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Starosta RT, Jensen N, Couteranis S, Slaugh R, Easterlin D, Tate V, Sams EI, Valle K, Akinwe T, Hou YCC, Turner TN, Cole FS, Milbrandt J, Dickson P. Using a new analytic approach for genotyping and phenotyping chromosome 9p deletion syndrome. Eur J Hum Genet 2024; 32:1095-1105. [PMID: 38972963 PMCID: PMC11369271 DOI: 10.1038/s41431-024-01667-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/16/2024] [Accepted: 06/26/2024] [Indexed: 07/09/2024] Open
Abstract
Using a new analytic method ("unique non-overlapping region" (UNOR) analysis), we characterized the genotypes and phenotypes of a large cohort of individuals diagnosed with chromosome 9p deletion syndrome (9PMS) and defined critical genomic regions. We extracted phenotypic information from 48 individuals with 9PMS from medical records and used a guided interview with caregivers to clarify ambiguities. Using high-resolution whole-genome sequencing for breakpoint definition, we aligned deletions and drew virtual breakpoints to obtain UNORs associated with phenotypic characteristics. We next extracted genotype and phenotype data for 57 individuals identified from a systematic review of the 9PMS literature and analyzed these as above. Common phenotypic features included developmental delay/intellectual disability, dysmorphic features, hypotonia, genital defects in XY individuals, psychiatric diagnoses, chronic constipation, atopic disease, vision problems, autism spectrum disorder, gastroesophageal reflux disease, trigonocephaly, congenital heart disease, and neonatal hypoglycemia. Our approach confirmed previous literature reports of an association of FREM1 with trigonocephaly and suggested a possible modifier element for this phenotype. In conclusion, the UNOR approach delineated phenotypic characteristics for 9PMS and confirmed the critical role of FREM1 and a possible long-distance regulatory element in pathogenesis of trigonocephaly that will need to be replicated in future studies.
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Affiliation(s)
- Rodrigo Tzovenos Starosta
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA.
| | - Nathaniel Jensen
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
| | - Sophia Couteranis
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
| | - Dawn Easterlin
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
| | - Victoria Tate
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
| | - Eleanor I Sams
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kostandin Valle
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Titilope Akinwe
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ying-Chen Claire Hou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - F Sessions Cole
- Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Patricia Dickson
- Division of Genetics and Genomic Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, 63110, USA
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2
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Pugnaloni F, Onesimo R, Blandino R, Putotto C, Versacci P, Delogu AB, Leoni C, Trevisan V, Croci I, Calì F, Digilio MC, Zampino G, Marino B, Calcagni G. Insights into the Cardiac Phenotype in 9p Deletion Syndrome: A Multicenter Italian Experience and Literature Review. Genes (Basel) 2023; 14:146. [PMID: 36672887 PMCID: PMC9859094 DOI: 10.3390/genes14010146] [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: 12/07/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023] Open
Abstract
Chromosome 9p deletion syndrome is a rare autosomal dominant disorder presenting with a broad spectrum of clinical features, including congenital heart defects (CHDs). To date, studies focused on a deep characterization of cardiac phenotype and function associated with this condition are lacking. We conducted a multicentric prospective observational study on a cohort of 10 patients with a molecular diagnosis of 9p deletion syndrome, providing a complete cardiological assessment through conventional echocardiography and tissue Doppler imaging echo modality. As a result, we were able to demonstrate that patients with 9p deletion syndrome without major CHDs may display subclinical cardiac structural changes and left-ventricle systolic and diastolic dysfunction. Albeit needing validation in a larger cohort, our findings support the idea that a complete cardiac assessment should be performed in patients with 9p deletion syndrome and should be integrated in the context of a long-term follow-up.
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Affiliation(s)
- Flaminia Pugnaloni
- Medical and Surgical Department of Fetus, Newborn and Infant, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
- Department of Pediatrics, Obstetrics and Gynecology, “Sapienza” University of Rome, Policlinico Umberto I, 00155 Rome, Italy
| | - Roberta Onesimo
- Rare Diseases Unit, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, 00168 Rome, Italy
- Pediatric Unit, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, 00168 Rome, Italy
| | - Rita Blandino
- Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Carolina Putotto
- Department of Pediatrics, Obstetrics and Gynecology, “Sapienza” University of Rome, Policlinico Umberto I, 00155 Rome, Italy
| | - Paolo Versacci
- Department of Pediatrics, Obstetrics and Gynecology, “Sapienza” University of Rome, Policlinico Umberto I, 00155 Rome, Italy
| | - Angelica Bibiana Delogu
- Pediatric Unit, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, 00168 Rome, Italy
- Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Chiara Leoni
- Rare Diseases Unit, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, 00168 Rome, Italy
- Pediatric Unit, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, 00168 Rome, Italy
| | - Valentina Trevisan
- Rare Diseases Unit, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, 00168 Rome, Italy
| | - Ileana Croci
- Multifactorial and Complex Diseases Research Area, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Federica Calì
- Department of Cardiac Surgery, Cardiology and Heart and Lung Transplant, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | | | - Giuseppe Zampino
- Rare Diseases Unit, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, 00168 Rome, Italy
- Pediatric Unit, Fondazione Policlinico Universitario Agostino Gemelli, IRCCS, 00168 Rome, Italy
- Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Bruno Marino
- Department of Pediatrics, Obstetrics and Gynecology, “Sapienza” University of Rome, Policlinico Umberto I, 00155 Rome, Italy
| | - Giulio Calcagni
- Department of Cardiac Surgery, Cardiology and Heart and Lung Transplant, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
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3
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Sams EI, Ng JK, Tate V, Claire Hou YC, Cao Y, Antonacci-Fulton L, Belhassan K, Neidich J, Mitra RD, Cole FS, Dickson P, Milbrandt J, Turner TN. From karyotypes to precision genomics in 9p deletion and duplication syndromes. HGG ADVANCES 2022; 3:100081. [PMID: 35047865 PMCID: PMC8756500 DOI: 10.1016/j.xhgg.2021.100081] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 12/21/2021] [Indexed: 11/27/2022] Open
Abstract
While 9p deletion and duplication syndromes have been studied for several years, small sample sizes and minimal high-resolution data have limited a comprehensive delineation of genotypic and phenotypic characteristics. In this study, we examined genetic data from 719 individuals in the worldwide 9p Network Cohort: a cohort seven to nine times larger than any previous study of 9p. Most breakpoints occur in bands 9p22 and 9p24, accounting for 35% and 38% of all breakpoints, respectively. Bands 9p11 and 9p12 have the fewest breakpoints, with each accounting for 0.6% of all breakpoints. The most common phenotype in 9p deletion and duplication syndromes is developmental delay, and we identified eight known neurodevelopmental disorder genes in 9p22 and 9p24. Since it has been previously reported that some individuals have a secondary structural variant related to the 9p variant, we examined our cohort for these variants and found 97 events. The top secondary variant involved 9q in 14 individuals (1.9%), including ring chromosomes and inversions. We identified a gender bias with significant enrichment for females (p = 0.0006) that may arise from a sex reversal in some individuals with 9p deletions. Genes on 9p were characterized regarding function, constraint metrics, and protein-protein interactions, resulting in a prioritized set of genes for further study. Finally, we achieved precision genomics in one child with a complex 9p structural variation using modern genomic technologies, demonstrating that long-read sequencing will be integral for some cases. Our study is the largest ever on 9p-related syndromes and provides key insights into genetic factors involved in these syndromes.
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Affiliation(s)
- Eleanor I. Sams
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey K. Ng
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Victoria Tate
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ying-Chen Claire Hou
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yang Cao
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Khadija Belhassan
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Julie Neidich
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robi D. Mitra
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - F. Sessions Cole
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Patricia Dickson
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
- Needleman Center for Neurometabolism and Axonal Therapeutics, St. Louis, MO, USA
| | - Tychele N. Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
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4
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Mohamed AM, Kamel AK, Eid MM, Eid OM, Mekkawy M, Hussein SH, Zaki MS, Esmail S, Afifi HH, El-Kamah GY, Otaify GA, El-Awady HA, Elaidy A, Essa MY, El-Ruby M, Ashaat EA, Hammad SA, Mazen I, Abdel-Salam GMH, Aglan M, Temtamy S. Chromosome 9p terminal deletion in nine Egyptian patients and narrowing of the critical region for trigonocephaly. Mol Genet Genomic Med 2021; 9:e1829. [PMID: 34609792 PMCID: PMC8606205 DOI: 10.1002/mgg3.1829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 05/22/2021] [Accepted: 09/07/2021] [Indexed: 11/30/2022] Open
Abstract
Background This study aimed to delineate the clinical phenotype of patients with 9p deletions, pinpoint the chromosomal breakpoints, and identify the critical region for trigonocephaly, which is a frequent finding in 9p terminal deletion. Methods We investigated a cohort of nine patients with chromosome 9p terminal deletions who all displayed developmental delay, intellectual disability, hypotonia, and dysmorphic features. Of them, eight had trigonocephaly, seven had brain anomalies, seven had autistic manifestations, seven had fair hair, and six had a congenital heart defect (CHD). Results Karyotyping revealed 9p terminal deletion in all patients, and patients 8 and 9 had additional duplication of other chromosomal segments. We used six bacterial artificial chromosome (BAC) clones that could identify the breakpoints at 17–20 Mb from the 9p terminus. Array CGH identified the precise extent of the deletion in six patients; the deleted regions ranged from 16 to 18.8 Mb in four patients, patient 8 had an 11.58 Mb deletion and patient 9 had a 2.3 Mb deletion. Conclusion The gene deletion in the 9p24 region was insufficient to cause ambiguous genitalia because six of the nine patients had normal genitalia. We suggest that the critical region for trigonocephaly lies between 11,575 and 11,587 Mb from the chromosome 9p terminus. To the best of our knowledge, this is the minimal critical region reported for trigonocephaly in 9p deletion syndrome, and it warrants further delineation.
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Affiliation(s)
- Amal M Mohamed
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Alaa K Kamel
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Maha M Eid
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Ola M Eid
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Mona Mekkawy
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Shymaa H Hussein
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Maha S Zaki
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Samira Esmail
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Hanan H Afifi
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Ghada Y El-Kamah
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Ghada A Otaify
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Heba Ahmed El-Awady
- Department of Pediatrics, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Aya Elaidy
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Mahmoud Y Essa
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Mona El-Ruby
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Engy A Ashaat
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Saida A Hammad
- Division of Human Genetics and Genome Research, Department of Human Cytogenetics, National Research Centre, Cairo, Egypt
| | - Inas Mazen
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Ghada M H Abdel-Salam
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Mona Aglan
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Samia Temtamy
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt
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5
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Gregoric Kumperscak H, Krgovic D, Drobnic Radobuljac M, Senica N, Zagorac A, Kokalj Vokac N. CNVs and Chromosomal Aneuploidy in Patients With Early-Onset Schizophrenia and Bipolar Disorder: Genotype-Phenotype Associations. Front Psychiatry 2020; 11:606372. [PMID: 33510659 PMCID: PMC7837028 DOI: 10.3389/fpsyt.2020.606372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/07/2020] [Indexed: 11/17/2022] Open
Abstract
Introduction: Early-onset schizophrenia (EOS) and bipolar disorder (EOB) start before the age of 18 years and have a more severe clinical course, a worse prognosis, and a greater genetic loading compared to the late-onset forms. Copy number variations (CNVs) are an important genetic factor in the etiology of psychiatric disorders. Therefore, this study aimed to analyze CNVs in patients with EOS and EOB and to establish genotype-phenotype relationships for contiguous gene syndromes or genes affected by identified CNVs. Methods: Molecular karyotyping was performed in 45 patients, 38 with EOS and seven with EOB hospitalized between 2010 and 2017. The exclusion criteria were medical or neurological disorders or IQ under 70. Detected CNVs were analyzed according to the standards and guidelines of the American College of Medical Genetics. Result: Molecular karyotyping showed CNVs in four patients with EOS (encompassing the PAK2, ADAMTS3, and ADAMTSL1 genes, and the 16p11.2 microduplication syndrome) and in two patients with EOB (encompassing the ARHGAP11B and PRODH genes). In one patient with EOB, a chromosomal aneuploidy 47, XYY was found. Discussion: Our study is the first study of CNVs in EOS and EOB patients in Slovenia. Our findings support the association of the PAK2, ARHGAP11B, and PRODH genes with schizophrenia and/or bipolar disorder. To our knowledge, this is also the first report of a multiplication of the ADAMTSL1 gene and the smallest deletion of the PAK2 gene in a patient with EOS, and one of the few reports of the 47, XYY karyotype in a patient with EOB.
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Affiliation(s)
- Hojka Gregoric Kumperscak
- Department of Pediatrics, University Medical Center Maribor, Maribor, Slovenia.,Medical Faculty, University of Maribor, Maribor, Slovenia
| | - Danijela Krgovic
- Medical Faculty, University of Maribor, Maribor, Slovenia.,Laboratory of Medical Genetics, University Medical Center Maribor, Maribor, Slovenia
| | - Maja Drobnic Radobuljac
- Unit for Intensive Child and Adolescent Psychiatry, Center for Mental Health, University Psychiatric Clinic Ljubljana, Ljubljana, Slovenia.,Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Senica
- Department of Pediatrics, University Medical Center Maribor, Maribor, Slovenia
| | - Andreja Zagorac
- Laboratory of Medical Genetics, University Medical Center Maribor, Maribor, Slovenia
| | - Nadja Kokalj Vokac
- Medical Faculty, University of Maribor, Maribor, Slovenia.,Laboratory of Medical Genetics, University Medical Center Maribor, Maribor, Slovenia
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6
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Aoi H, Mizuguchi T, Ceroni JR, Kim VEH, Furquim I, Honjo RS, Iwaki T, Suzuki T, Sekiguchi F, Uchiyama Y, Azuma Y, Hamanaka K, Koshimizu E, Miyatake S, Mitsuhashi S, Takata A, Miyake N, Takeda S, Itakura A, Bertola DR, Kim CA, Matsumoto N. Comprehensive genetic analysis of 57 families with clinically suspected Cornelia de Lange syndrome. J Hum Genet 2019; 64:967-978. [PMID: 31337854 DOI: 10.1038/s10038-019-0643-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/03/2019] [Accepted: 07/09/2019] [Indexed: 12/19/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a rare multisystem disorder with specific dysmorphic features. Pathogenic genetic variants encoding cohesion complex subunits and interacting proteins (e.g., NIPBL, SMC1A, SMC3, HDAC8, and RAD21) are the major causes of CdLS. However, there are many clinically diagnosed cases of CdLS without pathogenic variants in these genes. To identify further genetic causes of CdLS, we performed whole-exome sequencing in 57 CdLS families, systematically evaluating both single nucleotides variants (SNVs) and copy number variations (CNVs). We identified pathogenic genetic changes in 36 out of 57 (63.2 %) families, including 32 SNVs and four CNVs. Two known CdLS genes, NIPBL and SMC1A, were mutated in 23 and two cases, respectively. Among the remaining 32 individuals, four genes (ANKRD11, EP300, KMT2A, and SETD5) each harbored a pathogenic variant in a single individual. These variants are known to be involved in CdLS-like. Furthermore, pathogenic CNVs were detected in NIPBL, MED13L, and EHMT1, along with pathogenic SNVs in ZMYND11, MED13L, and PHIP. These three latter genes were involved in diseases other than CdLS and CdLS-like. Systematic clinical evaluation of all patients using a recently proposed clinical scoring system showed that ZMYND11, MED13L, and PHIP abnormality may cause CdLS or CdLS-like.
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Affiliation(s)
- Hiromi Aoi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - José Ricard Ceroni
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Veronica Eun Hue Kim
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Isabel Furquim
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Rachel S Honjo
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Takuma Iwaki
- Department of Pediatrics, University Hospital, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Toshifumi Suzuki
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Oncology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Atsuo Itakura
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Débora R Bertola
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Chong Ae Kim
- Clinical Genetics Unit, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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7
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Entire FGF12 duplication by complex chromosomal rearrangements associated with West syndrome. J Hum Genet 2019; 64:1005-1014. [PMID: 31311986 DOI: 10.1038/s10038-019-0641-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/23/2019] [Accepted: 06/26/2019] [Indexed: 11/09/2022]
Abstract
Complex rearrangements of chromosomes 3 and 9 were found in a patient presenting with severe epilepsy, developmental delay, dysmorphic facial features, and skeletal abnormalities. Molecular cytogenetic analysis revealed 46,XX.ish der(9)(3qter→3q28::9p21.1→9p22.3::9p22.3→9qter)(RP11-368G14+,RP11-299O8-,RP11-905L2++,RP11-775E6++). Her dysmorphic features are consistent with 3q29 microduplication syndrome and inv dup del(9p). Trio-based WES of the patient revealed no pathogenic single nucleotide variants causing epilepsy, but confirmed a 3q28q29 duplication involving FGF12, which encodes fibroblast growth factor 12. FGF12 positively regulates the activity of voltage-gated sodium channels. Recently, only one recurrent gain-of-function variant [NM_021032.4:c.341G>A:p.(Arg114His)] in FGF12 was found in a total of 10 patients with severe early-onset epilepsy. We propose that the patient's entire FGF12 duplication may be analogous to the gain-of-function variant in FGF12 in the epileptic phenotype of this patient.
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8
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Colangelo M, Alfonsi M, Palka C, Zio ED, Renzo SD, Guanciali-Franchi P, Palka G. Case report of newborn with de novo partial trisomy 2q31.2–37.3 and monosomy 9p24.3. J Genet 2018. [DOI: 10.1007/s12041-017-0879-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Sgardioli IC, de Mello Copelli M, Monteiro FP, Dos Santos AP, Lustosa Mendes E, Paiva Vieira T, Gil-da-Silva-Lopes VL. Diagnostic Approach to Microdeletion Syndromes Based on 22q11.2 Investigation: Challenges in Four Cases. Mol Syndromol 2017; 8:244-252. [PMID: 28878608 DOI: 10.1159/000477598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2017] [Indexed: 01/18/2023] Open
Abstract
In the last few decades, different methods for the detection of genomic imbalances, such as the microdeletion syndromes, were developed. The 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion syndrome and presents wide clinical heterogeneity. The aim of this study was to describe 4 unusual cases of genomic imbalances found in individuals with suspected microdeletion syndromes. Different methods were necessary to complete the diagnosis and to obtain information for genetic counseling. The study was retrospective and descriptive. From August 2014 to December 2015, 39 individuals were assessed using FISH and/or MLPA; in 15 cases, chromosomal microarray (CMA) analysis was carried out. Of 39 registered individuals, we found deletions in the 22q11.2 region in 10 individuals (8 individuals with 22q11.2DS and 2 individuals presenting with atypical deletions in the 22q11.2 region: 1 distal deletion and 1 central deletion). In one case with a typical 22q11.2 deletion, a familial balanced translocation was detected. In another case without a 22q11.2 deletion, a 6p duplication concomitant with a 9p deletion was detected by CMA. Clinical data are reported and diagnostic investigations are discussed. Essential aspects for the understanding of different diagnostic techniques of genomic imbalances are considered, and the 4 cases described underline the complexity and the difficulties involved in the diagnostic process. The approach is informative for clinical practice and may be applied in other contexts of genomic imbalance investigation in microdeletion syndromes.
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Affiliation(s)
- Ilária C Sgardioli
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Matheus de Mello Copelli
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Fabíola P Monteiro
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Ana P Dos Santos
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Elaine Lustosa Mendes
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Társis Paiva Vieira
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Vera L Gil-da-Silva-Lopes
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, São Paulo, Brazil
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10
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Lara-Navarro IJ, Córdova-Fletes C, García-Ruiz A, Rivera H. A further inv dup/del 9p de novo rearrangement. Reappraisal of 25 instances. GENE REPORTS 2015. [DOI: 10.1016/j.genrep.2015.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Clinical and molecular delineation of duplication 9p24.3q21.11 in a patient with psychotic behavior. Gene 2015; 560:124-7. [PMID: 25667990 DOI: 10.1016/j.gene.2015.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 02/01/2015] [Accepted: 02/06/2015] [Indexed: 12/11/2022]
Abstract
This article describes a 19-year-old female with mild facial dysmorphism, asociality, decreased school performance, and psychotic behavior in whom the karyotype showed an extra-chromosomal marker characterized as 9p24.3-9q21.11 duplication by array-CGH. The 69Mbp duplicated segment in this patient includes the critical 9p duplication syndrome region, the GLDC and C90RF72 genes associated with psychotic behavior and other conduct disorders, and a potential locus for autism.
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12
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Post-zygotic breakage of a dicentric chromosome results in mosaicism for a telocentric 9p marker chromosome in a boy with developmental delay. Gene 2014; 533:403-10. [DOI: 10.1016/j.gene.2013.09.090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/20/2013] [Accepted: 09/25/2013] [Indexed: 02/07/2023]
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13
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Quinonez SC, Park JM, Rabah R, Owens KM, Yashar BM, Glover TW, Keegan CE. 9p partial monosomy and disorders of sex development: Review and postulation of a pathogenetic mechanism. Am J Med Genet A 2013; 161A:1882-96. [DOI: 10.1002/ajmg.a.36018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/27/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Shane C. Quinonez
- Department of Pediatrics, Division of Genetics; University of Michigan; Ann Arbor; Michigan
| | - John M. Park
- Department of Urology; University of Michigan; Ann Arbor; Michigan
| | - Raja Rabah
- Department of Pathology; University of Michigan; Ann Arbor; Michigan
| | - Kailey M. Owens
- Department of Pediatrics, Division of Genetics; University of Michigan; Ann Arbor; Michigan
| | - Beverly M. Yashar
- Department of Human Genetics; University of Michigan; Ann Arbor; Michigan
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