhanced vesicle release probability. Short hairpin-mediated knockdown of Cyfip1 coupled with expression of mutant Cyfip1 proteins indicates that the presynaptic alterations are caused by dysregulation of the WAVE regulatory complex. Such dysregulation occurs downstream of Rac1 as acute exposure to Rac1 inhibitors rescues presynaptic responses in culture and in hippocampal slices. The data serve to highlight an early and essential role for Cyfip1 in the generation of normally functioning synapses and suggest a means by which changes in Cyfip1 levels could impact the generation of neural networks and contribute to abnormal and maladaptive behaviors. SIGNIFICANCE STATEMENT Several developmental brain disorders have been associated with gene duplications and deletions that serve to increase or decrease levels of encoded proteins. Cyfip1 is one such protein, but the role it plays in brain development is poorly understood. We asked whether decreased Cyfip1 levels altered the function of developing synapses. The data show that synapses with reduced Cyfip1 are larger and release neurotransmitter more rapidly. These effects are due to Cyfip1's role in actin polymerization and are reversed by expression of a Cyfip1 mutant protein retaining actin regulatory function or by inhibiting Rac1. Thus, Cyfip1 has a more prominent early role regulating presynaptic activity during a stage of development when activity helps to define neural pathways.
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Parental origin impairment of synaptic functions and behaviors in cytoplasmic FMRP interacting protein 1 (Cyfip1) deficient mice. Brain Res 2015; 1629:340-50. [PMID: 26474913 DOI: 10.1016/j.brainres.2015.10.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 09/01/2015] [Accepted: 10/06/2015] [Indexed: 11/30/2022]
Abstract
CYFIP1 maps to the interval between proximal breakpoint 1 (BP1) and breakpoint 2 (BP2) of chromosomal 15q11-q13 deletions that are implicated in the Angelman (AS) and Prader-Willi syndrome (PWS). There is only one breakpoint (BP3) at the distal end of deletion. CYFIP1 is deleted in AS patients with the larger class I deletion (BP1 to BP3) and the neurological presentations in these patients are more severe than that of patients with class II (BP2 to BP3) deletion. The haploinsufficiency of CYFIP1 is hypothesized to contribute to more severe clinical presentations in class I AS patients. The expression of CYFIP1 is suggested to be bi-allelic in literature but the possibility of parental origin of expression is not completely excluded. We generated and characterized Cyfip1 mutant mice. Homozygous Cyfip1 mice were early embryonic lethal. However, there was a parental origin specific effect between paternal Cyfip1 deficiency (m+/p-) and maternal deficiency (m-/p+) on both synaptic transmissions and behaviors in hippocampal CA1 synapses despite no evidence supporting the parental origin difference for the expression. Both m-/p+ and m+/p- showed the impaired input-output response and paired-pulse facilitation. While the long term-potentiation and group I mGluR mediated long term depression induced by DHPG was not different between Cyfip1 m-/p+ and m+/p- mice, the initial DHPG induced response was significantly enhanced in m-/p+ but not in m+/p- mice. m+/p- but not m-/p+ mice displayed increased freezing in cued fear conditioning and abnormal transitions in zero-maze test. The impaired synaptic transmission and behaviors in haploinsufficiency of Cyfip1 mice provide the evidence supporting the role of CYFIP1 modifying the clinical presentation of class I AS patients and in human neuropsychiatric disorders.
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Das DK, Tapias V, D'Aiuto L, Chowdari KV, Francis L, Zhi Y, Ghosh BA, Surti U, Tischfield J, Sheldon M, Moore JC, Fish K, Nimgaonkar V. Genetic and morphological features of human iPSC-derived neurons with chromosome 15q11.2 (BP1-BP2) deletions. MOLECULAR NEUROPSYCHIATRY 2015; 1:116-123. [PMID: 26528485 DOI: 10.1159/000430916] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Copy number variation on chromosome 15q11.2 (BP1-BP2) causes deletion of CYFIP1, NIPA1, NIPA2 and TUBGCP5; it also affects brain structure and elevates risk for several neurodevelopmental disorders that are associated with dendritic spine abnormalities. In rodents, altered cyfip1 expression changes dendritic spine morphology, motivating analyses of human neuronal cells derived from iPSCs (iPSC-neurons). METHODS iPSCs were generated from a mother and her offspring, both carrying the 15q11.2 (BP1-BP2) deletion, and a non-deletion control. Gene expression in the deletion region was estimated using quantitative real-time PCR assays. Neural progenitor cells (NPCs) and iPSC-neurons were characterized using immunocytochemistry. RESULTS CYFIP1, NIPA1, NIPA2 and TUBGCP5 gene expression was lower in iPSCs, NPCs and iPSC-neurons from the mother and her offspring in relation to control cells. CYFIP1 and PSD95 protein levels were lower in iPSC-neurons derived from the CNV bearing individuals using Western blot analysis. At 10 weeks post-differentiation, iPSC-neurons appeared to show dendritic spines and qualitative analysis suggested that dendritic morphology was altered in 15q11.2 deletion subjects compared with control cells. CONCLUSIONS The 15q11.2 (BP1-BP2) deletion is associated with reduced expression of four genes in iPSC-derived neuronal cells; it may also be associated altered iPSC-neuron dendritic morphology.
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Affiliation(s)
- D K Das
- University of Pittsburgh School of Medicine, Dept of Psychiatry
| | - V Tapias
- University of Pittsburgh, Dept. of Neurology
| | - L D'Aiuto
- University of Pittsburgh School of Medicine, Dept of Psychiatry
| | - K V Chowdari
- University of Pittsburgh School of Medicine, Dept of Psychiatry
| | - L Francis
- University of Pittsburgh School of Medicine, Dept of Psychiatry
| | - Y Zhi
- University of Pittsburgh School of Medicine, Dept of Psychiatry ; Tsinghua University School of Medicine
| | | | - U Surti
- University of Pittsburgh School of Medicine, Dept. of Pathology ; University of Pittsburgh, Graduate School of Public Health, Department of Human Genetics
| | - J Tischfield
- Dept. of Genetics and The Human Genome Institute of New Jersey, Rutgers, The State University of New Jersey
| | - M Sheldon
- Dept. of Genetics and The Human Genome Institute of New Jersey, Rutgers, The State University of New Jersey
| | - J C Moore
- Dept. of Genetics and The Human Genome Institute of New Jersey, Rutgers, The State University of New Jersey
| | - K Fish
- University of Pittsburgh School of Medicine, Dept of Psychiatry
| | - V Nimgaonkar
- University of Pittsburgh School of Medicine, Dept of Psychiatry ; University of Pittsburgh, Graduate School of Public Health, Department of Human Genetics
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Hashemi B, Bassett A, Chitayat D, Chong K, Feldman M, Flanagan J, Goobie S, Kawamura A, Lowther C, Prasad C, Siu V, So J, Tung S, Speevak M, Stavropoulos DJ, Carter MT. Deletion of 15q11.2(BP1-BP2) region: Further evidence for lack of phenotypic specificity in a pediatric population. Am J Med Genet A 2015; 167A:2098-102. [DOI: 10.1002/ajmg.a.37134] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/13/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Bita Hashemi
- Division of Clinical and Metabolics Genetics, Department of Pediatrics; The Hospital for Sick Children, University of Toronto; Toronto Ontario Canada
| | - Anne Bassett
- Clinical Genetics Research Program; Center for Addiction and Mental Health; Toronto Ontario Canada
| | - David Chitayat
- Division of Clinical and Metabolics Genetics, Department of Pediatrics; The Hospital for Sick Children, University of Toronto; Toronto Ontario Canada
- The Prenatal Diagnosis and Medical Genetics Program; Mount Sinai Hospital; Toronto Ontario Canada
| | - Karen Chong
- The Prenatal Diagnosis and Medical Genetics Program; Mount Sinai Hospital; Toronto Ontario Canada
| | - Mark Feldman
- Divison of Pediatric Medicine, Department of Pediatrics; The Hospital for Sick Children, University of Toronto; Toronto Ontario Canada
| | | | - Sharan Goobie
- Department of Pediatrics; Western University Children's Hospital Research Institute; London Ontario Canada
| | - Anne Kawamura
- Division of Developmental Pediatrics; Holland Bloorview Kids Rehabilitation Hospital; Toronto Ontario Canada
| | - Chelsea Lowther
- Clinical Genetics Research Program; Center for Addiction and Mental Health; Toronto Ontario Canada
| | - Chitra Prasad
- Department of Pediatrics; Western University Children's Hospital Research Institute; London Ontario Canada
| | - Victoria Siu
- Department of Pediatrics; Western University Children's Hospital Research Institute; London Ontario Canada
| | - Joyce So
- The Fred A. Litwin Family Center in Genetic Medicine; University Health Network and Mount Sinai Hospital; Toronto Canada
- Neurogenetics Lab, Neuroscience Research Department; Center for Addiction and Mental Health; Toronto Ontario Canada
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children; Laboratory Medicine and Pathobiology, University of Toronto; Toronto Ontario Canada
| | - Sharon Tung
- Genetics Program; North Bay Parry Sound District Health Unit; North Bay Ontario Canada
| | - Marsha Speevak
- Department of Laboratory Medicine and Pathobiology; University of Toronto; Toronto Ontario Canada
| | - Dimitri J. Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children; Laboratory Medicine and Pathobiology, University of Toronto; Toronto Ontario Canada
| | - Melissa T. Carter
- Division of Clinical and Metabolics Genetics, Department of Pediatrics; The Hospital for Sick Children, University of Toronto; Toronto Ontario Canada
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15q11.2 microdeletion (BP1–BP2) and developmental delay, behaviour issues, epilepsy and congenital heart disease: A series of 52 patients. Eur J Med Genet 2015; 58:140-7. [DOI: 10.1016/j.ejmg.2015.01.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 01/04/2015] [Indexed: 12/29/2022]
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Cox DM, Butler MG. The 15q11.2 BP1-BP2 microdeletion syndrome: a review. Int J Mol Sci 2015; 16:4068-82. [PMID: 25689425 PMCID: PMC4346944 DOI: 10.3390/ijms16024068] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/03/2015] [Accepted: 02/10/2015] [Indexed: 11/16/2022] Open
Abstract
Patients with the 15q11.2 BP1–BP2 microdeletion can present with developmental and language delay, neurobehavioral disturbances and psychiatric problems. Autism, seizures, schizophrenia and mild dysmorphic features are less commonly seen. The 15q11.2 BP1–BP2 microdeletion involving four genes (i.e., TUBGCP5, CYFIP1, NIPA1, NIPA2) is emerging as a recognized syndrome with a prevalence ranging from 0.57%–1.27% of patients presenting for microarray analysis which is a two to four fold increase compared with controls. Review of clinical features from about 200 individuals were grouped into five categories and included developmental (73%) and speech (67%) delays; dysmorphic ears (46%) and palatal anomalies (46%); writing (60%) and reading (57%) difficulties, memory problems (60%) and verbal IQ scores ≤75 (50%); general behavioral problems, unspecified (55%) and abnormal brain imaging (43%). Other clinical features noted but not considered as common were seizures/epilepsy (26%), autism spectrum disorder (27%), attention deficit disorder (ADD)/attention deficit hyperactivity disorder (ADHD) (35%), schizophrenia/paranoid psychosis (20%) and motor delay (42%). Not all individuals with the deletion are clinically affected, yet the collection of findings appear to share biological pathways and presumed genetic mechanisms. Neuropsychiatric and behavior disturbances and mild dysmorphic features are associated with genomic imbalances of the 15q11.2 BP1–BP2 region, including microdeletions, but with an apparent incomplete penetrance and variable expressivity.
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Affiliation(s)
- Devin M Cox
- Departments of Psychiatry & Behavioral Sciences, University of Kansas Medical Center, 3901 Rainbow Boulevard, MS 4015, Kansas City, KS 66160, USA.
| | - Merlin G Butler
- Departments of Psychiatry & Behavioral Sciences, University of Kansas Medical Center, 3901 Rainbow Boulevard, MS 4015, Kansas City, KS 66160, USA.
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Rudd DS, Axelsen M, Epping EA, Andreasen NC, Wassink TH. A genome-wide CNV analysis of schizophrenia reveals a potential role for a multiple-hit model. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:619-26. [PMID: 25228354 DOI: 10.1002/ajmg.b.32266] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 07/21/2014] [Indexed: 12/30/2022]
Abstract
Schizophrenia is a chronic and severe psychiatric disorder that is highly heritable. While both common and rare genetic variants contribute to disease risk, many questions still remain about disease etiology. We performed a genome-wide analysis of copy number variants (CNVs) in 166 schizophrenia subjects and 52 psychiatrically healthy controls. First, overall CNV characteristics were compared between cases and controls. The only statistically significant finding was that deletions comprised a greater proportion of CNVs in cases. High interest CNVs were then identified as conservative using the following filtering criteria: (i) known deleterious CNVs; (ii) CNVs > 1 Mb that were novel (not found in a database of control individuals); and (iii) CNVs < 1 Mb that were novel and that overlapped the coding region of a gene of interest. Cases did not harbor a higher proportion of conservative CNVs in comparison to controls. However, similar to previous reports, cases had a slightly higher proportion of individuals with clinically significant CNVs (known deleterious or conservative CNVs > 1 Mb) or with multiple conservative CNVs. Two case individuals with the highest burden of conservative CNVs also share a recurrent 15q11.2 BP1-2 deletion, indicating a role for a potential multiple-hit CNV model for schizophrenia. In total, we report three 15q11.2 BP1-2 deletion individuals with schizophrenia, adding to a growing body of evidence that this CNV is involved in disease etiology.
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Affiliation(s)
- Danielle S Rudd
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa; Department of Psychiatry, University of Iowa, Iowa City, Iowa
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The Psychological Challenges of Replacing Conventional Karyotyping with Genomic SNP Array Analysis in Prenatal Testing. J Clin Med 2014; 3:713-23. [PMID: 26237473 PMCID: PMC4449635 DOI: 10.3390/jcm3030713] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/21/2014] [Accepted: 06/16/2014] [Indexed: 01/15/2023] Open
Abstract
Pregnant couples tend to prefer a maximum of information about the health of their fetus. Therefore, we implemented whole genome microarray instead of conventional karyotyping (CK) for all indications for prenatal diagnosis (PND). The array detects more clinically relevant anomalies, including early onset disorders, not related to the indication and more genetic anomalies of yet unquantifiable risk, so-called susceptibility loci (SL) for mainly neurodevelopmental disorders. This manuscript highlights the psychological challenges in prenatal genetic counselling when using the array and provides counselling suggestions. First, we suggest that pre-test decision counselling should emphasize deliberation about what pregnant couples wish to learn about the future health of their fetus more than information about possible outcomes. Second, pregnant couples need support in dealing with SL. Therefore, in order to consider the SL in a proportionate perspective, the presence of phenotypes associated with SL in the family, the incidence of a particular SL in control populations and in postnatally ascertained patients needs highlighting during post-test genetic counselling. Finally, the decision that couples need to make about the course of their pregnancy is more complicated when the expected phenotype is variable and not quantifiable. Therefore, during post-test psychological counseling, couples should concretize the options of continuing and ending their pregnancy; all underlying feelings and thoughts should be made explicit, as well as the couple’s resources, in order to attain adequate decision-making. As such, pre- and post-test counselling aids pregnant couples in handling the uncertainties that may accompany offering a broader scope of genetic PND using the array.
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Chaste P, Sanders SJ, Mohan KN, Klei L, Song Y, Murtha MT, Hus V, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Lord C, Mane SM, Martin DM, Morrow EM, Walsh CA, Sutcliffe JS, State MW, Martin CL, Devlin B, Beaudet AL, Cook EH, Kim SJ. Modest impact on risk for autism spectrum disorder of rare copy number variants at 15q11.2, specifically breakpoints 1 to 2. Autism Res 2014; 7:355-62. [PMID: 24821083 PMCID: PMC6003409 DOI: 10.1002/aur.1378] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 03/19/2014] [Indexed: 01/24/2023]
Abstract
The proximal region of chromosome 15 is one of the genomic hotspots for copy number variants (CNVs). Among the rearrangements observed in this region, CNVs from the interval between the common breakpoints 1 and 2 (BP1 and BP2) have been reported cosegregating with autism spectrum disorder (ASD). Although evidence supporting an association between BP1-BP2 CNVs and autism accumulates, the magnitude of the effect of BP1-BP2 CNVs remains elusive, posing a great challenge to recurrence-risk counseling. To gain further insight into their pathogenicity for ASD, we estimated the penetrance of the BP1-BP2 CNVs for ASD as well as their effects on ASD-related phenotypes in a well-characterized ASD sample (n = 2525 families). Transmission disequilibrium test revealed significant preferential transmission only for the duplicated chromosome in probands (20T:9NT). The penetrance of the BP1-BP2 CNVs for ASD was low, conferring additional risks of 0.3% (deletion) and 0.8% (duplication). Stepwise regression analyses suggest a greater effect of the CNVs on ASD-related phenotype in males and when maternally inherited. Taken together, the results are consistent with BP1-BP2 CNVs as risk factors for autism. However, their effect is modest, more akin to that seen for common variants. To be consistent with the current American College of Medical Genetics guidelines for interpretation of postnatal CNV, the BP1-BP2 deletion and duplication CNVs would probably best be classified as variants of uncertain significance (VOUS): they appear to have an impact on risk, but one so modest that these CNVs do not merit pathogenic status.
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Affiliation(s)
- Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- FondaMental Foundation, Créteil, France
| | - Stephan J. Sanders
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, University of California at San Francisco, California, USA
| | - Kommu N. Mohan
- Department of Biological Sciences, BITS Pilani-Hyderabad Campus, Hyderabad, India
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Youeun Song
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michael T. Murtha
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Vanessa Hus
- Department of Psychology, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer K. Lowe
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - A. Jeremy Willsey
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, University of California at San Francisco, California, USA
| | - Daniel Moreno-De-Luca
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Timothy W. Yu
- Division of Genetics, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric Fombonne
- Department of Psychiatry, Oregon Health & Science University, Portland, Oregon, USA
| | - Daniel Geschwind
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Dorothy E. Grice
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
| | - David H. Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Catherine Lord
- Center for Autism and the Developing Brain, Weill Cornell Medical College, White Plains, New York, USA
| | | | - Donna M. Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Eric M. Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
- Department of Psychiatry and Human Behavior, Brown University, Providence, Rhode Island, USA
| | - Christopher A. Walsh
- Howard Hughes Medical Institute and Division of Genetics, Children's Hospital Boston, and Neurology and Pediatrics, Harvard Medical School Center for Life Sciences, Boston, Massachusetts, USA
| | - James S. Sutcliffe
- Departments of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Matthew W. State
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, University of California at San Francisco, California, USA
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Arthur L. Beaudet
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Soo-Jeong Kim
- Center for Integrative Brain Research, Seattle Children's Research Institute & Department of Psychiatry and Behavioral Science, University of Washington, Seattle, WA, USA
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Cafferkey M, Ahn JW, Flinter F, Ogilvie C. Phenotypic features in patients with 15q11.2(BP1-BP2) deletion: further delineation of an emerging syndrome. Am J Med Genet A 2014; 164A:1916-22. [PMID: 24715682 DOI: 10.1002/ajmg.a.36554] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 03/05/2014] [Indexed: 12/13/2022]
Abstract
15q11.2 deletions flanked by BP1 and BP2 of the Prader-Willi/Angelman syndrome region have recently been linked to a range of neurodevelopment disorders including intellectual disability, speech and language delay, motor delay, autism spectrum disorders, epilepsy, and schizophrenia. Array CGH analysis of 14,605 patients referred for diagnostic cytogenetic testing found that 83 patients (0.57%) carried the 15q11.2(BP1-BP2) deletion. Phenotypic frequencies in the deleted cohort (n = 83) were compared with frequencies in the non-deleted cohort (n = 14,522); developmental delay, motor delay, and speech and language delay were all more prevalent in the deleted cohort. Notably, motor delay was significantly more common (OR = 6.37). These data indicate that developmental delay, motor delay, and speech and language delay are common clinical features associated with this deletion, providing substantial evidence to support this CNV as a susceptibility locus for a spectrum of neurodevelopmental disorders. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Michiala Cafferkey
- Department of Medical and Molecular Genetics, King's College, London, UK
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Congenital Arthrogryposis: An Extension of the 15q11.2 BP1-BP2 Microdeletion Syndrome? Case Rep Genet 2014; 2014:127258. [PMID: 24778887 PMCID: PMC3978403 DOI: 10.1155/2014/127258] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 12/10/2013] [Indexed: 11/18/2022] Open
Abstract
The proximal 15q11–q13 region contains 5 breakpoints (BP1–BP5). The BP1-BP2 region spans approximately 500 kb and contains four evolutionarily conserved genes. The genes in this region are known to play a role in central nervous system development and/or function. Microdeletions within the 15q11.2 BP1-BP2 region have been reported in patients with neurological dysfunction, developmental delays, behavioral problems, and dysmorphic features. We report two unrelated subjects with the 15q11.2 BP1-BP2 microdeletion and presenting with congenital arthrogryposis, a feature which has not been previously reported as part of this newly recognized microdeletion syndrome. While arthrogryposis seen in these two subjects may be coincidental, we propose that congenital arthrogryposis may result from neurological dysfunction and involvement of the microdeletion of the 15q11.2 BP1-BP2 region, further expanding the phenotype of this microdeletion syndrome. We encourage others to report patients with this chromosome microdeletion and neurological findings to further characterize the clinical phenotype.
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Duplication of the 15q11-q13 region: clinical and genetic study of 30 new cases. Eur J Med Genet 2013; 57:5-14. [PMID: 24239951 DOI: 10.1016/j.ejmg.2013.10.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/31/2013] [Indexed: 11/23/2022]
Abstract
BACKGROUND 15q11-q13 region is an area of well-known susceptibility to genomic rearrangements, in which several breakpoints have been identified (BP1-BP5). Duplication of this region is observed in two instances: presence of a supernumerary marker chromosome (SMC) derived of chromosome 15, or interstitial tandem duplication. Duplications are clinically characterized by a variable phenotype that includes central hypotonia, developmental delay, speech delay, seizure, minor dysmorphic features and autism. METHODS Retrospective clinical and molecular study of 30 unrelated patients who were identified among the patients seen at the genetic clinics of Robert DEBRE hospital with microduplication of the 15q11-q13 region. RESULTS Fifteen patients presented with a supernumerary marker derived from chromosome 15. In fourteen cases the SMC was of large size, encompassing the Prader-Willi/Angelman critical region. All but one was maternal in origin. One patient had a PWS-like phenotype in absence of maternal UPD. In one case, the marker had a smaller size and contained only the BP1-BP2 region. Fifteen patients presented with interstitial duplication. Four cases were inherited from phenotypically normal parents (3 maternal and 1 paternal). Phenotypic features were somewhat variable and 57% presented with autism. Twelve patients showed cerebral anomalies and 18 patients had an abnormal EEG with a typical, recognizable pattern of excessive diffuse rapid spikes in the waking record, similar to the pattern observed after benzodiazepine exposure. Duplication of paternally expressed genes MKRN3, MAGEL2 and NDN in two autistic patients without extra material of a neighboring region enhances their likelihood to be genes related to autism.
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De Wolf V, Brison N, Devriendt K, Peeters H. Genetic counseling for susceptibility loci and neurodevelopmental disorders: the del15q11.2 as an example. Am J Med Genet A 2013; 161A:2846-54. [PMID: 24123946 DOI: 10.1002/ajmg.a.36209] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 07/26/2013] [Indexed: 01/09/2023]
Abstract
In recent years, several recurrent copy number variations (CNVs) that confer risk of neurodevelopmental disorders have been identified (e.g., del and dup 16p11.2, del15q13.3, del and dup 1q21.1, del16p13.3, del15q11.2). They are often inherited from an unaffected parent and lack phenotypic specificity. Although there is growing evidence from association studies to consider them as susceptibility CNVs, their clinical utility is debated. Yet the clinician is frequently challenged to deal with these counseling situations without guidelines or consensus. In this report, counseling issues and research opportunities are discussed, with the recurrent 15q11.2 BP1-BP2 (including CYFIP1, NIPA1, NIPA2, TUBGCP5) as an example. Several clinical reports have been published describing patients with del15q11.2 featuring intellectual disability, developmental delay, neurological problems, autism spectrum disorder (ASD), attention problems, speech delay, and dysmorphism. The del15q11.2 was found to be significantly associated with intellectual disability, schizophrenia, epilepsy, and ASD. In this report we discuss how patient-specific and family-specific information may alter the interpretation of del15q11.2 as a contributing factor to the disorder in practical counseling situations. In addition, an association study for ASD in a Belgian Flemish cohort and an overview of reported association studies, clinical reports and genomics data for del15q11.2 are presented.
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Affiliation(s)
- Veerle De Wolf
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
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29
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De Rubeis S, Pasciuto E, Li K, Fernández E, Di Marino D, Buzzi A, Ostroff L, Klann E, Zwartkruis FJ, Komiyama N, Grant SG, Poujol C, Choquet D, Achsel T, Posthuma D, Smit A, Bagni C. CYFIP1 coordinates mRNA translation and cytoskeleton remodeling to ensure proper dendritic spine formation. Neuron 2013; 79:1169-82. [PMID: 24050404 PMCID: PMC3781321 DOI: 10.1016/j.neuron.2013.06.039] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2013] [Indexed: 11/30/2022]
Abstract
The CYFIP1/SRA1 gene is located in a chromosomal region linked to various neurological disorders, including intellectual disability, autism, and schizophrenia. CYFIP1 plays a dual role in two apparently unrelated processes, inhibiting local protein synthesis and favoring actin remodeling. Here, we show that brain-derived neurotrophic factor (BDNF)-driven synaptic signaling releases CYFIP1 from the translational inhibitory complex, triggering translation of target mRNAs and shifting CYFIP1 into the WAVE regulatory complex. Active Rac1 alters the CYFIP1 conformation, as demonstrated by intramolecular FRET, and is key in changing the equilibrium of the two complexes. CYFIP1 thus orchestrates the two molecular cascades, protein translation and actin polymerization, each of which is necessary for correct spine morphology in neurons. The CYFIP1 interactome reveals many interactors associated with brain disorders, opening new perspectives to define regulatory pathways shared by neurological disabilities characterized by spine dysmorphogenesis.
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Affiliation(s)
- Silvia De Rubeis
- VIB Center for Biology of Disease, KULeuven, 3000 Leuven, Belgium
- Center for Human Genetics and Leuven Institute for Neuroscience and Disease (LIND), KULeuven, 3000 Leuven, Belgium
| | - Emanuela Pasciuto
- VIB Center for Biology of Disease, KULeuven, 3000 Leuven, Belgium
- Center for Human Genetics and Leuven Institute for Neuroscience and Disease (LIND), KULeuven, 3000 Leuven, Belgium
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Medical Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Esperanza Fernández
- VIB Center for Biology of Disease, KULeuven, 3000 Leuven, Belgium
- Center for Human Genetics and Leuven Institute for Neuroscience and Disease (LIND), KULeuven, 3000 Leuven, Belgium
| | - Daniele Di Marino
- VIB Center for Biology of Disease, KULeuven, 3000 Leuven, Belgium
- Center for Human Genetics and Leuven Institute for Neuroscience and Disease (LIND), KULeuven, 3000 Leuven, Belgium
| | - Andrea Buzzi
- VIB Center for Biology of Disease, KULeuven, 3000 Leuven, Belgium
- Center for Human Genetics and Leuven Institute for Neuroscience and Disease (LIND), KULeuven, 3000 Leuven, Belgium
| | | | - Eric Klann
- Center for Neural Science, New York University, New York, NY 10003, USA
| | - Fried J.T. Zwartkruis
- Molecular Cancer Research, Center for Biomedical Genetics and Cancer Genomics Center, University Medical Center Utrecht, 3584 CG Utrecht
| | - Noboru H. Komiyama
- Centre for Clinical Brain Sciences and Centre for Neuroregeneration, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Seth G.N. Grant
- Centre for Clinical Brain Sciences and Centre for Neuroregeneration, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Christel Poujol
- CNRS, Bordeaux Imaging Center, UMS 3420, 33000 Bordeaux, France
- University of Bordeaux, UMS 3420, 33077, Bordeaux, France
| | - Daniel Choquet
- CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, 33000 Bordeaux, France
- University of Bordeaux, UMR 5297, 33077, Bordeaux, France
| | - Tilmann Achsel
- VIB Center for Biology of Disease, KULeuven, 3000 Leuven, Belgium
- Center for Human Genetics and Leuven Institute for Neuroscience and Disease (LIND), KULeuven, 3000 Leuven, Belgium
| | - Danielle Posthuma
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Medical Center Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Medical Center Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus University Medical Center/Sophia Child Hospital, 3000 CB Rotterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Medical Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Claudia Bagni
- VIB Center for Biology of Disease, KULeuven, 3000 Leuven, Belgium
- Center for Human Genetics and Leuven Institute for Neuroscience and Disease (LIND), KULeuven, 3000 Leuven, Belgium
- Department of Biomedicine and Prevention, University “Tor Vergata,” 00133 Rome, Italy
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30
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Zhao Q, Li T, Zhao X, Huang K, Wang T, Li Z, Ji J, Zeng Z, Zhang Z, Li K, Feng G, St Clair D, He L, Shi Y. Rare CNVs and tag SNPs at 15q11.2 are associated with schizophrenia in the Han Chinese population. Schizophr Bull 2013; 39:712-9. [PMID: 22317777 PMCID: PMC3627771 DOI: 10.1093/schbul/sbr197] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Rare copy number variations (CNVs) were involved in the etiology of neuropsychiatric disorders, and some of them appeared to be shared risk factors for several different diseases. One of those promising loci is the CNV at 15q11.2, including 4 genes, TUBGCP5, CYFIP1, NIPA2, and NIPA1. Several studies showed that microdeletions at this locus were significant associated with schizophrenia. In the current study, we investigated the role of both rare CNVs and common single nucleotide polymorphisms (SNPs) at 15q11.2 in schizophrenia in the Chinese Han population. METHODS We screened deletions at 15q11.2 in 2058 schizophrenia patients and 3275 normal controls in Chinese Han population by Affymetrix 500K/6.0 SNP arrays and SYBR green real-time polymerase chain reaction and then validated deletions by multiplex ligation-dependent probe amplification and Taqman real-time assays. We successfully genotyped 27 tag SNPs in total and tested associations in 1144 schizophrenia cases and 1144 normal controls. RESULTS We found a triple increase of deletions in cases over controls, with OR=4.45 (95% CI=1.36-14.60) and P=.014. In the analysis of common SNPs, we found that the most significant SNP in schizophrenia was rs4778334 (OR=.72, 95% CI=0.60-0.87, allelic P=.0056 after permutation, genotypic P=.015 after permutation). We also found SNP rs1009153 in CYFIP1 was associated with schizophrenia (OR=0.82, 95% CI=0.73-0.93, allelic P=.044 after permutation). CONCLUSION We found that both rare deletions and common variants at 15q11.2 were associated with schizophrenia in the Chinese Han population.
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Affiliation(s)
- Qian Zhao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China,Changning Mental Health Center, Bio-X Institutes Affiliated Hospital, Shanghai Jiao Tong University, 299 XieHe Road, Shanghai 200042, People's Republic of China
| | - Tao Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China,Changning Mental Health Center, Bio-X Institutes Affiliated Hospital, Shanghai Jiao Tong University, 299 XieHe Road, Shanghai 200042, People's Republic of China
| | - XinZhi Zhao
- Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Ke Huang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ti Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - ZhiQiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jue Ji
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhen Zeng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhao Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Kan Li
- East China University of Science and Technology, Shanghai, People's Republic of China
| | - GuoYin Feng
- Shanghai Institute of Mental Health, Shanghai, People's Republic of China
| | - David St Clair
- Department of Mental Health, University of Aberdeen, Aberdeen, UK
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China,Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China,Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, China,Institute for Nutritional Sciences, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - YongYong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People's Republic of China,Changning Mental Health Center, Bio-X Institutes Affiliated Hospital, Shanghai Jiao Tong University, 299 XieHe Road, Shanghai 200042, People's Republic of China,Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, China,To whom correspondence should be addressed; tel: 86-21-62933338, fax: 86-21-62933338, e-mail:
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Grayton HM, Fernandes C, Rujescu D, Collier DA. Copy number variations in neurodevelopmental disorders. Prog Neurobiol 2012; 99:81-91. [DOI: 10.1016/j.pneurobio.2012.07.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 07/20/2011] [Accepted: 07/09/2012] [Indexed: 10/28/2022]
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Haploinsufficiency of Cyfip1 produces fragile X-like phenotypes in mice. PLoS One 2012; 7:e42422. [PMID: 22900020 PMCID: PMC3416859 DOI: 10.1371/journal.pone.0042422] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 07/09/2012] [Indexed: 11/22/2022] Open
Abstract
Background Copy number variation (CNV) at the 15q11.2 region, which includes a gene that codes for CYFIP1 (cytoplasmic FMR1 interacting protein 1), has been implicated in autism, intellectual disability and additional neuropsychiatric phenotypes. In the current study we studied the function of Cyfip1 in synaptic physiology and behavior, using mice with a disruption of the Cyfip1 gene. Methodology/Principal Findings We observed that in Cyfip1 heterozygous mice metabotropic glutamate receptor (mGluR)-dependent long-term depression (LTD) induced by paired-pulse low frequency stimulation (PP-LFS) was significantly increased in comparison to wildtype mice. In addition, mGluR-LTD was not affected in the presence of protein synthesis inhibitor in the Cyfip1 heterozygous mice, while the same treatment inhibited LTD in wildtype littermate controls. mGluR-agonist (RS)-3,5-dihydroxyphenylglycine (DHPG)-induced LTD was also significantly increased in hippocampal slices from Cyfip1 heterozygous mice and again showed independence from protein synthesis only in the heterozygous animals. Furthermore, we observed that the mammalian Target of Rapamycin (mTOR) inhibitor rapamycin was only effective at reducing mGluR-LTD in wildtype animals. Behaviorally, Cyfip1 heterozygous mice showed enhanced extinction of inhibitory avoidance. Application of both mGluR5 and mGluR1 antagonist to slices from Cyfip1 heterozygous mice reversed the increase in DHPG-induced LTD in these mice. Conclusions/Significance These results demonstrate that haploinsufficiency of Cyfip1 mimics key aspects of the phenotype of Fmr1 knockout mice and are consistent with the hypothesis that these effects are mediated by interaction of Cyfip1 and Fmrp in regulating activity-dependent translation. The data provide support for a model where CYFIP1 haploinsufficiency in patients results in intermediate phenotypes increasing risk for neuropsychiatric disorders.
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Madrigal I, Rodríguez-Revenga L, Xunclà M, Milà M. 15q11.2 microdeletion and FMR1 premutation in a family with intellectual disabilities and autism. Gene 2012; 508:92-5. [PMID: 22842191 DOI: 10.1016/j.gene.2012.07.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 06/04/2012] [Accepted: 07/15/2012] [Indexed: 12/20/2022]
Abstract
Genomic rearrangements of chromosome 15q11-q13 are responsible for diverse phenotypes including intellectual disabilities and autism. 15q11.2 deletion, implicating common PWS/AS breakpoints BP1-BP2, has been described in patients with delayed motor and speech development and behavioural problems. Here we report the clinical and molecular characterisation of a maternally inherited BP1-BP2 deletion in two siblings with intellectual, motor and speech delay, autistic syndrome disorder and several dysmorphic features. One of the patients was also a carrier of an FMR1 allele in the low premutation range. The four genes within the deletion were under-expressed in all deletion carriers but FMR1 mRNA levels remained normal. Our results suggest that BP1-BP2 deletion could be considered as a risk factor for neuropsychological phenotypes and that it presents with variable clinical expressivity.
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Crespi BJ, Crofts HJ. Association testing of copy number variants in schizophrenia and autism spectrum disorders. J Neurodev Disord 2012; 4:15. [PMID: 22958593 PMCID: PMC3436704 DOI: 10.1186/1866-1955-4-15] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 05/30/2012] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Autism spectrum disorders and schizophrenia have been associated with an overlapping set of copy number variant loci, but the nature and degree of overlap in copy number variants (deletions compared to duplications) between these two disorders remains unclear. METHODS We systematically evaluated three lines of evidence: (1) the statistical bases for associations of autism spectrum disorders and schizophrenia with a set of the primary CNVs thus far investigated, from previous studies; (2) data from case series studies on the occurrence of these CNVs in autism spectrum disorders, especially among children, and (3) data on the extent to which the CNVs were associated with intellectual disability and developmental, speech, or language delays. We also conducted new analyses of existing data on these CNVs in autism by pooling data from seven case control studies. RESULTS Four of the CNVs considered, dup 1q21.1, dup 15q11-q13, del 16p11.2, and dup 22q11.21, showed clear statistical evidence as autism risk factors, whereas eight CNVs, del 1q21.1, del 3q29, del 15q11.2, del 15q13.3, dup 16p11.2, dup 16p13.1, del 17p12, and del 22q11.21, were strongly statistically supported as risk factors for schizophrenia. Three of the CNVs, dup 1q21.1, dup 16p11.2, and dup 16p13.1, exhibited statistical support as risk factors for both autism and schizophrenia, although for each of these CNVs statistical significance was nominal for tests involving one of the two disorders. For the CNVs that were statistically associated with schizophrenia but were not statistically associated with autism, a notable number of children with the CNVs have been diagnosed with autism or ASD; children with these CNVs also demonstrate a high incidence of intellectual disability and developmental, speech, or language delays. CONCLUSIONS These findings suggest that although CNV loci notably overlap between autism and schizophrenia, the degree of strongly statistically supported overlap in specific CNVs at these loci remains limited. These analyses also suggest that relatively severe premorbidity to CNV-associated schizophrenia in children may sometimes be diagnosed as autism spectrum disorder.
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Affiliation(s)
- Bernard J Crespi
- Department of Biosciences, Simon Fraser University, Burnaby, BC, V5A 1 S6, Canada
| | - Helen J Crofts
- Department of Biosciences, Simon Fraser University, Burnaby, BC, V5A 1 S6, Canada
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Affiliation(s)
- Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA.
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36
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Leblond CS, Heinrich J, Delorme R, Proepper C, Betancur C, Huguet G, Konyukh M, Chaste P, Ey E, Rastam M, Anckarsäter H, Nygren G, Gillberg IC, Melke J, Toro R, Regnault B, Fauchereau F, Mercati O, Lemière N, Skuse D, Poot M, Holt R, Monaco AP, Järvelä I, Kantojärvi K, Vanhala R, Curran S, Collier DA, Bolton P, Chiocchetti A, Klauck SM, Poustka F, Freitag CM, Waltes R, Kopp M, Duketis E, Bacchelli E, Minopoli F, Ruta L, Battaglia A, Mazzone L, Maestrini E, Sequeira AF, Oliveira B, Vicente A, Oliveira G, Pinto D, Scherer SW, Zelenika D, Delepine M, Lathrop M, Bonneau D, Guinchat V, Devillard F, Assouline B, Mouren MC, Leboyer M, Gillberg C, Boeckers TM, Bourgeron T. Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders. PLoS Genet 2012; 8:e1002521. [PMID: 22346768 PMCID: PMC3276563 DOI: 10.1371/journal.pgen.1002521] [Citation(s) in RCA: 308] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 12/11/2011] [Indexed: 01/15/2023] Open
Abstract
Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disorders with a complex inheritance pattern. While many rare variants in synaptic proteins have been identified in patients with ASD, little is known about their effects at the synapse and their interactions with other genetic variations. Here, following the discovery of two de novo SHANK2 deletions by the Autism Genome Project, we identified a novel 421 kb de novo SHANK2 deletion in a patient with autism. We then sequenced SHANK2 in 455 patients with ASD and 431 controls and integrated these results with those reported by Berkel et al. 2010 (n = 396 patients and n = 659 controls). We observed a significant enrichment of variants affecting conserved amino acids in 29 of 851 (3.4%) patients and in 16 of 1,090 (1.5%) controls (P = 0.004, OR = 2.37, 95% CI = 1.23-4.70). In neuronal cell cultures, the variants identified in patients were associated with a reduced synaptic density at dendrites compared to the variants only detected in controls (P = 0.0013). Interestingly, the three patients with de novo SHANK2 deletions also carried inherited CNVs at 15q11-q13 previously associated with neuropsychiatric disorders. In two cases, the nicotinic receptor CHRNA7 was duplicated and in one case the synaptic translation repressor CYFIP1 was deleted. These results strengthen the role of synaptic gene dysfunction in ASD but also highlight the presence of putative modifier genes, which is in keeping with the "multiple hit model" for ASD. A better knowledge of these genetic interactions will be necessary to understand the complex inheritance pattern of ASD.
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Affiliation(s)
- Claire S. Leblond
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 “Genes, synapses and cognition,” Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
| | - Jutta Heinrich
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Richard Delorme
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 “Genes, synapses and cognition,” Institut Pasteur, Paris, France
- Assistance Publique-Hôpitaux de Paris, Robert Debré Hospital, Department of Child and Adolescent Psychiatry, Paris, France
| | | | - Catalina Betancur
- INSERM, U952, Paris, France
- CNRS, UMR 7224, Paris, France
- UPMC Univ Paris 06, Paris, France
| | - Guillaume Huguet
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 “Genes, synapses and cognition,” Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
| | - Marina Konyukh
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 “Genes, synapses and cognition,” Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
| | - Pauline Chaste
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 “Genes, synapses and cognition,” Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
| | - Elodie Ey
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 “Genes, synapses and cognition,” Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
| | - Maria Rastam
- Department of Clinical Sciences in Lund, Lund University, Lund, Sweden
| | | | - Gudrun Nygren
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Göteborg, Sweden
| | - I. Carina Gillberg
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Göteborg, Sweden
| | - Jonas Melke
- Institute of Neuroscience and Physiology, Department of Pharmacology, Gothenburg University, Göteborg, Sweden
| | - Roberto Toro
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 “Genes, synapses and cognition,” Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
| | - Beatrice Regnault
- Eukaryote Genotyping Platform, Genopole, Institut Pasteur, Paris, France
| | - Fabien Fauchereau
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 “Genes, synapses and cognition,” Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
| | - Oriane Mercati
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 “Genes, synapses and cognition,” Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
| | - Nathalie Lemière
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 “Genes, synapses and cognition,” Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
| | - David Skuse
- Behavioural and Brain Sciences Unit, Institute of Child Health, University College London, London, United Kingdom
| | - Martin Poot
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Richard Holt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anthony P. Monaco
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Katri Kantojärvi
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Raija Vanhala
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Sarah Curran
- Academic Department of Child and Adolescent Psychiatry, Institute of Psychiatry, King's College London, London, United Kingdom
| | - David A. Collier
- Social Genetic Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Patrick Bolton
- Academic Department of Child and Adolescent Psychiatry, Institute of Psychiatry, King's College London, London, United Kingdom
- Social Genetic Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Andreas Chiocchetti
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sabine M. Klauck
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Fritz Poustka
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University, Frankfurt am Main, Germany
| | - Christine M. Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University, Frankfurt am Main, Germany
| | - Regina Waltes
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University, Frankfurt am Main, Germany
| | - Marnie Kopp
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University, Frankfurt am Main, Germany
| | - Eftichia Duketis
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University, Frankfurt am Main, Germany
| | - Elena Bacchelli
- Department of Biology, University of Bologna, Bologna, Italy
| | | | - Liliana Ruta
- Division of Child Neurology and Psychiatry, Department of Paediatrics, University of Catania, Catania, Italy
| | - Agatino Battaglia
- Stella Maris Clinical Research Institute for Child and Adolescent Neuropsychiatry, Pisa, Italy
| | - Luigi Mazzone
- Division of Child Neurology and Psychiatry, Department of Pediatrics, University of Catania, Catania, Italy
| | - Elena Maestrini
- Department of Biology, University of Bologna, Bologna, Italy
| | - Ana F. Sequeira
- Instituto Nacional de Saude Dr Ricardo Jorge, Lisbon, Portugal
- Instituto Gulbenkian de Ciencia, Oeiras, Portugal
- Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Barbara Oliveira
- Instituto Nacional de Saude Dr Ricardo Jorge, Lisbon, Portugal
- Instituto Gulbenkian de Ciencia, Oeiras, Portugal
- Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Astrid Vicente
- Instituto Nacional de Saude Dr Ricardo Jorge, Lisbon, Portugal
- Instituto Gulbenkian de Ciencia, Oeiras, Portugal
- Center for Biodiversity, Functional and Integrative Genomics, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Guiomar Oliveira
- Unidade Neurodesenvolvimento e Autismo, Centro Investigação e Formação Clinica, Hospital Pediátrico Coimbra e Faculdade Medicina, Universidade Coimbra, Coimbra, Portugal
| | - Dalila Pinto
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | | | | | | | - Dominique Bonneau
- INSERM U771 and CNRS 6214, Angers, France
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, Angers, France
| | - Vincent Guinchat
- CADIPA–Centre de Ressources Autisme Rhône-Alpes, Saint Egrève, France
| | | | | | - Marie-Christine Mouren
- Assistance Publique-Hôpitaux de Paris, Robert Debré Hospital, Department of Child and Adolescent Psychiatry, Paris, France
| | - Marion Leboyer
- INSERM, U955, Psychiatrie Génétique, Créteil, France
- Université Paris Est, Faculté de Médecine, Créteil, France
- AP-HP, Hôpital H. Mondor–A. Chenevier, Département de Psychiatrie, Créteil, France
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Göteborg, Sweden
- Institute of Child Health, University College London, London, United Kingdom
| | | | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 “Genes, synapses and cognition,” Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
- * E-mail:
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Genetics and Epigenetics of Autism Spectrum Disorders. RESEARCH AND PERSPECTIVES IN NEUROSCIENCES 2012. [DOI: 10.1007/978-3-642-27913-3_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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De Rubeis S, Bagni C. Regulation of molecular pathways in the Fragile X Syndrome: insights into Autism Spectrum Disorders. J Neurodev Disord 2011; 3:257-69. [PMID: 21842222 PMCID: PMC3167042 DOI: 10.1007/s11689-011-9087-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Accepted: 07/07/2011] [Indexed: 11/01/2022] Open
Abstract
The Fragile X syndrome (FXS) is a leading cause of intellectual disability (ID) and autism. The disease is caused by mutations or loss of the Fragile X Mental Retardation Protein (FMRP), an RNA-binding protein playing multiple functions in RNA metabolism. The expression of a large set of neuronal mRNAs is altered when FMRP is lost, thus causing defects in neuronal morphology and physiology. FMRP regulates mRNA stability, dendritic targeting, and protein synthesis. At synapses, FMRP represses protein synthesis by forming a complex with the Cytoplasmic FMRP Interacting Protein 1 (CYFIP1) and the cap-binding protein eIF4E. Here, we review the clinical, genetic, and molecular aspects of FXS with a special focus on the receptor signaling that regulates FMRP-dependent protein synthesis. We further discuss the FMRP-CYFIP1 complex and its potential relevance for ID and autism.
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Affiliation(s)
- Silvia De Rubeis
- Center for Human Genetics, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
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39
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Srebniak M, Boter M, Oudesluijs G, Joosten M, Govaerts L, Van Opstal D, Galjaard RJH. Application of SNP array for rapid prenatal diagnosis: implementation, genetic counselling and diagnostic flow. Eur J Hum Genet 2011; 19:1230-7. [PMID: 21694736 DOI: 10.1038/ejhg.2011.119] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We report on the validation and implementation of the HumanCytoSNP-12 array (Illumina) (HCS) in prenatal diagnosis. In total, 64 samples were used to validate the Illumina platform (20 with a known (sub) microscopic chromosome abnormality, 5 with known maternal cell contamination (MCC) and 39 normal control samples). There were no false-positive or false-negative results. In addition to the diagnostic possibilities of arrayCGH, the HCS allows detection of regions of homozygosity (ROH), triploidy and helps recognising MCC. Moreover, in two cases of MCC, a deletion was correctly detected. Furthermore we found out that only about 50 ng of DNA is required, which allows a reporting time of only 3 days. We also present a prospective pilot study of 61 fetuses with ultrasound abnormalities and a normal karyotype tested with HCS. In 4 out of 61 (6.5%) fetuses, a clinically relevant abnormality was detected. We designed and present pre-test genetic counselling information on categories of possible test outcomes. On the basis of this information, about 90% of the parents chose to be informed about adverse health outcomes of their future child at infancy and childhood, and 55% also about outcomes at an adult stage. The latter issue regarding the right of the future child itself to decide whether or not to know this information needs to be addressed.
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Affiliation(s)
- Malgorzata Srebniak
- Department of Clinical Genetics, Erasmus Medical Center, Dr Molewaterplein 50, Rotterdam, The Netherlands.
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40
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von der Lippe C, Rustad C, Heimdal K, Rødningen O. 15q11.2 microdeletion – Seven new patients with delayed development and/or behavioural problems. Eur J Med Genet 2011; 54:357-60. [DOI: 10.1016/j.ejmg.2010.12.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 12/14/2010] [Indexed: 11/30/2022]
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Abstract
AbstractRecent genome-wide association studies in schizophrenia have provided strongest evidence for association and this strengthened when the affected phenotype included bipolar disorder suggesting that genes may not always associate with operationalised diagnostic entities. Several further large Genome Wide Association (GWA) studies on schizophrenia are under way and identified and replicated further loci in well-powered cohorts. The last 2 years have also witnessed an explosion of interest in human Copy Number Variants (CNVs). Deletions recently identified in schizophrenia (1q21.1; 2p16.3; 15q11.2; 15q13.3) have also been most recently found in further neurodevelopmental diseases. Thus, a significant fraction of individuals with neurodevelopmental diseases including schizophrenia carry CNVs and many will be defined as “genomic disorders” in the coming years. These findings could represent a decisive step towards understanding the causes of this severe mental disorder as well as developing new potential treatments. There is new hope that these new avenues will help understanding the neurobiology of schizophrenia in more depth leading to the development of new innovative diagnostic tools and therapies as was the case after the discovery of rare APP and presenilin 1 and 2 mutations in Alzheimer's disease.
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42
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Sempere Pérez A, Manchón Trives I, Palazón Azorín I, Alcaraz Más L, Pérez Lledó E, Galán Sánchez F. [15Q11.2 (BP1-BP2) microdeletion, a new syndrome with variable expressivity]. An Pediatr (Barc) 2011; 75:58-62. [PMID: 21419731 DOI: 10.1016/j.anpedi.2011.01.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 01/31/2011] [Indexed: 11/19/2022] Open
Abstract
The case of a boy with psychomotor retardation and dysmorphic features is presented. He has a 1.5 Mb 15q11.2 microdeletion of paternal origin diagnosed by aCGH. The deletion is located between breakpoints BP1 and BP2 of the Prader-Willi/Angelman syndromes critical region. Clinical features in our patient fit well with those described in ten cases of pure BP1-BP2 deletion published to date.
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Affiliation(s)
- A Sempere Pérez
- Neuropediatría, Hospital General Universitario, Alicante, España
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43
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Microdeletion/microduplication of proximal 15q11.2 between BP1 and BP2: a susceptibility region for neurological dysfunction including developmental and language delay. Hum Genet 2011; 130:517-28. [PMID: 21359847 DOI: 10.1007/s00439-011-0970-4] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 02/10/2011] [Indexed: 10/18/2022]
Abstract
The proximal long arm of chromosome 15 has segmental duplications located at breakpoints BP1-BP5 that mediate the generation of NAHR-related microdeletions and microduplications. The classical Prader-Willi/Angelman syndrome deletion is flanked by either of the proximal BP1 or BP2 breakpoints and the distal BP3 breakpoint. The larger Type I deletions are flanked by BP1 and BP3 in both Prader-Willi and Angelman syndrome subjects. Those with this deletion are reported to have a more severe phenotype than individuals with either Type II deletions (BP2-BP3) or uniparental disomy 15. The BP1-BP2 region spans approximately 500 kb and contains four evolutionarily conserved genes that are not imprinted. Reports of mutations or disturbed expression of these genes appear to impact behavioral and neurological function in affected individuals. Recently, reports of deletions and duplications flanked by BP1 and BP2 suggest an association with speech and motor delays, behavioral problems, seizures, and autism. We present a large cohort of subjects with copy number alteration of BP1 to BP2 with common phenotypic features. These include autism, developmental delay, motor and language delays, and behavioral problems, which were present in both cytogenetic groups. Parental studies demonstrated phenotypically normal carriers in several instances, and mildly affected carriers in others, complicating phenotypic association and/or causality. Possible explanations for these results include reduced penetrance, altered gene dosage on a particular genetic background, or a susceptibility region as reported for other areas of the genome implicated in autism and behavior disturbances.
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Hou A, Lin SP, Ho SY, Chen CFJ, Lin HY, Chen YJ, Huang CY, Chiu HC, Chuang CK, Chen KS. Genetic studies of Prader-Willi patients provide evidence for conservation of genomic architecture in proximal chromosome 15q. Ann Hum Genet 2011; 75:211-21. [PMID: 21198515 DOI: 10.1111/j.1469-1809.2010.00633.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Prader-Willi syndrome (PWS) is a neurogenetic disorder associated with recurrent genomic recombination involving low copy repeats (LCRs) located in the human chromosome 15q11-q13. Previous studies of PWS patients from Asia suggested that there is a higher incidence of deletion and lower incidence of maternal uniparental disomy (mUPD) compared to that of Western populations. In this report, we present genetic etiology of 28 PWS patients from Taiwan. Consistent with the genetic etiology findings from Western populations, the type II deletion appears to be the most common deletion subtype. Furthermore, the ratio of the two most common deletion subtypes and the ratio of the maternal heterodisomy to isodisomy cases observed from this study are in agreement with previous findings from Western populations. In addition, we identified and further mapped the deletion breakpoints in two patients with atypical deletions using array CGH (comparative genomic hybridization). Despite the relatively small numbers of patients in each subgroup, our findings suggest that the genomic architecture responsible for the recurrent recombination in PWS is conserved in Taiwanese of the Han Chinese heritage and Western populations, thereby predisposing chromosome 15q11-q13 to a similar risk of rearrangements.
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Affiliation(s)
- Aihua Hou
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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45
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Pedersen K, Wiechec E, Madsen BE, Overgaard J, Hansen LL. A simple way to evaluate self-designed probes for tumor specific Multiplex Ligation-dependent Probe Amplification (MLPA). BMC Res Notes 2010; 3:179. [PMID: 20579386 PMCID: PMC2913922 DOI: 10.1186/1756-0500-3-179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 06/26/2010] [Indexed: 11/30/2022] Open
Abstract
Background The Multiplex Ligation-dependent Probe Amplification (MLPA) is widely used for analysis of copy number variations (CNVs) in single or multiple loci. MLPA is a versatile methodology and important tool in cancer research; it provides precise information on increased or decreased copy number at specific loci as opposed to loss of heterozygosity (LOH) studies based upon microsatellite analysis. Pre-designed MLPA kits and software are commercially available to analyze multiple exons, genes, and genomic regions. However, an increasing demand for new gene specific assays makes it necessary to self-design new MLPA probes for which the available software may not be applicable. During evaluation of new self-designed reference probes, we encountered a number of problems, especially when applying the MLPA methodology to tumor samples. Findings DNA samples from 48 unaffected individuals and 145 breast cancer patients were used to evaluate 11 self-designed MLPA probes and determine the cut-off values for CNV, before applying the MLPA probes to normalize the target probes in a cohort of affected individuals. To test the calculation strategy, three probes were designed to cover regions in Regulator of G-protein Signaling 8 (RGS8), which we previously have identified as being affected by allelic imbalance by LOH analysis across RGS8 in the cohort comprising 145 breast tumors. Agreement between the LOH results and the results obtained by each of the three MLPA probes in RGS8 was found for 64%, 73%, and 91%, of the analyzed samples, respectively. Conclusion Here, we present a straightforward method, based upon the normalization pattern in both unaffected and affected individuals, to evaluate self-designed reference probes and to calculate CNV for the MLPA assay with specific focus on the difficulties when analyzing tumor DNA.
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Affiliation(s)
- Kristina Pedersen
- Institute of Human Genetics, The Bartholin building, Wilhelm Meyers Allé 4, University of Aarhus, DK-8000 Aarhus C, Denmark.
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46
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van der Zwaag B, Staal WG, Hochstenbach R, Poot M, Spierenburg HA, de Jonge MV, Verbeek NE, van ’t Slot R, van Es MA, Staal FJ, Freitag CM, Buizer-Voskamp JE, Nelen MR, van den Berg LH, van Amstel HKP, van Engeland H, Burbach JPH. A co-segregating microduplication of chromosome 15q11.2 pinpoints two risk genes for autism spectrum disorder. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:960-6. [PMID: 20029941 PMCID: PMC2933514 DOI: 10.1002/ajmg.b.31055] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
High resolution genomic copy-number analysis has shown that inherited and de novo copy-number variations contribute significantly to autism pathology, and that identification of small chromosomal aberrations related to autism will expedite the discovery of risk genes involved. Here, we report a microduplication of chromosome 15q11.2, spanning only four genes, co-segregating with autism in a Dutch pedigree, identified by SNP microarray analysis, and independently confirmed by FISH and MLPA analysis. Quantitative RT-PCR analysis revealed over 70% increase in peripheral blood mRNA levels for the four genes present in the duplicated region in patients, and RNA in situ hybridization on mouse embryonic and adult brain sections revealed that two of the four genes, CYFIP1 and NIPA1, were highly expressed in the developing mouse brain. These findings point towards a contribution of microduplications at chromosome 15q11.2 to autism, and highlight CYFIP1 and NIPA1 as autism risk genes functioning in axonogenesis and synaptogenesis. Thereby, these findings further implicate defects in dosage-sensitive molecular control of neuronal connectivity in autism. However, the prevalence of this microduplication in patient samples was statistically not significantly different from control samples (0.94% in patients vs. 0.42% controls, P = 0.247), which suggests that our findings should be interpreted with caution and indicates the need for studies that include large numbers of control subjects to ascertain the impact of these changes on a population scale.
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Affiliation(s)
- Bert van der Zwaag
- Rudolf Magnus Institute of Neuroscience, Department of Neuroscience and Pharmacology, UMC Utrecht, Utrecht, the Netherlands
| | - Wouter G Staal
- Rudolf Magnus Institute of Neuroscience, Department of Child and Adolescent Psychiatry, UMC Utrecht, Utrecht, the Netherlands
| | | | - Martin Poot
- Department of Medical Genetics, UMC Utrecht, the Netherlands
| | - Henk A Spierenburg
- Rudolf Magnus Institute of Neuroscience, Department of Neuroscience and Pharmacology, UMC Utrecht, Utrecht, the Netherlands
| | - Maretha V de Jonge
- Rudolf Magnus Institute of Neuroscience, Department of Child and Adolescent Psychiatry, UMC Utrecht, Utrecht, the Netherlands
| | | | - R. van ’t Slot
- Complex Genetics Section, Department of Biomedical Genetics, UMC Utrecht, Utrecht, the Netherlands
| | - Michael A van Es
- Rudolf Magnus Institute of Neuroscience, Department of Neurology, UMC Utrecht, Utrecht, the Netherlands
| | - Frank J Staal
- Department of Immunology, Erasmus MC, Rotterdam, the Netherlands
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Saarland University Hospital, Homburg, Germany
| | - Jacobine E Buizer-Voskamp
- Complex Genetics Section, Department of Biomedical Genetics, UMC Utrecht, Utrecht, the Netherlands, Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marcel R Nelen
- Department of Medical Genetics, UMC Utrecht, the Netherlands
| | - Leonard H van den Berg
- Rudolf Magnus Institute of Neuroscience, Department of Neurology, UMC Utrecht, Utrecht, the Netherlands
| | | | - Herman van Engeland
- Rudolf Magnus Institute of Neuroscience, Department of Child and Adolescent Psychiatry, UMC Utrecht, Utrecht, the Netherlands
| | - J Peter H Burbach
- Rudolf Magnus Institute of Neuroscience, Department of Neuroscience and Pharmacology, UMC Utrecht, Utrecht, the Netherlands
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47
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Need AC, Goldstein DB. Whole genome association studies in complex diseases: where do we stand? DIALOGUES IN CLINICAL NEUROSCIENCE 2010. [PMID: 20373665 PMCID: PMC3181943 DOI: 10.31887/dcns.2010.12.1/aneed] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hundreds of genome-wide association studies have been performed in recent years in order to try to identify common variants that associate with complex disease. These have met with varying success. Some of the strongest effects of common variants have been found in lateonset diseases and in drug response. The major histocompatibility complex has also shown very strong association with a variety of disorders. Although there have been some notable success stories in neuropsychiatric genetics, on the whole, common variation has explained little of the high heritability of these traits. In contrast, early studies of rare copy number variants have led rapidly to a number of genes and loci that strongly associate with neuropsychiatric disorders. It is likely that the use of whole-genome sequencing to extend the study of rare variation in neuropsychiatry will greatly advance our understanding of neuropsychiatric genetics.
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Affiliation(s)
- Anna C Need
- Institute for Genome Sciences and Policy, Center for Human Genome Variation, Duke University, Durham, North Carolina 27708, USA
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48
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The role of DNA copy number variation in schizophrenia. Biol Psychiatry 2009; 66:1005-12. [PMID: 19748074 DOI: 10.1016/j.biopsych.2009.07.027] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 07/21/2009] [Accepted: 07/21/2009] [Indexed: 11/23/2022]
Abstract
Schizophrenia is a major psychiatric disease with strong evidence of genetic risk factors. Recent studies based on genome-wide study of copy number variations (CNVs) have detected novel recurrent submicroscopic copy number changes, including recurrent deletions at 1q21.11, 15q11.3, 15q13.3, and the recurrent CNV at the 2p16.3 neurexin 1 locus. These schizophrenia susceptibility CNV loci demonstrate that schizophrenia is, at least in part, genetic in origin and provide the basis for further investigation of mutations associated with the disease. The studies combined have also established the role of rare and-in sporadic cases-de novo variants in schizophrenia. Furthermore, neuronal-related genes and genetic pathways are starting to emerge from the CNV loci associated with schizophrenia. Here, we review the major findings in the recent literature, which begin to unravel the genetic and biological architecture of this complex human neuropsychiatric disorder.
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49
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Shaikh TH, Gai X, Perin JC, Glessner JT, Xie H, Murphy K, O'Hara R, Casalunovo T, Conlin LK, D'Arcy M, Frackelton EC, Geiger EA, Haldeman-Englert C, Imielinski M, Kim CE, Medne L, Annaiah K, Bradfield JP, Dabaghyan E, Eckert A, Onyiah CC, Ostapenko S, Otieno FG, Santa E, Shaner JL, Skraban R, Smith RM, Elia J, Goldmuntz E, Spinner NB, Zackai EH, Chiavacci RM, Grundmeier R, Rappaport EF, Grant SF, White PS, Hakonarson H. High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications. Genome Res 2009; 19:1682-90. [PMID: 19592680 PMCID: PMC2752118 DOI: 10.1101/gr.083501.108] [Citation(s) in RCA: 290] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Accepted: 06/17/2009] [Indexed: 01/19/2023]
Abstract
We present a database of copy number variations (CNVs) detected in 2026 disease-free individuals, using high-density, SNP-based oligonucleotide microarrays. This large cohort, comprised mainly of Caucasians (65.2%) and African-Americans (34.2%), was analyzed for CNVs in a single study using a uniform array platform and computational process. We have catalogued and characterized 54,462 individual CNVs, 77.8% of which were identified in multiple unrelated individuals. These nonunique CNVs mapped to 3272 distinct regions of genomic variation spanning 5.9% of the genome; 51.5% of these were previously unreported, and >85% are rare. Our annotation and analysis confirmed and extended previously reported correlations between CNVs and several genomic features such as repetitive DNA elements, segmental duplications, and genes. We demonstrate the utility of this data set in distinguishing CNVs with pathologic significance from normal variants. Together, this analysis and annotation provides a useful resource to assist with the assessment of CNVs in the contexts of human variation, disease susceptibility, and clinical molecular diagnostics.
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Affiliation(s)
- Tamim H. Shaikh
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Xiaowu Gai
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Juan C. Perin
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Joseph T. Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Hongbo Xie
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kevin Murphy
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Ryan O'Hara
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Tracy Casalunovo
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Laura K. Conlin
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Monica D'Arcy
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Edward C. Frackelton
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Elizabeth A. Geiger
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Chad Haldeman-Englert
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Marcin Imielinski
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Cecilia E. Kim
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Livija Medne
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Kiran Annaiah
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Jonathan P. Bradfield
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Elvira Dabaghyan
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Andrew Eckert
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Chioma C. Onyiah
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Svetlana Ostapenko
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - F. George Otieno
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Erin Santa
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Julie L. Shaner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Robert Skraban
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Ryan M. Smith
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Josephine Elia
- Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Elizabeth Goldmuntz
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
- Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Nancy B. Spinner
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Elaine H. Zackai
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Rosetta M. Chiavacci
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Robert Grundmeier
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Division of General Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Eric F. Rappaport
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Struan F.A. Grant
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Peter S. White
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Hakon Hakonarson
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Division of Pulmonary Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
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50
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Depienne C, Moreno-De-Luca D, Heron D, Bouteiller D, Gennetier A, Delorme R, Chaste P, Siffroi JP, Chantot-Bastaraud S, Benyahia B, Trouillard O, Nygren G, Kopp S, Johansson M, Rastam M, Burglen L, Leguern E, Verloes A, Leboyer M, Brice A, Gillberg C, Betancur C. Screening for genomic rearrangements and methylation abnormalities of the 15q11-q13 region in autism spectrum disorders. Biol Psychiatry 2009; 66:349-59. [PMID: 19278672 DOI: 10.1016/j.biopsych.2009.01.025] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 01/18/2009] [Accepted: 01/21/2009] [Indexed: 11/30/2022]
Abstract
BACKGROUND Maternally derived duplications of the 15q11-q13 region are the most frequently reported chromosomal aberrations in autism spectrum disorders (ASD). Prader-Willi and Angelman syndromes, caused by 15q11-q13 deletions or abnormal methylation of imprinted genes, are also associated with ASD. However, the prevalence of these disorders in ASD is unknown. The aim of this study was to assess the frequency of 15q11-q13 rearrangements in a large sample of patients ascertained for ASD. METHODS A total of 522 patients belonging to 430 families were screened for deletions, duplications, and methylation abnormalities involving 15q11-q13 with multiplex ligation-dependent probe amplification (MLPA). RESULTS We identified four patients with 15q11-q13 abnormalities: a supernumerary chromosome 15, a paternal interstitial duplication, and two subjects with Angelman syndrome, one with a maternal deletion and the other with a paternal uniparental disomy. CONCLUSIONS Our results show that abnormalities of the 15q11-q13 region are a significant cause of ASD, accounting for approximately 1% of cases. Maternal interstitial 15q11-q13 duplications, previously reported to be present in 1% of patients with ASD, were not detected in our sample. Although paternal duplications of chromosome 15 remain phenotypically silent in the majority of patients, they can give rise to developmental delay and ASD in some subjects, suggesting that paternally expressed genes in this region can contribute to ASD, albeit with reduced penetrance compared with maternal duplications. These findings indicate that patients with ASD should be routinely screened for 15q genomic imbalances and methylation abnormalities and that MLPA is a reliable, rapid, and cost-effective method to perform this screening.
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Affiliation(s)
- Christel Depienne
- INSERM U679, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
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