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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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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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Liang D, Wang Y, Ji X, Hu H, Zhang J, Meng L, Lin Y, Ma D, Jiang T, Jiang H, Asan, Song L, Guo J, Hu P, Xu Z. Clinical application of whole-genome low-coverage next-generation sequencing to detect and characterize balanced chromosomal translocations. Clin Genet 2016; 91:605-610. [PMID: 27491356 DOI: 10.1111/cge.12844] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/31/2016] [Accepted: 08/01/2016] [Indexed: 11/28/2022]
Abstract
Individuals carrying balanced translocations have a high risk of birth defects, recurrent spontaneous abortions and infertility. Thus, the detection and characterization of balanced translocations is important to reveal the genetic background of the carriers and to provide proper genetic counseling. Next-generation sequencing (NGS), which has great advantages over other methods such as karyotyping and fluorescence in situ hybridization (FISH), has been used to detect disease-associated breakpoints. Herein, to evaluate the application of this technology to detect balanced translocations in the clinic, we performed a parental study for prenatal cases with unbalanced translocations. Eight candidate families with potential balanced translocations were investigated using two strategies in parallel, low-coverage whole-genome sequencing (WGS) followed-up by Sanger sequencing and G-banding karyotype coupled with FISH. G-banding analysis revealed three balanced translocations, and FISH detected two cryptic submicroscopic balanced translocations. Consistently, WGS detected five balanced translocations and mapped all the breakpoints by Sanger sequencing. Analysis of the breakpoints revealed that six genes were disrupted in the four apparently healthy carriers. In summary, our result suggested low-coverage WGS can detect balanced translocations reliably and can map breakpoints precisely compared with conventional procedures. WGS may replace cytogenetic methods in the diagnosis of balanced translocation carriers in the clinic.
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Affiliation(s)
- D Liang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Y Wang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - X Ji
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - H Hu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - J Zhang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - L Meng
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Y Lin
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - D Ma
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - T Jiang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - H Jiang
- Clinical Laboratory of BGI Health, BGI, Shenzhen, China
| | - Asan
- Binhai Genomics Institute, BGI-Tianjin, BGI-shenzhen, Tianjin, China.,Tianjin Translational Genomics Center, BGI-Tianjin, BGI-shenzhen, Tianjin, China
| | - L Song
- Binhai Genomics Institute, BGI-Tianjin, BGI-shenzhen, Tianjin, China.,Tianjin Translational Genomics Center, BGI-Tianjin, BGI-shenzhen, Tianjin, China
| | - J Guo
- Binhai Genomics Institute, BGI-Tianjin, BGI-shenzhen, Tianjin, China.,Tianjin Translational Genomics Center, BGI-Tianjin, BGI-shenzhen, Tianjin, China
| | - P Hu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Z Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
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Xu XJ, Lv F, Liu Y, Wang JY, Song YW, Asan, Wang JW, Song LJ, Jiang Y, Wang O, Xia WB, Xing XP, Li M. A cryptic balanced translocation involving COL1A2 gene disruption cause a rare type of osteogenesis imperfecta. Clin Chim Acta 2016; 460:33-9. [DOI: 10.1016/j.cca.2016.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/11/2016] [Indexed: 12/25/2022]
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