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Jeong H, Dishuck PC, Yoo D, Harvey WT, Munson KM, Lewis AP, Kordosky J, Garcia GH, Yilmaz F, Hallast P, Lee C, Pastinen T, Eichler EE. Structural polymorphism and diversity of human segmental duplications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597452. [PMID: 38895457 PMCID: PMC11185583 DOI: 10.1101/2024.06.04.597452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Segmental duplications (SDs) contribute significantly to human disease, evolution, and diversity yet have been difficult to resolve at the sequence level. We present a population genetics survey of SDs by analyzing 170 human genome assemblies where the majority of SDs are fully resolved using long-read sequence assembly. Excluding the acrocentric short arms, we identify 173.2 Mbp of duplicated sequence (47.4 Mbp not present in the telomere-to-telomere reference) distinguishing fixed from structurally polymorphic events. We find that intrachromosomal SDs are among the most variable with rare events mapping near their progenitor sequences. African genomes harbor significantly more intrachromosomal SDs and are more likely to have recently duplicated gene families with higher copy number when compared to non-African samples. A comparison to a resource of 563 million full-length Iso-Seq reads identifies 201 novel, potentially protein-coding genes corresponding to these copy number polymorphic SDs.
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Affiliation(s)
- Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Altos Labs, San Diego, CA, USA
| | - Philip C. Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - William T. Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P. Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jennifer Kordosky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Gage H. Garcia
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Feyza Yilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Tomi Pastinen
- Children’s Mercy Hospital and University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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2
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Stokes G, Li Z, Talaba N, Genthe W, Brix MB, Pham B, Wienhold MD, Sandok G, Hernan R, Wynn J, Tang H, Tabima DM, Rodgers A, Hacker TA, Chesler NC, Zhang P, Murad R, Yuan JXJ, Shen Y, Chung WK, McCulley DJ. Rescuing lung development through embryonic inhibition of histone acetylation. Sci Transl Med 2024; 16:eadc8930. [PMID: 38295182 DOI: 10.1126/scitranslmed.adc8930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
A major barrier to the impact of genomic diagnosis in patients with congenital malformations is the lack of understanding regarding how sequence variants contribute to disease pathogenesis and whether this information could be used to generate patient-specific therapies. Congenital diaphragmatic hernia (CDH) is among the most common and severe of all structural malformations; however, its underlying mechanisms are unclear. We identified loss-of-function sequence variants in the epigenomic regulator gene SIN3A in two patients with complex CDH. Tissue-specific deletion of Sin3a in mice resulted in defects in diaphragm development, lung hypoplasia, and pulmonary hypertension, the cardinal features of CDH and major causes of CDH-associated mortality. Loss of SIN3A in the lung mesenchyme resulted in reduced cellular differentiation, impaired cell proliferation, and increased DNA damage. Treatment of embryonic Sin3a mutant mice with anacardic acid, an inhibitor of histone acetyltransferase, reduced DNA damage, increased cell proliferation and differentiation, improved lung and pulmonary vascular development, and reduced pulmonary hypertension. These findings demonstrate that restoring the balance of histone acetylation can improve lung development in the Sin3a mouse model of CDH.
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Affiliation(s)
- Giangela Stokes
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | - Zhuowei Li
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | - Nicole Talaba
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | - William Genthe
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Maria B Brix
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Betty Pham
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | | | - Gracia Sandok
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Rebecca Hernan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Haiyang Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Diana M Tabima
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Allison Rodgers
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Timothy A Hacker
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Naomi C Chesler
- Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center and Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Pan Zhang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Rabi Murad
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jason X-J Yuan
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yufeng Shen
- Department of Systems Biology, Department of Biomedical Informatics, and JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David J McCulley
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
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3
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Honkanen M, Otava U, Viskari H, Rantala S, Outinen T, Toiminen H, Syrjänen J. Hypogammaglobulinemia with T-cell defects and autoimmune manifestations associated with chromosome 15q24 microdeletion. Scand J Immunol 2023; 98:e13324. [PMID: 39007955 DOI: 10.1111/sji.13324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 07/16/2024]
Affiliation(s)
- Meeri Honkanen
- Department of Internal Medicine, Tampere University Hospital and Faculty of Medicine and Life Sciences, Tampere University, Tampere, Finland
| | - Ulla Otava
- Department of Internal Medicine, Tampere University Hospital and Faculty of Medicine and Life Sciences, Tampere University, Tampere, Finland
| | - Hanna Viskari
- Department of Internal Medicine, Tampere University Hospital and Faculty of Medicine and Life Sciences, Tampere University, Tampere, Finland
| | - Sari Rantala
- Department of Internal Medicine, Tampere University Hospital and Faculty of Medicine and Life Sciences, Tampere University, Tampere, Finland
| | - Tuula Outinen
- Department of Internal Medicine, Tampere University Hospital and Faculty of Medicine and Life Sciences, Tampere University, Tampere, Finland
| | - Heidi Toiminen
- Department of Clinical Genetics, Tampere University Hospital and Faculty of Medicine and Life Sciences, Tampere University, Tampere, Finland
| | - Jaana Syrjänen
- Department of Internal Medicine, Tampere University Hospital and Faculty of Medicine and Life Sciences, Tampere University, Tampere, Finland
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4
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Wu D, Wu Y, Lan Y, Lan S, Zhong Z, Li D, Zheng Z, Wang H, Ma L. Chromosomal Aberrations in Pediatric Patients With Moderate/Severe Developmental Delay/Intellectual Disability With Abundant Phenotypic Heterogeneities: A Single-Center Study. Pediatr Neurol 2023; 147:72-81. [PMID: 37566956 DOI: 10.1016/j.pediatrneurol.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/26/2023] [Accepted: 06/06/2023] [Indexed: 08/13/2023]
Abstract
BACKGROUND This study aimed to examine the clinical usefulness of chromosome microarray (CMA) for selective implementation in patients with unexplained moderate or severe developmental delay/intellectual disability (DD/ID) and/or combined with different dysphonic features in the Han Chinese population. METHODS We retrospectively analyzed data on 122 pediatric patients with unexplained isolated moderate/severe DD/ID with or without autism spectrum disorders, epilepsy, dystonia, and congenital abnormalities from a single-center neurorehabilitation clinic in southern China. RESULTS A total of 46 probands (37.7%) had abnormal CMA results among the 122 study patients. With the exclusion of aneuploidies, uniparental disomies, and multiple homozygotes, 37 patients harbored 39 pathogenic copy number variations (pCNVs) (median [interquartile range] size: 3.57 [1.6 to 7.1] Mb; 33 deletions and 6 duplications), enriched in chromosomes 5, 7, 15, 17, and 22, with a markedly high prevalence of Angelman/Prader-Willi syndrome (24.3% [nine of 37]). Three rare deletions in the regions 5q33.2q34, 17p13.2, and 13q33.2 were reported, with specific delineation of clinical phenotypes. The frequencies of pCNVs were 18%, 33.3%, 38.89%, 41.67%, and 100% for patients with 1, 2, 3, 4, and 5 study phenotypes, respectively; patients with more concomitant abnormalities in the heart, brain, craniofacial region, and/or other organs had a higher CMA diagnostic yield and pCNV prevalence (P < 0.05). CONCLUSIONS Clinical application of CMA as a first-tier test among patients with moderate/severe DD/ID combined with congenital structural anomalies improved diagnostic yields and the quality of clinical management in this series of patients.
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Affiliation(s)
- Dan Wu
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China; Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
| | - Yi Wu
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yulong Lan
- Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia; Department of Cardiology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Shaocong Lan
- Guangdong Medical College, Zhanjiang, Guangdong, China
| | - Zhiwei Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Duo Li
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zexin Zheng
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Hongwu Wang
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
| | - Lian Ma
- Department of Pediatrics, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China; Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen, Guangdong, China; Shenzhen Public Service Platform of Molecular Medicine in Pediatric Hematology and Oncology, Shenzhen, Guangdong, China; Department of Pediatrics, The Third Affiliated Hospital of Guangzhou Medical University (The Women and Children's Hospital of Guangzhou Medical University), Guangzhou, Guangdong, China.
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5
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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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Giovenale AMG, Ruotolo G, Soriano AA, Turco EM, Rotundo G, Casamassa A, D’Anzi A, Vescovi AL, Rosati J. Deepening the understanding of CNVs on chromosome 15q11-13 by using hiPSCs: An overview. Front Cell Dev Biol 2023; 10:1107881. [PMID: 36684422 PMCID: PMC9852989 DOI: 10.3389/fcell.2022.1107881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/16/2022] [Indexed: 01/09/2023] Open
Abstract
The human α7 neuronal nicotinic acetylcholine receptor gene (CHRNA7) is widely expressed in the central and peripheral nervous systems. This receptor is implicated in both brain development and adult neurogenesis thanks to its ability to mediate acetylcholine stimulus (Ach). Copy number variations (CNVs) of CHRNA7 gene have been identified in humans and are genetically linked to cognitive impairments associated with multiple disorders, including schizophrenia, bipolar disorder, epilepsy, Alzheimer's disease, and others. Currently, α7 receptor analysis has been commonly performed in animal models due to the impossibility of direct investigation of the living human brain. But the use of model systems has shown that there are very large differences between humans and mice when researchers must study the CNVs and, in particular, the CNV of chromosome 15q13.3 where the CHRNA7 gene is present. In fact, human beings present genomic alterations as well as the presence of genes of recent origin that are not present in other model systems as well as they show a very heterogeneous symptomatology that is associated with both their genetic background and the environment where they live. To date, the induced pluripotent stem cells, obtained from patients carrying CNV in CHRNA7 gene, are a good in vitro model for studying the association of the α7 receptor to human diseases. In this review, we will outline the current state of hiPSCs technology applications in neurological diseases caused by CNVs in CHRNA7 gene. Furthermore, we will discuss some weaknesses that emerge from the overall analysis of the published articles.
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Affiliation(s)
- Angela Maria Giada Giovenale
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Giorgia Ruotolo
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Amata Amy Soriano
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Elisa Maria Turco
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giovannina Rotundo
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Alessia Casamassa
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Angela D’Anzi
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Angelo Luigi Vescovi
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy,*Correspondence: Jessica Rosati, ; Angelo Luigi Vescovi,
| | - Jessica Rosati
- Cellular Reprogramming Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy,*Correspondence: Jessica Rosati, ; Angelo Luigi Vescovi,
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7
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AYAZ A, GEZDIRICI A, YILMAZ GULEC E, OZALP Ö, KOSEOGLU AH, DOGRU Z, YALCINTEPE S. Diagnostic Value of Microarray Method in Autism Spectrum Disorder, Intellectual Disability, and Multiple Congenital Anomalies and Some Candidate Genes for Autism: Experience of Two Centers. Medeni Med J 2022; 37:180-193. [PMID: 35735171 PMCID: PMC9234369 DOI: 10.4274/mmj.galenos.2022.70962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Objective: This study aimed to demonstrate the diagnostic value of microarray testing in autism spectrum disorder, intellectual disability, and multiple congenital anomalies of unknown etiology, as well as to report some potential candidate genes for autism. Methods: Microarray analysis records between January 2016 and December 2017 from two Genetic Diagnostic Centers in Turkey, Kanuni Sultan Suleyman and Adana Numune Training and Research Hospital, were compiled. Detected copy number variations (CNVs) were classified as benign, likely benign, variants of uncertain significance (VUS), likely pathogenic, and pathogenic according to American College of Medical Genetics and Genomics guidelines. The clinical findings of the some patients and the literature data were compared. Results: In 109 (24.5%) of 445 patients, a total of 163 CNVs with reporting criterion feature were detected. Sixty-nine (42%) and 8 (5%) of these were evaluated as pathogenic and likely pathogenic, respectively. Fifteen (9%) CNVs were also evaluated as VUS. Pathogenic or likely pathogenic CNVs were detected in 61 (13.6%) of 445 patients. Conclusions: We found that the probability of elucidating the etiology of microarray method in autism spectrum disorder, intellectual disability, and multiple congenital anomalies is 13.6% with a percentage similar to the literature. We suggest that the MYT1L, PXDN, TPO, and AUTS2 genes are all strong candidate genes for autism spectrum disorders. We detailed the clinical findings of the cases and reported that some CNV regions in the genome may be associated with autism.
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8
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Penon-Portmann M, Carlston CM, Martin PM, Slavotinek A. Exome Sequencing Identifies a Novel <b><i>SIN3A</i></b> Variant in a Patient with Witteveen-Kolk Syndrome. Mol Syndromol 2022; 13:337-342. [PMID: 36158056 PMCID: PMC9421682 DOI: 10.1159/000520042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 09/23/2021] [Indexed: 12/03/2022] Open
Abstract
Witteveen-Kolk syndrome (WITKOS; OMIM #613406) is a recently described, rare neurodevelopmental syndrome characterized by mild intellectual disability and a recognizable facial gestalt. WITKOS is caused by heterozygous loss-of-function variants in SIN3A. It shares some features with 15q24 deletion syndrome but to date has only been described in a limited number of patients mostly of Northern European ancestry. Here, we report the first patient with Hispanic ancestry to our knowledge diagnosed with WITKOS, who has a novel, truncating variant in the SIN3A gene. Clinical exome sequencing performed in-house using a custom bioinformatics pipeline identified a de novo heterozygous, nonsense variant in SIN3A, c.1015C>T (p.Gln339Ter) that has not been previously described in the literature. This 3-year-old boy with WITKOS demonstrated classic features including mild developmental delay and triangular facies with hypotelorism and deep-set, hooded eyes. This patient supports the currently described phenotype for WITKOS in more diverse populations.
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Affiliation(s)
- Monica Penon-Portmann
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Colleen M. Carlston
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
| | - Pierre-Marie Martin
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Anne Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
- *Anne Slavotinek,
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Quinonez SC, Terefework Z. The introduction of clinical genetic testing in Ethiopia: Experiences and lessons learned. Am J Med Genet A 2021; 185:2995-3004. [PMID: 34169623 DOI: 10.1002/ajmg.a.62396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/22/2021] [Accepted: 05/31/2021] [Indexed: 11/08/2022]
Abstract
Limited data are available on genetic testing laboratories in low- and middle-income countries including those in sub-Saharan Africa (SSA). To characterize the need for genetic testing in SSA we describe the experience of MRC-ET Advanced Laboratory, a genetic testing laboratory in Ethiopia. Test results were analyzed based on indication(s) for testing, referral category, and diagnostic yield. A total of 1311 tests were run using the full MRC-Holland catalogue of Multiplex-Ligation Probe Amplification assays. Of all samples, 77% were postnatal samples, 15% products of conception (POC), and 8% amniotic samples. Of postnatal samples, the most common testing categories were multiple congenital anomalies (32%), disorders of sex development (17%), and Obstetrics/Gynecology (16%). Forty-three percent of postnatal samples were diagnostic, 11% were variants of uncertain significance (VUS), and 46% were normal with Trisomy 21 the most common diagnosis. Of POC samples, 10% were diagnostic, 34% revealed VUSs, and 55% were normal with Trisomy 18 the most common diagnosis. Of amniotic samples 17.5% were diagnostic, 3% revealed VUSs, and 79% were normal with Trisomy 18 the most common diagnosis. There is increasing demand for genetic testing in Ethiopia. Diagnostic genetic testing in SSA deserves increased attention as testing platforms become more affordable.
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Affiliation(s)
- Shane C Quinonez
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, USA.,Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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10
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Mosley TJ, Johnston HR, Cutler DJ, Zwick ME, Mulle JG. Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders. BMC Med Genomics 2021; 14:154. [PMID: 34107974 PMCID: PMC8190997 DOI: 10.1186/s12920-021-00999-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Structural rearrangements of the genome, which generally occur during meiosis and result in large-scale (> 1 kb) copy number variants (CNV; deletions or duplications ≥ 1 kb), underlie genomic disorders. Recurrent pathogenic CNVs harbor similar breakpoints in multiple unrelated individuals and are primarily formed via non-allelic homologous recombination (NAHR). Several pathogenic NAHR-mediated recurrent CNV loci demonstrate biases for parental origin of de novo CNVs. However, the mechanism underlying these biases is not well understood. METHODS We performed a systematic, comprehensive literature search to curate parent of origin data for multiple pathogenic CNV loci. Using a regression framework, we assessed the relationship between parental CNV origin and the male to female recombination rate ratio. RESULTS We demonstrate significant association between sex-specific differences in meiotic recombination and parental origin biases at these loci (p = 1.07 × 10-14). CONCLUSIONS Our results suggest that parental origin of CNVs is largely influenced by sex-specific recombination rates and highlight the need to consider these differences when investigating mechanisms that cause structural variation.
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Affiliation(s)
- Trenell J Mosley
- Graduate Program in Genetics and Molecular Biology, Laney Graduate School, Emory University, 201 Dowman Drive, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Emory Integrated Computational Core, Emory University, 101 Woodruff Circle, Atlanta, GA, 30322, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Drive, Atlanta, GA, 30322, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA.
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA.
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Balasubramanian M, Dingemans AJM, Albaba S, Richardson R, Yates TM, Cox H, Douzgou S, Armstrong R, Sansbury FH, Burke KB, Fry AE, Ragge N, Sharif S, Foster A, De Sandre-Giovannoli A, Elouej S, Vasudevan P, Mansour S, Wilson K, Stewart H, Heide S, Nava C, Keren B, Demirdas S, Brooks AS, Vincent M, Isidor B, Küry S, Schouten M, Leenders E, Chung WK, Haeringen AV, Scheffner T, Debray FG, White SM, Palafoll MIV, Pfundt R, Newbury-Ecob R, Kleefstra T. Comprehensive study of 28 individuals with SIN3A-related disorder underscoring the associated mild cognitive and distinctive facial phenotype. Eur J Hum Genet 2021; 29:625-636. [PMID: 33437032 PMCID: PMC8115148 DOI: 10.1038/s41431-020-00769-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 11/08/2022] Open
Abstract
Witteveen-Kolk syndrome (OMIM 613406) is a recently defined neurodevelopmental syndrome caused by heterozygous loss-of-function variants in SIN3A. We define the clinical and neurodevelopmental phenotypes related to SIN3A-haploinsufficiency in 28 unreported patients. Patients with SIN3A variants adversely affecting protein function have mild intellectual disability, growth and feeding difficulties. Involvement of a multidisciplinary team including a geneticist, paediatrician and neurologist should be considered in managing these patients. Patients described here were identified through a combination of clinical evaluation and gene matching strategies (GeneMatcher and Decipher). All patients consented to participate in this study. Mean age of this cohort was 8.2 years (17 males, 11 females). Out of 16 patients ≥ 8 years old assessed, eight (50%) had mild intellectual disability (ID), four had moderate ID (22%), and one had severe ID (6%). Four (25%) did not have any cognitive impairment. Other neurological symptoms such as seizures (4/28) and hypotonia (12/28) were common. Behaviour problems were reported in a minority. In patients ≥2 years, three were diagnosed with Autism Spectrum Disorder (ASD) and four with Attention Deficit Hyperactivity Disorder (ADHD). We report 27 novel variants and one previously reported variant. 24 were truncating variants; three were missense variants and one large in-frame gain including exons 10-12.
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Affiliation(s)
- Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK.
- Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK.
| | - Alexander J M Dingemans
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Shadi Albaba
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Ruth Richardson
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Trust, Newcastle, UK
| | - Thabo M Yates
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Helen Cox
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Sofia Douzgou
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Ruth Armstrong
- East Anglian Medical Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Francis H Sansbury
- All Wales Medical Genomics Service, NHS Wales Cardiff and Vale University Health Board, Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Katherine B Burke
- All Wales Medical Genomics Service, NHS Wales Cardiff and Vale University Health Board, Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Andrew E Fry
- All Wales Medical Genomics Service, NHS Wales Cardiff and Vale University Health Board, Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Nicola Ragge
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Saba Sharif
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Alison Foster
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Annachiara De Sandre-Giovannoli
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
- Department of Medical Genetics, La Timone Children's Hospital, Marseille, France
- Biological Resource Center (CRB-TAC), Assistance Publique Hôpitaux de Marseille, La Timone Children's Hospital, Marseille, France
| | - Sahar Elouej
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - Pradeep Vasudevan
- Leicester Clinical Genetics Service, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Sahar Mansour
- Clinical Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Kate Wilson
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Solveig Heide
- Clinical Genetics Service, GH Pitié-Salpêtrière, Pitié Salpêtrière Hospital, APHP Sorbonne University, Paris, France
| | - Caroline Nava
- Clinical Genetics Service, GH Pitié-Salpêtrière, Pitié Salpêtrière Hospital, APHP Sorbonne University, Paris, France
| | - Boris Keren
- Clinical Genetics Service, GH Pitié-Salpêtrière, Pitié Salpêtrière Hospital, APHP Sorbonne University, Paris, France
| | - Serwet Demirdas
- Department of Clinical Genetics, Erasmus Medical Centre, Erasmus University, Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus Medical Centre, Erasmus University, Rotterdam, the Netherlands
| | - Marie Vincent
- Service de Génétique Médicale, CHU de Nantes, 44000, Nantes, France
- Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000, Nantes, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, 44000, Nantes, France
- Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000, Nantes, France
| | - Sebastien Küry
- Service de Génétique Médicale, CHU de Nantes, 44000, Nantes, France
- Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000, Nantes, France
| | - Meyke Schouten
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Erika Leenders
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, USA
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Thomas Scheffner
- Klinik für Kinder- und Jugendmedizin, Perinatal- und Stoffwechselzentrum, Reutlingen, Germany
| | - Francois-Guillaume Debray
- Metabolic Unit-Department of Medical Genetics, CHU & University Liège Domaine L Sart-Tilman Bât B35, B-4000, Liège, Belgium
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Maria Irene Valenzuela Palafoll
- Department of Clinical and Molecular Genetics, University Hospital Vall d´Hebron and Medicine Genetics Group, Valle Hebron Research Institute, Barcelona, Spain
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ruth Newbury-Ecob
- University Hospitals Bristol NHS Foundation Trust, Clinical Genetics, St. Michael's Hospital, Bristol, UK
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
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12
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Prenatal diagnosis and molecular cytogenetic characterization of a chromosome 15q24 microdeletion. Taiwan J Obstet Gynecol 2021; 59:432-436. [PMID: 32416893 DOI: 10.1016/j.tjog.2020.03.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2019] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE We present prenatal diagnosis, molecular cytogenetic characterization and genetic counseling of a chromosome 15q24 microdeletion of paternal origin. CASE REPORT A 34-year-old primigravid woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 46,XY. Simultaneous array comparative genomic hybridization (aCGH) analysis on amniotic fluid revealed a de novo 2.571-Mb microdeletion of 15q24.1-q24.2. Prenatal ultrasound findings were unremarkable except persistent left superior vena cava and enlarged coronary sinus. The woman requested repeat amniocentesis at 22 weeks of gestation, and aCGH analysis confirmed the result of arr 15q24.1q24.2 (72,963,970-75,535,330) × 1.0 [GRCh37 (hg19)] and a 15q24 microdeletion encompassing the genes of STRA6, CYP11A1, SEMA7A, ARID3B, CYP1A1, CYP1A2, CSK and CPLX3. The parents did not have such a deletion, and polymorphic DNA marker analysis confirmed a paternal origin of the de novo deletion. Metaphase fluorescence in situ hybridization analysis confirmed a 15q24 deletion. The parents elected to terminate the pregnancy, and a malformed fetus was delivered with characteristic facial dysmorphism. CONCLUSION Simultaneous aCGH analysis of uncultured amniocytes at amniocentesis may help to detect rare de novo microdeletion disorders.
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13
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Nees SN, Chung WK. Genetic Basis of Human Congenital Heart Disease. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036749. [PMID: 31818857 DOI: 10.1101/cshperspect.a036749] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Congenital heart disease (CHD) is the most common major congenital anomaly with an incidence of ∼1% of live births and is a significant cause of birth defect-related mortality. The genetic mechanisms underlying the development of CHD are complex and remain incompletely understood. Known genetic causes include all classes of genetic variation including chromosomal aneuploidies, copy number variants, and rare and common single-nucleotide variants, which can be either de novo or inherited. Among patients with CHD, ∼8%-12% have a chromosomal abnormality or aneuploidy, between 3% and 25% have a copy number variation, and 3%-5% have a single-gene defect in an established CHD gene with higher likelihood of identifying a genetic cause in patients with nonisolated CHD. These genetic variants disrupt or alter genes that play an important role in normal cardiac development and in some cases have pleiotropic effects on other organs. This work reviews some of the most common genetic causes of CHD as well as what is currently known about the underlying mechanisms.
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Affiliation(s)
| | - Wendy K Chung
- Department of Pediatrics.,Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
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14
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van Dongen LCM, Wingbermühle E, Dingemans AJM, Bos-Roubos AG, Vermeulen K, Pop-Purceleanu M, Kleefstra T, Egger JIM. Behavior and cognitive functioning in Witteveen-Kolk syndrome. Am J Med Genet A 2020; 182:2384-2390. [PMID: 32783353 PMCID: PMC7540409 DOI: 10.1002/ajmg.a.61775] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/19/2020] [Accepted: 06/19/2020] [Indexed: 01/08/2023]
Abstract
Witteveen-Kolk syndrome (WITKOS) is a rare neurodevelopmental disorder characterized by developmental delay/intellectual disability, facial dysmorphisms, and short stature. The syndrome is caused by loss of function of switch-insensitive 3 transcription regulator family member A (SIN3A). Regarding behavioral functioning, Autism Spectrum Disorders (ASD), obsessive-compulsive behaviors, as well as Attention-Deficit/Hyperactivity Disorder symptoms (ADHD) have been suggested. The present study explores various aspects of neurocognitive functioning in five individuals (age range 10-23) with WITKOS. Medical records and results of extensive neuropsychological assessment are used to describe developmental trajectories and neurocognitive profiles. Systematic analysis of medical records displays developmental difficulties described as ASD or ADHD in childhood, sleep problems and internalizing problems during adolescence. Results of cognitive assessments indicate profoundly disabled (n = 1), mildly disabled (n = 2), borderline (n = 1), and average (n = 1) levels of intelligence. Furthermore, results indicate weaknesses in speed of information processing/sustained attention in all participants, and difficulties in planning and maintaining overview in three participants. Furthermore, parent reports of behavioral functioning primarily suggest problems in social functioning. Implications of both cognitive problems and social-emotional vulnerabilities for counseling are discussed and supplemented with suggestions for interventions.
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Affiliation(s)
- Linde C M van Dongen
- Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ellen Wingbermühle
- Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Stevig Specialized and Forensic Care for People with Intellectual Disability, Oostrum, The Netherlands
| | | | - Anja G Bos-Roubos
- Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Karlijn Vermeulen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Intellectual Disabilities, Karakter Child and Adolescent Psychiatry, Ede, The Netherlands
| | - Monica Pop-Purceleanu
- Department of Psychiatry, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jos I M Egger
- Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Stevig Specialized and Forensic Care for People with Intellectual Disability, Oostrum, The Netherlands
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15
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A de-novo 15q24.2 deletion involving SIN3A is associated with emotional, behavioural, motor problems and hypersensitivity in a girl with above average intelligence and typical facial features. Clin Dysmorphol 2020; 29:210-213. [PMID: 32639238 DOI: 10.1097/mcd.0000000000000337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Liu Y, Zhang Y, Zarrei M, Dong R, Yang X, Zhao D, Scherer SW, Gai Z. Refining critical regions in 15q24 microdeletion syndrome pertaining to autism. Am J Med Genet B Neuropsychiatr Genet 2020; 183:217-226. [PMID: 31953991 DOI: 10.1002/ajmg.b.32778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 11/29/2019] [Accepted: 12/16/2019] [Indexed: 12/26/2022]
Abstract
Chromosome 15q24 microdeletion syndrome is characterized by developmental delay, facial dysmorphism, hearing loss, hypotonia, recurrent infection, and other congenital malformations including microcephaly, scoliosis, joint laxity, digital anomalies, as well as sometimes having autism spectrum disorder (ASD) and attention deficit hyperactivity disorder. Here, we report a boy with a 2.58-Mb de novo deletion at chromosome 15q24. He is diagnosed with ASD and having multiple phenotypes similar to those reported in cases having 15q24 microdeletion syndrome. To delineate the critical genes and region that might be responsible for these phenotypes, we reviewed all previously published cases. We observe a potential minimum critical region of 650 kb (LCR15q24A-B) affecting NEO1 among other genes that might pertinent to individuals with ASD carrying this deletion. In contrast, a previously defined minimum critical region downstream of the 650-kb interval (LCR15q24B-D) is more likely associated with the developmental delay, facial dysmorphism, recurrent infection, and other congenital malformations. As a result, the ASD phenotype in this individual is potentially attributed by genes particularly NEO1 within the newly proposed critical region.
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Affiliation(s)
- Yi Liu
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Yanqing Zhang
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rui Dong
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Xiaomeng Yang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Dongmei Zhao
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
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17
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Liu Y, Mapow B. Coexistence of urogenital malformations in a female fetus with de novo 15q24 microdeletion and a literature review. Mol Genet Genomic Med 2020; 8:e1265. [PMID: 32400031 PMCID: PMC7336734 DOI: 10.1002/mgg3.1265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022] Open
Abstract
Background 15q24 microdeletion is a relatively new syndrome caused by nonallelic homologous recombination (NAHR) between low‐copy repeats (LCRs) in the 15q24 chromosome region. This syndrome is characterized by a spectrum of clinical symptoms including global developmental delay, intellectual disability, facial dysmorphisms, and congenital malformations of the extremities, eye, gastrointestinal tract, genitourinary system, and genitalia. Method Molecular cytogenetic analysis was performed using whole genome single‐nucleotide polymorphism (SNP) microarray analysis. Autopsy examination including gross and microscopic examination were performed. In addition, a thorough review of the literature on 15q24 microdeletion was completed and summarized in table format. Result Molecular cytogenetic analysis revealed a 3.88 MB interstitial deletion within 15q24.1 to 15q24.3 (74,353,735–78,228,485 bp) in our case. Autopsy examination showed congenital malformations within the genitourinary system and genitalia, including left kidney agenesis and uterus didelphys. After thorough literature review, we found a series of midline defects associated with 15q24 microdeletion syndrome. Conclusion We report the first case of coexistence of urogenital abnormalities, including left kidney agenesis and uterus didelphys, with 15q24 microdeletion syndrome, which is also associated with midline defects secondary to abnormal development. Since 15q24 microdeletion syndrome is a relatively new entity, fully characterizing its variation and severity requires additional examination of the genetics, molecular profile and structural and functional abnormalities in affected patients. Due to the limited data in the literature, statistical analysis of abnormalities in each organ system is not possible. However, we can predict that novel genetic pathways involving cell migration, adhesion, apoptosis, and embryo development might be discovered with the advanced study of 15q24 microdeletion syndrome.
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Affiliation(s)
- Yaobin Liu
- Department of Pathology, Pennsylvania Hospital, Philadelphia, Pennsylvania, USA
| | - Beth Mapow
- Department of Pathology and Laboratory Medicine, Jefferson Health New jersey, Cherry Hill, New Jersey, USA
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18
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Maggiolini FAM, Cantsilieris S, D’Addabbo P, Manganelli M, Coe BP, Dumont BL, Sanders AD, Pang AWC, Vollger MR, Palumbo O, Palumbo P, Accadia M, Carella M, Eichler EE, Antonacci F. Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus. PLoS Genet 2019; 15:e1008075. [PMID: 30917130 PMCID: PMC6436712 DOI: 10.1371/journal.pgen.1008075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/07/2019] [Indexed: 11/19/2022] Open
Abstract
Human chromosome 15q25 is involved in several disease-associated structural rearrangements, including microdeletions and chromosomal markers with inverted duplications. Using comparative fluorescence in situ hybridization, strand-sequencing, single-molecule, real-time sequencing and Bionano optical mapping analyses, we investigated the organization of the 15q25 region in human and nonhuman primates. We found that two independent inversions occurred in this region after the fission event that gave rise to phylogenetic chromosomes XIV and XV in humans and great apes. One of these inversions is still polymorphic in the human population today and may confer differential susceptibility to 15q25 microdeletions and inverted duplications. The inversion breakpoints map within segmental duplications containing core duplicons of the GOLGA gene family and correspond to the site of an ancestral centromere, which became inactivated about 25 million years ago. The inactivation of this centromere likely released segmental duplications from recombination repression typical of centromeric regions. We hypothesize that this increased the frequency of ectopic recombination creating a hotspot of hominid inversions where dispersed GOLGA core elements now predispose this region to recurrent genomic rearrangements associated with disease.
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Affiliation(s)
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Pietro D’Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Michele Manganelli
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Beth L. Dumont
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - Ashley D. Sanders
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, Heidelberg, Germany
| | | | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Orazio Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Pietro Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital “Cardinale G. Panico”, Via San Pio X n°4, Tricase, LE, Italy
| | - Massimo Carella
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States of America
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
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19
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Wang R, Lei T, Fu F, Li R, Jing X, Yang X, Liu J, Li D, Liao C. Application of chromosome microarray analysis in patients with unexplained developmental delay/intellectual disability in South China. Pediatr Neonatol 2019; 60:35-42. [PMID: 29631977 DOI: 10.1016/j.pedneo.2018.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 01/22/2018] [Accepted: 03/20/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND AND METHODS Chromosome microarray analysis (CMA) is currently the first-tier diagnostic assay for the evaluation of developmental delay (DD) and intellectual disability (ID) with unknown etiology. Here, we present our clinical experience in implementing whole-genome high-resolution single nucleotide polymorphism (SNP) arrays to investigate 489 patients with unexplained DD/ID in whom standard karyotyping analyses showed normal karyotypes. This study aimed to assess the usefulness of CMA for clinical diagnostic testing in the Chinese population. RESULTS A total of 489 children were classified into three groups: isolated DD/ID (n = 358), DD/ID with epilepsy (n = 49), and DD/ID with other structural anomalies (n = 82). We identified 126 cases (25.8%, 126/489) of pathogenic copy number variants (CNVs) by CMA, including 89 (24.9%, 89/358) with isolated DD/ID, 13 (26.5%, 13/49) with DD/ID with epilepsy, and 24 (29.3%, 24/82) with DD/ID with other structural anomalies. Among the 126 cases of pathogenic CNVs, 79 cases were identified as microdeletion/microduplication syndromes, among which 76 cases were classified as common syndromes, and 3 cases were classified as rare syndromes, including 15q24 microdeletion syndrome, Xq28 microduplication syndrome and Lowe syndrome. Additionally, there were forty-seven cases of non-syndromic pathogenic CNVs. The ABAT, FTSJ1, DYNC1H1, and SETBP1 genes were identified as DD/ID candidate genes. CONCLUSION Our findings suggest the necessity of CMA as a routine diagnostic test for unexplained DD/ID in South China.
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Affiliation(s)
- Rongyue Wang
- Southern Medical University, Guangzhou, 510515, Guangdong, China; The Second Hospital affiliated to Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Tingying Lei
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Xiangyi Jing
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Xin Yang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Juan Liu
- Foshan Women and Children's Hospital, Foshan, 528000, Guangdong, China
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Can Liao
- Southern Medical University, Guangzhou, 510515, Guangdong, China; Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China.
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20
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Pierpont ME, Brueckner M, Chung WK, Garg V, Lacro RV, McGuire AL, Mital S, Priest JR, Pu WT, Roberts A, Ware SM, Gelb BD, Russell MW. Genetic Basis for Congenital Heart Disease: Revisited: A Scientific Statement From the American Heart Association. Circulation 2018; 138:e653-e711. [PMID: 30571578 PMCID: PMC6555769 DOI: 10.1161/cir.0000000000000606] [Citation(s) in RCA: 349] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review provides an updated summary of the state of our knowledge of the genetic contributions to the pathogenesis of congenital heart disease. Since 2007, when the initial American Heart Association scientific statement on the genetic basis of congenital heart disease was published, new genomic techniques have become widely available that have dramatically changed our understanding of the causes of congenital heart disease and, clinically, have allowed more accurate definition of the pathogeneses of congenital heart disease in patients of all ages and even prenatally. Information is presented on new molecular testing techniques and their application to congenital heart disease, both isolated and associated with other congenital anomalies or syndromes. Recent advances in the understanding of copy number variants, syndromes, RASopathies, and heterotaxy/ciliopathies are provided. Insights into new research with congenital heart disease models, including genetically manipulated animals such as mice, chicks, and zebrafish, as well as human induced pluripotent stem cell-based approaches are provided to allow an understanding of how future research breakthroughs for congenital heart disease are likely to happen. It is anticipated that this review will provide a large range of health care-related personnel, including pediatric cardiologists, pediatricians, adult cardiologists, thoracic surgeons, obstetricians, geneticists, genetic counselors, and other related clinicians, timely information on the genetic aspects of congenital heart disease. The objective is to provide a comprehensive basis for interdisciplinary care for those with congenital heart disease.
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21
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Narumi-Kishimoto Y, Araki N, Migita O, Kawai T, Okamura K, Nakabayashi K, Kaname T, Ozawa Y, Ozawa H, Takada F, Hata K. Novel SIN3A mutation identified in a Japanese patient with Witteveen-Kolk syndrome. Eur J Med Genet 2018; 62:103547. [PMID: 30267900 DOI: 10.1016/j.ejmg.2018.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/06/2018] [Accepted: 09/26/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Yoko Narumi-Kishimoto
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan; Medical Genome Center, National Research Institute for Child Health and Development, Tokyo, Japan; Department of Medical Genetics, Kitasato University, Sagamihara, Japan; Department of Neuro-pediatrics, Shimada Ryouiku Center Hachiouji, Tokyo, Japan.
| | - Naomi Araki
- Department of Medical Genetics, Kitasato University, Sagamihara, Japan
| | - Ohsuke Migita
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan; Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yuri Ozawa
- Department of Neuro-pediatrics, Shimada Ryouiku Center Hachiouji, Tokyo, Japan
| | - Hiroshi Ozawa
- Department of Neuro-pediatrics, Shimada Ryouiku Center Hachiouji, Tokyo, Japan
| | - Fumio Takada
- Department of Medical Genetics, Kitasato University, Sagamihara, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
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22
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Huynh MT, Lambert AS, Tosca L, Petit F, Philippe C, Parisot F, Benoît V, Linglart A, Brisset S, Tran CT, Tachdjian G, Receveur A. 15q24.1 BP4-BP1 microdeletion unmasking paternally inherited functional polymorphisms combined with distal 15q24.2q24.3 duplication in a patient with epilepsy, psychomotor delay, overweight, ventricular arrhythmia. Eur J Med Genet 2018; 61:459-464. [PMID: 29549028 DOI: 10.1016/j.ejmg.2018.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/05/2017] [Accepted: 03/10/2018] [Indexed: 11/25/2022]
Abstract
15q24 microdeletion and microduplication syndromes are genetic disorders caused by non-allelic homologous recombination between low-copy repeats (LCRs) in the 15q24 chromosome region. Individuals with 15q24 microdeletion and microduplication syndromes share a common 1.2 Mb critical interval, spanning from LCR15q24B to LCR15q24C. Patients with 15q24 microdeletion syndrome exhibit distinct dysmorphic features, microcephaly, variable developmental delay, multiples congenital anomalies while individuals with reciprocal 15q24 microduplication syndrome show mild developmental delay, facial dysmorphism associated with skeletal and genital abnormalities. We report the first case of a 10 year-old girl presenting mild developmental delay, psychomotor retardation, epilepsy, ventricular arrhythmia, overweight and idiopathic central precocious puberty. 180K array-CGH analysis identified a 1.38 Mb heterozygous interstitial 15q24.1 BP4-BP1 microdeletion including HCN4 combined with a concomitant 2.6 Mb heterozygous distal 15q24.2q24.3 microduplication. FISH analysis showed that both deletion and duplication occurred de novo in the proband. Of note, both copy number imbalances did not involve the 1.2 Mb minimal deletion/duplication critical interval of the 15q24.1q24.2 chromosome region (74.3-75.5 Mb). Sequencing of candidate genes for epilepsy and obesity showed that the proband was hemizygous for paternal A-at risk allele of BBS4 rs7178130 and NPTN rs7171755 predisposing to obesity, epilepsy and intellectual deficits. Our study highlights the complex interaction of functional polymorphisms and/or genetic variants leading to variable clinical manifestations in patients with submicroscopic chromosomal aberrations.
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Affiliation(s)
- Minh-Tuan Huynh
- APHP, Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France; Faculté de Médecine Paris Sud, Université Paris-Sud, 94276 Le Kremlin-Bicêtre cedex, France; Pham Ngoc Thach Medical University, Ho Chi Minh city, Viet Nam.
| | - Anne-Sophie Lambert
- APHP, Service d'Endocrinologie et de Diabétologie Pédiatrique, Hôpitaux Universitaires Paris-Sud, Hôpital Kremlin-Bicêtre, 94275 Le Kremlin-Bicêtre, France
| | - Lucie Tosca
- APHP, Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France; Faculté de Médecine Paris Sud, Université Paris-Sud, 94276 Le Kremlin-Bicêtre cedex, France
| | - François Petit
- APHP, Laboratoire de Génétique Moléculaire, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France
| | - Christophe Philippe
- Laboratoire de Génétique Chromosomique et Moléculaire, Plateau technique de Biologie, CHU de Dijon, Dijon, France
| | - Frédéric Parisot
- APHP, Laboratoire de Génétique Moléculaire, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France
| | - Virginie Benoît
- APHP, Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France
| | - Agnès Linglart
- APHP, Service d'Endocrinologie et de Diabétologie Pédiatrique, Hôpitaux Universitaires Paris-Sud, Hôpital Kremlin-Bicêtre, 94275 Le Kremlin-Bicêtre, France
| | - Sophie Brisset
- APHP, Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France; Faculté de Médecine Paris Sud, Université Paris-Sud, 94276 Le Kremlin-Bicêtre cedex, France
| | - Cong Toai Tran
- Pham Ngoc Thach Medical University, Ho Chi Minh city, Viet Nam
| | - Gérard Tachdjian
- APHP, Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France; Faculté de Médecine Paris Sud, Université Paris-Sud, 94276 Le Kremlin-Bicêtre cedex, France
| | - Aline Receveur
- APHP, Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud, Hôpital Antoine Béclère, 92140 Clamart, France
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23
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Ahram DF, Al-Sarraj Y, Taha RZ, Elhag SF, Al-Shaban FA, El-Shanti H, Kambouris M. A chromosomal microdeletion of 15q in a female patient with epilepsy, ID, and autism spectrum disorder: a case report. Clin Case Rep 2017; 5:1013-1017. [PMID: 28588858 PMCID: PMC5457985 DOI: 10.1002/ccr3.945] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/19/2017] [Accepted: 03/09/2017] [Indexed: 11/15/2022] Open
Abstract
15q deletions have been described in association with intellectual disability and autism spectrum disorder (ASD). Previous reports have supported the role of 15q24 low copy repeats (LCRs) in mediating alternatively sized genomic rearrangements. Based on our reported finding of a 15q24 deletion coinciding with two LCR regions in a patient with epilepsy and ASD, we recommend that patients with 15q24 deletions be evaluated for ASD for early institution of therapy.
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Affiliation(s)
- Dina F Ahram
- Division of Nephrology College of Physicians and Surgeons Columbia University New York City New York
| | - Yasser Al-Sarraj
- Medical Genetics Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Doha Qatar
| | - Rowaida Z Taha
- Medical Genetics Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Doha Qatar
| | - Saba F Elhag
- Medical Genetics Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Doha Qatar
| | - Fouad A Al-Shaban
- Medical Genetics Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Doha Qatar
| | - Hatem El-Shanti
- Pediatrics University of Jordan Amman Jordan.,Pediatrics University of Iowa Iowa City Iowa
| | - Marios Kambouris
- Pathology-Genetics Sidra Medical and Research Center Doha Qatar.,Genetics Yale University School of Medicine New Haven Connecticut
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24
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NEIL1 is a candidate gene associated with common variable immunodeficiency in a patient with a chromosome 15q24 deletion. Clin Immunol 2017; 176:71-76. [PMID: 28093361 DOI: 10.1016/j.clim.2017.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 02/07/2023]
Abstract
We report the first patient with an interstitial deletion of chromosome 15q24.1-q24.3 associated with common variable immunodeficiency (CVID). The 18-year old female patient's clinical and immunological phenotype was compared with 8 additional previously published patients with chr15q24 deletions. A CGH analysis estimated the deletion to be 3.767Mb in size (chr15: 74,410,916-78,178,418) and the result was confirmed using qRT-PCR. We defined an immune-related commonly deleted region (ICDR) within the chromosomal band 15q24.2, deleted in all four patients with different forms of antibody deficiencies. Mutations in the 14 genes within this ICDR were not identified in the remaining allele in our patient by WES and gene expression analyses showed haploinsufficiency of all the genes. Among these genes, we consider Nei Like DNA Glycosylase 1 (NEIL1) as a likely candidate gene due to its crucial role in B-cell activation and terminal differentiation.
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25
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Firouzabadi SG, Kariminejad R, Vameghi R, Darvish H, Ghaedi H, Banihashemi S, Firouzkouhi Moghaddam M, Jamali P, Mofidi Tehrani HF, Dehghani H, Narooie-Nejad M, Jamshidi J, Tafakhori A, Sadabadi S, Najmabadi H, Behjati F. Copy Number Variants in Patients with Autism and Additional Clinical Features: Report of VIPR2 Duplication and a Novel Microduplication Syndrome. Mol Neurobiol 2016; 54:7019-7027. [PMID: 27796743 DOI: 10.1007/s12035-016-0202-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/11/2016] [Indexed: 10/20/2022]
Abstract
Autism is a common neurodevelopmental disorder estimated to affect 1 in 68 children. Many studies have shown the role of copy number variants (CNVs) as a major contributor in the etiology of autism with the overall detection rate of about 10-15 % and over 20 % when syndromic forms of autism exist. In this study, we used array CGH to identify CNVs in 15 Iranian patients with autism. To elevate our diagnostic yield, we selected the sporadic patients who had additional clinical features including intellectual disability (ID), craniofacial anomaly, and seizure. Six out of 15 patients showed clinically relevant CNVs including pathogenic and likely pathogenic copy number gains or losses. We report a novel gene duplication syndrome (10q21.2q21.3 microduplication) and present a new evidence for VIPR2 duplication, as a candidate gene for autism. Furthermore, we describe the first manifesting carrier female with deletion of SLC6A8 and BCAP31 genes on Xq28. Our findings suggest that there might be a higher prevalence of clinically significant CNVs in patients with autism and additional clinical manifestations. The CNV analysis in such patients could lead to the discovery of novel syndromes as well as unraveling the etiology of autism.
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Affiliation(s)
| | | | - Roshanak Vameghi
- Pediatric Neurorehabilitation Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Darvish
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ghaedi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Susan Banihashemi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mahboubeh Firouzkouhi Moghaddam
- Child and Adolescent Psychiatry Department, Zahedan University of Medical Sciences, Zahedan, Iran.,Research Center for Children and Adolescents Health, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | | | - Hossein Dehghani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mehrnaz Narooie-Nejad
- Genetics of Non-communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Javad Jamshidi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Abbas Tafakhori
- Department of Neurology, School of Medicine, Imam Khomeini Hospital and Iranian Center of Neurological Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeid Sadabadi
- Bahar Education and Rehabilitation Center for the handicapped, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Farkhondeh Behjati
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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26
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Witteveen JS, Willemsen MH, Dombroski TCD, van Bakel NHM, Nillesen WM, van Hulten JA, Jansen EJR, Verkaik D, Veenstra-Knol HE, van Ravenswaaij-Arts CMA, Wassink-Ruiter JSK, Vincent M, David A, Le Caignec C, Schieving J, Gilissen C, Foulds N, Rump P, Strom T, Cremer K, Zink AM, Engels H, de Munnik SA, Visser JE, Brunner HG, Martens GJM, Pfundt R, Kleefstra T, Kolk SM. Haploinsufficiency of MeCP2-interacting transcriptional co-repressor SIN3A causes mild intellectual disability by affecting the development of cortical integrity. Nat Genet 2016; 48:877-87. [PMID: 27399968 DOI: 10.1038/ng.3619] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 06/15/2016] [Indexed: 12/13/2022]
Abstract
Numerous genes are associated with neurodevelopmental disorders such as intellectual disability and autism spectrum disorder (ASD), but their dysfunction is often poorly characterized. Here we identified dominant mutations in the gene encoding the transcriptional repressor and MeCP2 interactor switch-insensitive 3 family member A (SIN3A; chromosome 15q24.2) in individuals who, in addition to mild intellectual disability and ASD, share striking features, including facial dysmorphisms, microcephaly and short stature. This phenotype is highly related to that of individuals with atypical 15q24 microdeletions, linking SIN3A to this microdeletion syndrome. Brain magnetic resonance imaging showed subtle abnormalities, including corpus callosum hypoplasia and ventriculomegaly. Intriguingly, in vivo functional knockdown of Sin3a led to reduced cortical neurogenesis, altered neuronal identity and aberrant corticocortical projections in the developing mouse brain. Together, our data establish that haploinsufficiency of SIN3A is associated with mild syndromic intellectual disability and that SIN3A can be considered to be a key transcriptional regulator of cortical brain development.
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Affiliation(s)
- Josefine S Witteveen
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Thaís C D Dombroski
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Nick H M van Bakel
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Willy M Nillesen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Josephus A van Hulten
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Eric J R Jansen
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Dave Verkaik
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Hermine E Veenstra-Knol
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | | | - Marie Vincent
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, Nantes, France
| | - Albert David
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, Nantes, France
| | - Cedric Le Caignec
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, Nantes, France.,Laboratoire de Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Faculté de Médecine, INSERM UMRS 957, Nantes, France
| | - Jolanda Schieving
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Nicola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton National Health Service Foundation Trust, Princess Anne Hospital, Southampton, UK.,Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Patrick Rump
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tim Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Sonja A de Munnik
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Jasper E Visser
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Neurology, Amphia Hospital Breda, Berda, the Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Gerard J M Martens
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Sharon M Kolk
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
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27
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Cáceres A, Esko T, Pappa I, Gutiérrez A, Lopez-Espinosa MJ, Llop S, Bustamante M, Tiemeier H, Metspalu A, Joshi PK, Wilsonx JF, Reina-Castillón J, Shin J, Pausova Z, Paus T, Sunyer J, Pérez-Jurado LA, González JR. Ancient Haplotypes at the 15q24.2 Microdeletion Region Are Linked to Brain Expression of MAN2C1 and Children's Intelligence. PLoS One 2016; 11:e0157739. [PMID: 27355585 PMCID: PMC4927142 DOI: 10.1371/journal.pone.0157739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/05/2016] [Indexed: 11/26/2022] Open
Abstract
The chromosome bands 15q24.1-15q24.3 contain a complex region with numerous segmental duplications that predispose to regional microduplications and microdeletions, both of which have been linked to intellectual disability, speech delay and autistic features. The region may also harbour common inversion polymorphisms whose functional and phenotypic manifestations are unknown. Using single nucleotide polymorphism (SNP) data, we detected four large contiguous haplotype-genotypes at 15q24 with Mendelian inheritance in 2,562 trios, African origin, high population stratification and reduced recombination rates. Although the haplotype-genotypes have been most likely generated by decreased or absent recombination among them, we could not confirm that they were the product of inversion polymorphisms in the region. One of the blocks was composed of three haplotype-genotypes (N1a, N1b and N2), which significantly correlated with intelligence quotient (IQ) in 2,735 children of European ancestry from three independent population cohorts. Homozygosity for N2 was associated with lower verbal IQ (2.4-point loss, p-value = 0.01), while homozygosity for N1b was associated with 3.2-point loss in non-verbal IQ (p-value = 0.0006). The three alleles strongly correlated with expression levels of MAN2C1 and SNUPN in blood and brain. Homozygosity for N2 correlated with over-expression of MAN2C1 over many brain areas but the occipital cortex where N1b homozygous highly under-expressed. Our population-based analyses suggest that MAN2C1 may contribute to the verbal difficulties observed in microduplications and to the intellectual disability of microdeletion syndromes, whose characteristic dosage increment and removal may affect different brain areas.
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Affiliation(s)
- Alejandro Cáceres
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- * E-mail: (AC); (JRG)
| | - Tõnu Esko
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
- Division of Endocrinology, Children’s Hospital Boston, Boston, Massachusetts, United States of America
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Irene Pappa
- School of Pedagogical and Educational Sciences, Erasmus University Rotterdam, Rotterdam, The Netherlands
- Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Armand Gutiérrez
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Maria-Jose Lopez-Espinosa
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO–Universitat Jaume I–Universitat de València, Valencia, Spain
| | - Sabrina Llop
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO–Universitat Jaume I–Universitat de València, Valencia, Spain
| | - Mariona Bustamante
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Genomics and Disease Group, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center-Sophia Children’s Hospital, Rotterdam, The Netherlands
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Peter K. Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
| | - James F. Wilsonx
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland
| | - Judith Reina-Castillón
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Jean Shin
- Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Zdenka Pausova
- Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Tomáš Paus
- Rotman Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Jordi Sunyer
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Luis A. Pérez-Jurado
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Juan R. González
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- * E-mail: (AC); (JRG)
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Deng HZ, You C, Xing Y, Chen KY, Zou XB. A Family-Based Association Study of CYP11A1 and CYP11B1 Gene Polymorphisms With Autism in Chinese Trios. J Child Neurol 2016; 31:733-7. [PMID: 26690694 DOI: 10.1177/0883073815620672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/09/2015] [Indexed: 11/16/2022]
Abstract
Autism spectrum disorder is a group of neurodevelopmental disorders with the higher prevalence in males. Our previous studies have indicated lower progesterone levels in the children with autism spectrum disorder, suggesting involvement of the cytochrome P-450scc gene (CYP11A1) and cytochrome P-45011beta gene (CYP11B1) as candidate genes in autism spectrum disorder. The aim of this study was to investigate the family-based genetic association between single-nucleotide polymorphisms, rs2279357 in the CYP11A1 gene and rs4534 and rs4541 in the CYP11B1 gene and autism spectrum disorder in Chinese children, which were selected according to the location in the coding region and 5' and 3' regions and minor allele frequencies of greater than 0.05 in the Chinese populations. The transmission disequilibrium test and case-control association analyses were performed in 100 Chinese Han autism spectrum disorder family trios. The genotype and allele frequency of the 3 single-nucleotide polymorphisms had no statistical difference between the children with autism spectrum disorder and their parents (P> .05). Transmission disequilibrium test analysis showed transmission disequilibrium of CYP11A1 gene rs2279357 single-nucleotide polymorphisms (χ(2)= 5.038,P< .001). Our findings provide further support for the hypothesis that a susceptibility gene for autism spectrum disorder exists within or near the CYP11A1 gene in the Han Chinese population.
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Affiliation(s)
- Hong-Zhu Deng
- Child Developmental-Behavioral Center, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China Equal contributors
| | - Cong You
- Child Developmental-Behavioral Center, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China Equal contributors
| | - Yu Xing
- Child Developmental-Behavioral Center, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Kai-Yun Chen
- Child Developmental-Behavioral Center, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiao-Bing Zou
- Child Developmental-Behavioral Center, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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29
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Unmasking a novel disease gene NEO1 associated with autism spectrum disorders by a hemizygous deletion on chromosome 15 and a functional polymorphism. Behav Brain Res 2016; 300:135-42. [DOI: 10.1016/j.bbr.2015.10.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 10/14/2015] [Accepted: 10/21/2015] [Indexed: 11/20/2022]
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30
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Palazón-Bru A, Ramírez-Prado D, Cortés E, Aguilar-Segura MS, Gil-Guillén VF. An inferential study of the phenotype for the chromosome 15q24 microdeletion syndrome: a bootstrap analysis. PeerJ 2016; 4:e1641. [PMID: 26925314 PMCID: PMC4768676 DOI: 10.7717/peerj.1641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/08/2016] [Indexed: 11/21/2022] Open
Abstract
In January 2012, a review of the cases of chromosome 15q24 microdeletion syndrome was published. However, this study did not include inferential statistics. The aims of the present study were to update the literature search and calculate confidence intervals for the prevalence of each phenotype using bootstrap methodology. Published case reports of patients with the syndrome that included detailed information about breakpoints and phenotype were sought and 36 were included. Deletions in megabase (Mb) pairs were determined to calculate the size of the interstitial deletion of the phenotypes studied in 2012. To determine confidence intervals for the prevalence of the phenotype and the interstitial loss, we used bootstrap methodology. Using the bootstrap percentiles method, we found wide variability in the prevalence of the different phenotypes (3–100%). The mean interstitial deletion size was 2.72 Mb (95% CI [2.35–3.10 Mb]). In comparison with our work, which expanded the literature search by 45 months, there were differences in the prevalence of 17% of the phenotypes, indicating that more studies are needed to analyze this rare disease.
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Affiliation(s)
- Antonio Palazón-Bru
- Department of Clinical Medicine, Miguel Hernández University, San Juan de Alicante, Alicante, Spain; Research Unit, Elda Hospital, Elda, Alicante, Spain
| | - Dolores Ramírez-Prado
- Clinical Analysis Department, Elda Hospital, Elda, Alicante, Spain; Pharmacology, Pediatrics and Organic Chemistry Department, Miguel Hernández University, San Juan de Alicante, Alicante, Spain
| | - Ernesto Cortés
- Pharmacology, Pediatrics and Organic Chemistry Department, Miguel Hernández University , San Juan de Alicante, Alicante , Spain
| | - María Soledad Aguilar-Segura
- Pharmacology, Pediatrics and Organic Chemistry Department, Miguel Hernández University , San Juan de Alicante, Alicante , Spain
| | - Vicente Francisco Gil-Guillén
- Department of Clinical Medicine, Miguel Hernández University, San Juan de Alicante, Alicante, Spain; Research Unit, Elda Hospital, Elda, Alicante, Spain
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31
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Inherited 15q24 microdeletion syndrome in twins and their father with phenotypic variability. Eur J Med Genet 2015; 58:111-5. [DOI: 10.1016/j.ejmg.2014.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 12/01/2014] [Indexed: 11/20/2022]
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32
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Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability. Nat Genet 2014; 46:1293-302. [PMID: 25326701 PMCID: PMC4244265 DOI: 10.1038/ng.3120] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 09/25/2014] [Indexed: 12/14/2022]
Abstract
Recurrent deletions of chromosome 15q13.3 associate with intellectual disability, schizophrenia, autism and epilepsy. To gain insight into its instability, we sequenced the region in patients, normal individuals and nonhuman primates. We discovered five structural configurations of the human chromosome 15q13.3 region ranging in size from 2 to 3 Mbp. These configurations arose recently (~0.5–0.9 million years ago) as a result of human-specific expansions of segmental duplications and two independent inversion events. All inversion breakpoints map near GOLGA8 core duplicons—a ~14 kbp primate-specific chromosome 15 repeat that became organized into larger palindromic structures. GOLGA8-flanked palindromes also demarcate the breakpoints of recurrent 15q13.3 microdeletions, the expansion of chromosome 15 segmental duplications in the human lineage, and independent structural changes in apes. The significant clustering (p=0.002) of breakpoints provides mechanistic evidence for the role of this core duplicon and its palindromic architecture in promoting evolutionary and disease-related instability of chromosome 15.
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33
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Watson CT, Marques-Bonet T, Sharp AJ, Mefford HC. The genetics of microdeletion and microduplication syndromes: an update. Annu Rev Genomics Hum Genet 2014; 15:215-244. [PMID: 24773319 DOI: 10.1146/annurev-genom-091212-153408] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chromosomal abnormalities, including microdeletions and microduplications, have long been associated with abnormal developmental outcomes. Early discoveries relied on a common clinical presentation and the ability to detect chromosomal abnormalities by standard karyotype analysis or specific assays such as fluorescence in situ hybridization. Over the past decade, the development of novel genomic technologies has allowed more comprehensive, unbiased discovery of microdeletions and microduplications throughout the human genome. The ability to quickly interrogate large cohorts using chromosome microarrays and, more recently, next-generation sequencing has led to the rapid discovery of novel microdeletions and microduplications associated with disease, including very rare but clinically significant rearrangements. In addition, the observation that some microdeletions are associated with risk for several neurodevelopmental disorders contributes to our understanding of shared genetic susceptibility for such disorders. Here, we review current knowledge of microdeletion/duplication syndromes, with a particular focus on recurrent rearrangement syndromes.
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Affiliation(s)
- Corey T Watson
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra/CSIC, 08003 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.,Centro Nacional de Análisis Genómico, 08023 Barcelona, Spain
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Heather C Mefford
- Department of Pediatrics, University of Washington, Seattle, Washington 98195
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34
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Carvill GL, Mefford HC. Microdeletion syndromes. Curr Opin Genet Dev 2013; 23:232-9. [PMID: 23664828 DOI: 10.1016/j.gde.2013.03.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 03/11/2013] [Accepted: 03/25/2013] [Indexed: 01/11/2023]
Abstract
The recent explosion in the implementation of genome-wide microarray technology to discover rare, pathogenic genomic rearrangements in a variety of diseases has led to the discovery of numerous microdeletion syndromes. It is now clear that these microdeletions are associated with extensive phenotypic heterogeneity and incomplete penetrance. A subset of recurrent microdeletions underpin diverse phenotypes, including intellectual disability, autism, epilepsy and neuropsychiatric disorders. Recent studies highlight a role for additional low frequency variants, or 'second hits' to account for this variability. The implementation of massively parallel sequencing and epigenetic models may provide a powerful prospective approach to the delineation of microdeletion syndrome phenotypes.
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Affiliation(s)
- Gemma L Carvill
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
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35
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Flore LA, Milunsky JM. Updates in the genetic evaluation of the child with global developmental delay or intellectual disability. Semin Pediatr Neurol 2012; 19:173-80. [PMID: 23245550 DOI: 10.1016/j.spen.2012.09.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Global developmental delay (GDD) and intellectual disability (ID) occur in up to 3% of the general population and are even more commonly encountered in the setting of the pediatric neurology clinic. New advances in technology and in the understanding of genetic disorders have led to changes in the diagnostic approach to a child with unexplained GDD or ID. Chromosomal microarray has become a first-line test for evaluation of patients in this population and has both significantly increased diagnostic yield and introduced new challenges in the interpretation of copy number variants of uncertain significance. The G-banded karyotype is now frequently utilized as an adjunct to the microarray rather than as a first-line test in individuals with GDD or ID. Fragile X DNA testing continues to be recommended in the initial evaluation of the child with GDD or ID. The presence or absence of certain cardinal features (such as microcephaly or macrocephaly, seizures, autism, abnormal neurologic examination, and facial dysmorphism) can be utilized to direct single-gene molecular testing. The availability of next-generation and massively parallel sequencing technologies has enabled the use of genetic testing panels, in which dozens of genes associated with GDD or ID may be rapidly analyzed. Most recently, the clinical availability of whole-genome and whole-exome sequencing has opened new possibilities for the evaluation of individuals with GDD or ID who have previously eluded a genetic diagnosis. Consultation with a medical geneticist is recommended when progressing beyond first-tier analyses to most efficiently prioritize testing.
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36
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Smith M, Flodman PL, Gargus JJ, Simon MT, Verrell K, Haas R, Reiner GE, Naviaux R, Osann K, Spence MA, Wallace DC. Mitochondrial and ion channel gene alterations in autism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1796-802. [PMID: 22538295 DOI: 10.1016/j.bbabio.2012.04.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 04/09/2012] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
Abstract
To evaluate the potential importance in autistic subjects of copy number variants (CNVs) that alter genes of relevance to bioenergetics, ionic metabolism, and synaptic function, we conducted a detailed microarray analysis of 69 autism probands and 35 parents, compared to 89 CEU HapMap controls. This revealed that the frequency CNVs of≥100kb and CNVs of≥10 Kb were markedly increased in probands over parents and in probands and parents over controls. Evaluation of CNVs≥1Mb by chromosomal FISH confirmed the molecular identity of a subset of the CNVs, some of which were associated with chromosomal rearrangements. In a number of the cases, CNVs were found to alter the copy number of genes that are important in mitochondrial oxidative phosphorylation (OXPHOS), ion and especially calcium transport, and synaptic structure. Hence, autism might result from alterations in multiple bioenergetic and metabolic genes required for mental function. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Affiliation(s)
- Moyra Smith
- Department of Pediatrics University of California, Irvine, CA, USA.
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37
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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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