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Buecking J, An Y, Bi W, Hinderhofer K, Theiß S, Slavotinek A, Schaaf CP. A Case of Prader-Willi Syndrome With a Deletion Including MAGEL2, NDN, and MKRN3, but Excluding SNRPN and SNORD116. Am J Med Genet A 2025:e64070. [PMID: 40231584 DOI: 10.1002/ajmg.a.64070] [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: 01/10/2025] [Revised: 03/14/2025] [Accepted: 03/18/2025] [Indexed: 04/16/2025]
Abstract
Prader-Willi syndrome (PWS) is a neurodevelopmental disorder typically caused by large deletions or imprinting defects on chromosome 15q11.2, encompassing multiple genes. While the contribution of individual genes to the PWS phenotype remains unclear, previous studies suggested that isolated deletions of MAGEL2, NDN, and MKRN3, excluding the SNRPN/SNORD116 locus, were insufficient to cause PWS. Here, we present a case report of a patient with an isolated deletion of MAGEL2, NDN, and MKRN3 who exhibits the full PWS phenotype, including neonatal hypotonia, developmental delay, hyperphagia, obesity, and behavioral issues. We explore the potential mechanisms underlying this case and investigate the potential contribution of the deleted genes to the observed phenotype. This case challenges previous findings and highlights the complexity of genotype-phenotype correlations in PWS. We compare the clinical data of our patient with previous reports and discuss the discrepancy with earlier findings. Our findings underscore the need for further research to fully elucidate the roles of individual genes within the PWS locus and the mechanisms underlying the phenotypic spectrum of this complex disorder.
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Affiliation(s)
- Jannis Buecking
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Yu An
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, California, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | | | - Susanne Theiß
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Anne Slavotinek
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, California, USA
- Department of Pediatrics, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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2
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Previdi A, Jordan P, Egloff C, Coussement A, Ahmed-Eli S, Tudal L, Bienvenu T, Picone O, Dupont JM. Prenatal diagnosis of a 15q24.1 microdeletion in a fetus with cerebral and urogenital abnormalities. Clin Genet 2024; 106:537-544. [PMID: 39012202 DOI: 10.1111/cge.14592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/21/2024] [Accepted: 07/05/2024] [Indexed: 07/17/2024]
Abstract
15q24.1 microdeletion syndrome is a recently described condition often resulting from non-allelic homologous recombination (NAHR). Typical clinical features include pre and post-natal growth retardation, facial dysmorphism, developmental delay and intellectual disability. Nonspecific urogenital, skeletal, and digit abnormalities may be present, although other congenital malformations are less frequent. Consequently, only one case was reported prenatally, complicating the genotype-phenotype correlation and the genetic counseling. We identified prenatally a second case, presenting with cerebral abnormalities including hydrocephaly, macrocephaly, cerebellum hypoplasia, vermis hypoplasia, rhombencephalosynapsis, right kidney agenesis with left kidney duplication and micropenis. Genome-wide aCGH assay allowed a diagnosis at 26 weeks of amenorrhea revealing a 1.6 Mb interstitial deletion on the long arm of chromosome 15 at 15q24.1-q24.2 (arr[GRCh37] 15q24.1q24.2(74,399,112_76,019,966)x1). A deep review of the literature was undertaken to further delineate the prenatal clinical features and the candidate genes involved in the phenotype. Cerebral malformations are typically nonspecific, but microcephaly appears to be the most frequent in postnatal cases. Our case is the first reported with a frank cerebellar involvement.
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Affiliation(s)
- Anaïk Previdi
- APHP.Centre-Université Paris Cité, Site Hôpital Cochin, Service de Médecine Génomique des Maladies de Système et d'Organe, Paris, France
| | - Pénélope Jordan
- APHP.Centre-Université Paris Cité, Site Hôpital Cochin, Service de Médecine Génomique des Maladies de Système et d'Organe, Paris, France
| | - Charles Egloff
- AP-HP.Nord-Université Paris Cité, Site Hôpital Louis Mourier, Service de Gynécologie Obstétrique, Colombes, France
| | - Aurélie Coussement
- APHP.Centre-Université Paris Cité, Site Hôpital Cochin, Service de Médecine Génomique des Maladies de Système et d'Organe, Paris, France
| | - Samira Ahmed-Eli
- APHP.Centre-Université Paris Cité, Site Hôpital Cochin, Service de Médecine Génomique des Maladies de Système et d'Organe, Paris, France
| | - Laure Tudal
- AP-HP.Nord-Université Paris Cité, Site Hôpital Louis Mourier, Service de Gynécologie Obstétrique, Colombes, France
| | - Thierry Bienvenu
- APHP.Centre-Université Paris Cité, Site Hôpital Cochin, Service de Médecine Génomique des Maladies de Système et d'Organe, Paris, France
| | - Olivier Picone
- AP-HP.Nord-Université Paris Cité, Site Hôpital Louis Mourier, Service de Gynécologie Obstétrique, Colombes, France
| | - Jean-Michel Dupont
- APHP.Centre-Université Paris Cité, Site Hôpital Cochin, Service de Médecine Génomique des Maladies de Système et d'Organe, Paris, France
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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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Drevet JR, Hallak J, Nasr-Esfahani MH, Aitken RJ. Reactive Oxygen Species and Their Consequences on the Structure and Function of Mammalian Spermatozoa. Antioxid Redox Signal 2022; 37:481-500. [PMID: 34913729 DOI: 10.1089/ars.2021.0235] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Significance: Among the 200 or so cell types that comprise mammals, spermatozoa have an ambiguous relationship with the reactive oxygen species (ROS) inherent in the consumption of oxygen that supports aerobic metabolism. Recent Advances: In this review, we shall see that spermatozoa need the action of ROS to reach their structural and functional maturity, but that due to intrinsic unique characteristics, they are, perhaps more than any other cell type, susceptible to oxidative damage. Recent studies have improved our knowledge of how oxidative damage affects sperm structures and functions. The focus of this review will be on how genetic and epigenetic oxidative alterations to spermatozoa can have dramatic unintended consequences in terms of both the support and the suppression of sperm function. Critical Issues: Oxidative stress can have dramatic consequences not only for the spermatozoon itself, but also, and above all, on its primary objective, which is to carry out fertilization and to ensure, in part, that the embryonic development program should lead to a healthy progeny. Future Directions: Sperm oxidative DNA damage largely affects the integrity of the paternal genetic material to such an extent that the oocyte may have difficulties in correcting it. Diagnostic and therapeutic actions should be considered more systematically, especially in men with difficulties to conceive. Research is underway to determine whether the epigenetic information carried by spermatozoa is also subject to changes mediated by pro-oxidative situations. Antioxid. Redox Signal. 37, 481-500.
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Affiliation(s)
- Joël R Drevet
- Faculty of Medicine, GReD Institute, INSERM U1103-CNRS UMR6293-Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jorge Hallak
- Androscience, Science and Innovation Center in Andrology and High-Complex Clinical and Research Andrology Laboratory, São Paulo, Brazil.,Division of Urology, University of São Paulo, São Paulo, Brazil.,Men's Health Study Group, Institute for Advanced Studies, University of São Paulo, São Paulo, Brazil.,Reproductive Toxicology Unit, Department of Pathology, University of São Paulo, São Paulo, Brazil
| | - Mohammad-Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.,Isfahan Fertility and Infertility Center, Isfahan, Iran
| | - Robert J Aitken
- Faculty of Science and Priority Research Center for Reproductive Sciences, The University of Newcastle, Callaghan, Australia.,Faculty of Health and Medicine, Priority Research Center for Reproductive Sciences, The University of Newcastle, Callaghan, Australia.,Hunter Medical Research Institute, New Lambton Heights, Australia
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Zhang Y, Liu X, Gao H, Cui W, Zhang B, Zhao Y. Molecular and phenotypic characteristics of 15q24 microdeletion in pediatric patients with developmental disorders. Mol Cytogenet 2021; 14:57. [PMID: 34922566 PMCID: PMC8684056 DOI: 10.1186/s13039-021-00574-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/03/2021] [Indexed: 11/18/2022] Open
Abstract
Chromosome 15q24 microdeletion is a rare genetic disorder characterized by development delay, facial dysmorphism, congenital malformations, and occasional autism spectrum disorder (ASD). In this study, we identified five cases of 15q24 microdeletion using multiplex ligation-dependent probe amplification (MLPA) technology in a cohort of patients with developmental delay and/or intellectual disability. Two of these five cases had deletions that overlapped with the previously defined 1.1 Mb region observed in most reported cases. Two cases had smaller deletions (< 0.57 Mb) in the 15q24.1 low copy repeat (LCR) B-C region. They presented significant neurobehavioral features, suggesting that this smaller interval is critical for core phenotypes of 15q24 microdeletion syndrome. One case had minimal homozygous deletion of less than 0.11 Mb in the 15q24.1 LCR B-C region, which contained CYP1A1 (cytochrome P450 family 1 subfamily A member 1) and EDC3 (enhancer of mRNA decapping 3) genes, resulting in poor immunity, severe laryngeal stridor, and lower limbs swelling. This study provides additional evidence of 15q24 microdeletion syndrome with genetic and clinical findings. The results will be of significance to pediatricians in their daily practice.
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Affiliation(s)
- Yuanyuan Zhang
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Xiaoliang Liu
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Haiming Gao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Wanting Cui
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Bijun Zhang
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Yanyan Zhao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China.
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6
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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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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: 6] [Impact Index Per Article: 1.2] [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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8
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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: 5] [Impact Index Per Article: 1.0] [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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Xavier MJ, Nixon B, Roman SD, Scott RJ, Drevet JR, Aitken RJ. Paternal impacts on development: identification of genomic regions vulnerable to oxidative DNA damage in human spermatozoa. Hum Reprod 2019; 34:1876-1890. [DOI: 10.1093/humrep/dez153] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
Abstract
STUDY QUESTION
Do all regions of the paternal genome within the gamete display equivalent vulnerability to oxidative DNA damage?
SUMMARY ANSWER
Oxidative DNA damage is not randomly distributed in mature human spermatozoa but is instead targeted, with particular chromosomes being especially vulnerable to oxidative stress.
WHAT IS KNOWN ALREADY
Oxidative DNA damage is frequently encountered in the spermatozoa of male infertility patients. Such lesions can influence the incidence of de novo mutations in children, yet it remains to be established whether all regions of the sperm genome display equivalent susceptibility to attack by reactive oxygen species.
STUDY DESIGN, SIZE, DURATION
Human spermatozoa obtained from normozoospermic males (n = 8) were split into equivalent samples and subjected to either hydrogen peroxide (H2O2) treatment or vehicle controls before extraction of oxidized DNA using a modified DNA immunoprecipitation (MoDIP) protocol. Specific regions of the genome susceptible to oxidative damage were identified by next-generation sequencing and validated in the spermatozoa of normozoospermic males (n = 18) and in patients undergoing infertility evaluation (n = 14).
PARTICIPANTS/MATERIALS, SETTING, METHODS
Human spermatozoa were obtained from normozoospermic males and divided into two identical samples prior to being incubated with either H2O2 (5 mm, 1 h) to elicit oxidative stress or an equal volume of vehicle (untreated controls). Alternatively, spermatozoa were obtained from fertility patients assessed as having high basal levels of oxidative stress within their spermatozoa. All semen samples were subjected to MoDIP to selectively isolate oxidized DNA, prior to sequencing of the resultant DNA fragments using a next-generation whole-genomic sequencing platform. Bioinformatic analysis was then employed to identify genomic regions vulnerable to oxidative damage, several of which were selected for real-time quantitative PCR (qPCR) validation.
MAIN RESULTS AND THE ROLE OF CHANCE
Approximately 9000 genomic regions, 150–1000 bp in size, were identified as highly vulnerable to oxidative damage in human spermatozoa. Specific chromosomes showed differential susceptibility to damage, with chromosome 15 being particularly sensitive to oxidative attack while the sex chromosomes were protected. Susceptible regions generally lay outside protamine- and histone-packaged domains. Furthermore, we confirmed that these susceptible genomic sites experienced a dramatic (2–15-fold) increase in their burden of oxidative DNA damage in patients undergoing infertility evaluation compared to normal healthy donors.
LIMITATIONS, REASONS FOR CAUTION
The limited number of samples analysed in this study warrants external validation, as do the implications of our findings. Selection of male fertility patients was based on high basal levels of oxidative stress within their spermatozoa as opposed to specific sub-classes of male factor infertility.
WIDER IMPLICATIONS OF THE FINDINGS
The identification of genomic regions susceptible to oxidation in the male germ line will be of value in focusing future analyses into the mutational load carried by children in response to paternal factors such as age, the treatment of male infertility using ART and paternal exposure to environmental toxicants.
STUDY FUNDING/COMPETING INTEREST(S)
Project support was provided by the University of Newcastle’s (UoN) Priority Research Centre for Reproductive Science. M.J.X. was a recipient of a UoN International Postgraduate Research Scholarship. B.N. is the recipient of a National Health and Medical Research Council of Australia Senior Research Fellowship. Authors declare no conflict of interest.
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Affiliation(s)
- M J Xavier
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - B Nixon
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - S D Roman
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Drug Development, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - R J Scott
- Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Medical Genetics, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- Division of Molecular Medicine, Pathology North, John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - J R Drevet
- GReD Laboratory, CNRS UMR6293—INSERM U1103—Clermont Université, Clermont-Ferrand, France
| | - R J Aitken
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
- Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Medical Genetics, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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10
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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: 1.1] [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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11
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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: 0.5] [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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12
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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: 1.4] [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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13
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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: 65] [Impact Index Per Article: 7.2] [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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14
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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: 0.2] [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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