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Li P, Dupont B, Hu Q, Crimi M, Shen Y, Lebedev I, Liehr T. The past, present, and future for constitutional ring chromosomes: A report of the international consortium for human ring chromosomes. HGG ADVANCES 2022; 3:100139. [PMID: 36187226 PMCID: PMC9519620 DOI: 10.1016/j.xhgg.2022.100139] [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: 12/03/2022] Open
Abstract
Human ring chromosomes (RCs) are rare diseases with an estimated newborn incidence of 1/50,000 and an annual occurrence of 2,800 patients globally. Over the past 60 years, banding cytogenetics, fluorescence in situ hybridization (FISH), chromosome microarray analysis (CMA), and whole-genome sequencing (WGS) has been used to detect an RC and further characterize its genomic alterations. Ring syndrome featuring sever growth retardation and variable intellectual disability has been considered as general clinical presentations for all RCs due to the cellular losses from the dynamic mosaicism of RC instability through mitosis. Cytogenomic heterogeneity ranging from simple complete RCs to complex rearranged RCs and variable RC intolerance with different relative frequencies have been observed. Clinical heterogeneity, including chromosome-specific deletion and duplication syndromes, gene-related organ and tissue defects, cancer predisposition to different types of tumors, and reproductive failure, has been reported in the literature. However, the patients with RCs reported in the literature accounted for less than 1% of its occurrence. Current diagnostic practice lacks laboratory standards for analyzing cellular behavior and genomic imbalances of RCs to evaluate the compound effects on patients. Under-representation of clinical cases and lack of comprehensive diagnostic analysis make it a challenge for evidence-based interpretation of clinico-cytogenomic correlations and recommendation of follow-up clinical management. Given recent advancements in genomic technologies and organized efforts by international collaborations and patient advocacy organizations, the prospective of standardized cytogenomic diagnosis and evidence-based clinical management for all patients with RCs could be achieved at an unprecedented global scale.
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Affiliation(s)
- Peining Li
- Clinical Cytogenetics Laboratory, Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Corresponding author
| | - Barbara Dupont
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, SC, USA
- Corresponding author
| | - Qiping Hu
- Department of Cell Biology and Genetics, Institute of Basic Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Marco Crimi
- Ring 14 International, Via Santa Maria Alla Porta 2, 20123 Milano, Italy
- Kaleidos SCS, Scientific Office, Via Moretti Andrea 20, 24121 Bergamo, Italy
| | - Yiping Shen
- Division of Genetics and Genomics, Boston Children’s Hospital, Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Igor Lebedev
- Laboratory of Ontogenetics, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk 634050, Russia
- Corresponding author
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, 07747 Jena, Germany
- Corresponding author
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Craig CP, Calamaro E, Fong CT, Iqbal AM, Paciorkowski AR, Zhang B. Diagnosis of FOXG1 syndrome caused by recurrent balanced chromosomal rearrangements: case study and literature review. Mol Cytogenet 2020; 13:40. [PMID: 33632291 PMCID: PMC7905679 DOI: 10.1186/s13039-020-00506-1] [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: 05/12/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Background The FOXG1 gene plays a vital role in mammalian brain differentiation and development. Intra- and intergenic mutations resulting in loss of function or altered expression of the FOXG1 gene cause FOXG1 syndrome. The hallmarks of this syndrome are severe developmental delay with absent verbal language, post-natal growth restriction, post-natal microcephaly, and a recognizable movement disorder characterized by chorea and dystonia.
Case presentation Here we describe a case of a 7-year-old male patient found to have a de novo balanced translocation between chromosome 3 at band 3q14.1 and chromosome 14 at band 14q12 via G-banding chromosome and Fluorescence In Situ Hybridization (FISH) analyses. This rearrangement disrupts the proximity of FOXG1 to a previously described smallest region of deletion overlap (SRO), likely resulting in haploinsufficiency. Conclusions This case adds to the growing body of literature implicating chromosomal structural variants in the manifestation of this disorder and highlights the vital role of cis-acting regulatory elements in the normal expression of this gene. Finally, we propose a protocol for reflex FISH analysis to improve diagnostic efficiency for patients with suspected FOXG1 syndrome.
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Affiliation(s)
- Connor P Craig
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA.,School of Medicine and Dentistry, University of Rochester, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Emily Calamaro
- Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Chin-To Fong
- Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Anwar M Iqbal
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA
| | - Alexander R Paciorkowski
- Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.,Department of Neurology, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.,Center for Neural Development and Disease, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.,Departments of Neuroscience and Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA
| | - Bin Zhang
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA. .,Department of Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY, 14642, USA.
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Circle-Seq: Isolation and Sequencing of Chromosome-Derived Circular DNA Elements in Cells. Methods Mol Biol 2020; 2119:165-181. [PMID: 31989524 DOI: 10.1007/978-1-0716-0323-9_15] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromosome-derived extrachromosomal circular DNA elements (eccDNAs) are detected in all eukaryotes examined so far. Here I describe the Circle-Seq protocol, applicable for physical enrichment of eccDNAs of a broad size range, combined with sequence confirmation of circular structures.Briefly, by concise alkaline treatment and gentle gravity flow-through an ion-exchange column, eccDNAs are enriched in the eluate fraction. EccDNAs are enzymatically isolated by extensive Plasmid-Safe DNase digestion of linear chromosomes and further enriched by φ29 rolling circle amplification. By means of high throughput sequencing of amplified eccDNA and custom eccDNA mapping software, around ten-thousand unique eccDNA types could be detected at nucleotide resolution in a million human muscle nuclei by this method.
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Hu Q, Chai H, Shu W, Li P. Human ring chromosome registry for cases in the Chinese population: re-emphasizing Cytogenomic and clinical heterogeneity and reviewing diagnostic and treatment strategies. Mol Cytogenet 2018; 11:19. [PMID: 29492108 PMCID: PMC5828142 DOI: 10.1186/s13039-018-0367-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/13/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Constitutional ring chromosomes are rare orphan chromosomal disorders. Ring chromosome syndrome featuring growth retardation and mild to intermediate intellectual disability is likely caused by the dynamic behavior of ring chromosome through cell cycles. Chromosomal and regional specific phenotypes likely result from segmental losses and gains during the ring formation. Although recent applications of genomic copy number and sequencing analyses revealed various ring chromosome structures from an increasing number of case studies, there was no organized effort for compilating and curating cytogenomic and clinical finding for ring chromosomes. METHODS A web-based interactive 'Human Ring Chromosome Registry' using Microsoft Access based relational database was developed to present genetic and phenotypic findings of ring chromosome cases. Chinese ring chromosome cases reported in the literature was reviewed and compiled as a testing data set to validate this registry. RESULTS A total of 113 cases of ring chromosomes were retrieved in all chromosomes except for chromosomes 16, 17 and 19. The most frequently seen ring chromosomes by a decreasing order of relative frequencies were ring 13 (14%), X (12%), 22 (10%), 15 (9%), 14 (7%), and 18 (7%). Genomic imbalances were detected in 18 out of 19 cases analyzed by microarray or sequencing. Variable clinical manifestations of developmental delay, dysmorphic facial features, intellectual disability, microcephaly, and hypotonia were noted in most autosomal rings. Chromosomal specific syndromic phenotypes included Wolf-Hirschhorn syndrome in a ring chromosome 4, cri-du-chat syndrome in a ring chromosome 5, epilepsy in ring chromosomes 14 and 20, Turner syndrome in ring chromosome X, and infertility in ring chromosomes 13, 21, 22 and Y. Effective growth hormone supplemental treatment for growth retardation in a ring chromosome 18 was noted. CONCLUSIONS Based on findings from these Chinese ring chromosome cases, guidelines for cytogenomic diagnosis and criteria for case registration were proposed. Further research to define underlying mechanisms of ring chromosome formation and dynamic mosaicism, to delineate the genotype-phenotype correlations, and to develop chromosome therapy for ring chromosomes were discussed.
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Affiliation(s)
- Qiping Hu
- Department of Cell Biology and Genetics, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021 China
- Laboratory of Clinical Cytogenetics and Genomics, Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - Hongyan Chai
- Laboratory of Clinical Cytogenetics and Genomics, Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
| | - Wei Shu
- Department of Cell Biology and Genetics, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021 China
| | - Peining Li
- Laboratory of Clinical Cytogenetics and Genomics, Department of Genetics, Yale School of Medicine, New Haven, CT 06520 USA
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Regulatory variants of FOXG1 in the context of its topological domain organisation. Eur J Hum Genet 2017; 26:186-196. [PMID: 29289958 DOI: 10.1038/s41431-017-0011-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 02/02/2023] Open
Abstract
FOXG1 syndrome is caused by FOXG1 intragenic point mutations, or by long-range position effects (LRPE) of intergenic structural variants. However, the size of the FOXG1 regulatory landscape is uncertain, because the associated topologically associating domain (TAD) in fibroblasts is split into two domains in embryonic stem cells (hESC). Indeed, it has been suggested that the pathogenetic mechanism of deletions that remove the stem-cell-specific TAD boundary may be enhancer adoption due to ectopic activity of enhancer(s) located in the distal hESC-TAD. Herein we map three de novo translocation breakpoints to the proximal regulatory domain of FOXG1. The classical FOXG1 syndrome in these and in other translocation patients, and in a patient with an intergenic deletion that removes the hESC-specific TAD boundary, do not support the hypothesised enhancer adoption as a main contributor to the FOXG1 syndrome. Also, virtual 4 C and HiC-interaction data suggest that the hESC-specific TAD boundary may not be critical for FOXG1 regulation in a majority of human cells and tissues, including brain tissues and a neuronal progenitor cell line. Our data support the importance of a critical regulatory region (SRO) proximal to the hESC-specific TAD boundary. We further narrow this critical region by a deletion distal to the hESC-specific boundary, associated with a milder clinical phenotype. The distance from FOXG1 to the SRO ( > 500 kb) highlight a limitation of ENCODE DNase hypersensitivity data for functional prediction of LRPE. Moreover, the SRO has little overlap with a cluster of frequently associating regions (FIREs) located in the proximal hESC-TAD.
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Rinaldi B, Vaisfeld A, Amarri S, Baldo C, Gobbi G, Magini P, Melli E, Neri G, Novara F, Pippucci T, Rizzi R, Soresina A, Zampini L, Zuffardi O, Crimi M. Guideline recommendations for diagnosis and clinical management of Ring14 syndrome-first report of an ad hoc task force. Orphanet J Rare Dis 2017; 12:69. [PMID: 28399932 PMCID: PMC5387247 DOI: 10.1186/s13023-017-0606-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/01/2017] [Indexed: 01/22/2023] Open
Abstract
Background Ring chromosome 14 syndrome is a rare chromosomal disorder characterized by early onset refractory epilepsy, intellectual disability, autism spectrum disorder and a number of diverse health issues. Results The aim of this work is to provide recommendations for the diagnosis and management of persons affected by ring chromosome 14 syndrome based on evidence from literature and experience of health professionals from different medical backgrounds who have followed for several years subjects affected by ring chromosome 14 syndrome. The literature search was performed in 2016. Original papers, meta-analyses, reviews, books and guidelines were reviewed and final recommendations were reached by consensus. Conclusion Conventional cytogenetics is the primary tool to identify a ring chromosome. Children with a terminal deletion of chromosome 14q ascertained by molecular karyotyping (CGH/SNP array) should be tested secondarily by conventional cytogenetics for the presence of a ring chromosome. Early diagnosis should be pursued in order to provide medical and social assistance by a multidisciplinary team. Clinical investigations, including neurophysiology for epilepsy, should be performed at the diagnosis and within the follow-up. Following the diagnosis, patients and relatives/caregivers should receive regular care for health and social issues. Epilepsy should be treated from the onset with anticonvulsive therapy. Likewise, feeding difficulties should be treated according to need. Nutritional assessment is recommended for all patients and nutritional support for malnourishment can include gastrostomy feeding in selected cases. Presence of autistic traits should be carefully evaluated. Many patients with ring chromosome 14 syndrome are nonverbal and thus maintaining their ability to communicate is always essential; every effort should be made to preserve their autonomy.
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Affiliation(s)
- Berardo Rinaldi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Alessandro Vaisfeld
- Institute of Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Sergio Amarri
- Pediatrics Unit, Department of Women's and Children's Health, IRCCS Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - Chiara Baldo
- Laboratory of Human Genetics, Galliera Hospital, Genoa, Italy
| | - Giuseppe Gobbi
- Child Neurology Unit, IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy
| | - Pamela Magini
- Medical Genetics Unit, Department of Medical and Surgical Sciences, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Erto Melli
- Ospedale S. Anna, Ambulatorio Oculistica, AUSL di Reggio Emilia, Reggio Emilia, Italy
| | - Giovanni Neri
- Institute of Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Francesca Novara
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, Department of Woman, Child and Urologic Diseases, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Romana Rizzi
- Neurology Unit, Department of Neuro-Motor Diseases, IRCCS Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - Annarosa Soresina
- Unit of Pediatric Immunology, Department of Pediatrics, University of Brescia, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Laura Zampini
- Department of Psychology, University of Milano-Bicocca, Milan, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Marco Crimi
- Ring14 International, Scientific office, Via Flavio Gioia, 5-42124, Reggio Emilia, Italy.
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Mehrjouy MM, Fonseca AC, Ehmke N, Tiffany B, Mencarelli MA, Novelli A, Bak M, Tommerup N. Regulatory Mutations of FOXG1 in the Context of Topological Domains. Cancer Genet 2016. [DOI: 10.1016/j.cancergen.2016.05.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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