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Zhang J, Xu Y, Liu Y, Yue L, Jin H, Chen Y, Wang D, Wang M, Chen G, Yang L, Zhang G, Zhang X, Li S, Zhao H, Zhao Y, Niu G, Gao Y, Cai Z, Yang F, Zhu C, Zhu D. Genetic Testing for Global Developmental Delay in Early Childhood. JAMA Netw Open 2024; 7:e2415084. [PMID: 38837156 PMCID: PMC11154162 DOI: 10.1001/jamanetworkopen.2024.15084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/03/2024] [Indexed: 06/06/2024] Open
Abstract
Importance Global developmental delay (GDD) is characterized by a complex etiology, diverse phenotypes, and high individual heterogeneity, presenting challenges for early clinical etiologic diagnosis. Cognitive impairment is the core symptom, and despite the pivotal role of genetic factors in GDD development, the understanding of them remains limited. Objectives To assess the utility of genetic detection in patients with GDD and to examine the potential molecular pathogenesis of GDD to identify targets for early intervention. Design, Setting, and Participants This multicenter, prospective cohort study enrolled patients aged 12 to 60 months with GDD from 6 centers in China from July 4, 2020, to August 31, 2023. Participants underwent trio whole exome sequencing (trio-WES) coupled with copy number variation sequencing (CNV-seq). Bioinformatics analysis was used to unravel pathogenesis and identify therapeutic targets. Main Outcomes and Measures The main outcomes of this study involved enhancing the rate of positive genetic diagnosis for GDD, broadening the scope of genetic testing indications, and investigating the underlying pathogenesis. The classification of children into levels of cognitive impairment was based on the developmental quotient assessed using the Gesell scale. Results The study encompassed 434 patients with GDD (262 [60%] male; mean [SD] age, 25.75 [13.24] months) with diverse degrees of cognitive impairment: mild (98 [23%]), moderate (141 [32%]), severe (122 [28%]), and profound (73 [17%]). The combined use of trio-WES and CNV-seq resulted in a 61% positive detection rate. Craniofacial abnormalities (odds ratio [OR], 2.27; 95% CI, 1.45-3.56), moderate or severe cognitive impairment (OR, 1.69; 95% CI, 1.05-2.70), and age between 12 and 24 months (OR, 1.57; 95% CI, 1.05-2.35) were associated with a higher risk of carrying genetic variants. Additionally, bioinformatics analysis suggested that genetic variants may induce alterations in brain development and function, which may give rise to cognitive impairment. Moreover, an association was found between the dopaminergic pathway and cognitive impairment. Conclusions and Relevance In this cohort study of patients with GDD, combining trio-WES with CNV-seq was a demonstrable, instrumental strategy for advancing the diagnosis of GDD. The close association among genetic variations, brain development, and clinical phenotypes contributed valuable insights into the pathogenesis of GDD. Notably, the dopaminergic pathway emerged as a promising focal point for potential targets in future precision medical interventions for GDD.
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Affiliation(s)
- Jiamei Zhang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yun Liu
- Kunming Children’s Hospital, Kunming, China
| | - Ling Yue
- Department of Neurological Rehabilitation, Children’s Hospital of Hebei Province, Shijiazhuang, China
| | - Hongfang Jin
- Qinghai Provincial Women and Children’s Hospital, Xining, China
| | | | - Dong Wang
- Department of Pediatric Neurology, Xi’an Children’s Hospital, Xi’an, China
| | - Mingmei Wang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Gongxun Chen
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Yang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangyu Zhang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoli Zhang
- Department of Pediatric Neurology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sansong Li
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huiling Zhao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yunxia Zhao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guohui Niu
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongqiang Gao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhijun Cai
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Changlian Zhu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Dengna Zhu
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Brewer BJ, Dunham MJ, Raghuraman MK. A unifying model that explains the origins of human inverted copy number variants. PLoS Genet 2024; 20:e1011091. [PMID: 38175827 PMCID: PMC10766186 DOI: 10.1371/journal.pgen.1011091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
With the release of the telomere-to-telomere human genome sequence and the availability of both long-read sequencing and optical genome mapping techniques, the identification of copy number variants (CNVs) and other structural variants is providing new insights into human genetic disease. Different mechanisms have been proposed to account for the novel junctions in these complex architectures, including aberrant forms of DNA replication, non-allelic homologous recombination, and various pathways that repair DNA breaks. Here, we have focused on a set of structural variants that include an inverted segment and propose that they share a common initiating event: an inverted triplication with long, unstable palindromic junctions. The secondary rearrangement of these palindromes gives rise to the various forms of inverted structural variants. We postulate that this same mechanism (ODIRA: origin-dependent inverted-repeat amplification) that creates the inverted CNVs in inherited syndromes also generates the palindromes found in cancers.
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Affiliation(s)
- Bonita J. Brewer
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Maitreya J. Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - M. K. Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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Nguyen HT, Khoa Huynh LA, Nguyen TV, Tran DH, Thu Tran TT, Khang Le ND, Le NAT, Pham TVN, Le MT, Quynh Pham TM, Nguyen TH, Van Nguyen TC, Nguyen TD, Tran Nguyen BQ, Phan MD, Giang H, Tran LS. Multimodal analysis of ctDNA methylation and fragmentomic profiles enhances detection of nonmetastatic colorectal cancer. Future Oncol 2022; 18:3895-3912. [PMID: 36524960 DOI: 10.2217/fon-2022-1041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aims: Early detection of colorectal cancer (CRC) provides substantially better survival rates. This study aimed to develop a blood-based screening assay named SPOT-MAS ('screen for the presence of tumor by DNA methylation and size') for early CRC detection with high accuracy. Methods: Plasma cell-free DNA samples from 159 patients with nonmetastatic CRC and 158 healthy controls were simultaneously analyzed for fragment length and methylation profiles. We then employed a deep neural network with fragment length and methylation signatures to build a classification model. Results: The model achieved an area under the curve of 0.989 and a sensitivity of 96.8% at 97% specificity in detecting CRC. External validation of our model showed comparable performance, with an area under the curve of 0.96. Conclusion: SPOT-MAS based on integration of cancer-specific methylation and fragmentomic signatures could provide high accuracy for early-stage CRC detection.
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Affiliation(s)
| | - Le Anh Khoa Huynh
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Department of Biostatistics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA
| | | | - Duc Huy Tran
- University Medical Center, Ho Chi Minh City, Vietnam
| | - Thuy Thi Thu Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Nguyen Duy Khang Le
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | | | | | - Minh-Triet Le
- University Medical Center, Ho Chi Minh City, Vietnam
| | - Thi Mong Quynh Pham
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Trong Hieu Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Thien Chi Van Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Thanh Dat Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Bui Que Tran Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Minh-Duy Phan
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
| | - Le Son Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam.,Gene Solutions, Ho Chi Minh City, Vietnam
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Burssed B, Zamariolli M, Bellucco FT, Melaragno MI. Mechanisms of structural chromosomal rearrangement formation. Mol Cytogenet 2022; 15:23. [PMID: 35701783 PMCID: PMC9199198 DOI: 10.1186/s13039-022-00600-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/31/2022] [Indexed: 12/31/2022] Open
Abstract
Structural chromosomal rearrangements result from different mechanisms of formation, usually related to certain genomic architectural features that may lead to genetic instability. Most of these rearrangements arise from recombination, repair, or replication mechanisms that occur after a double-strand break or the stalling/breakage of a replication fork. Here, we review the mechanisms of formation of structural rearrangements, highlighting their main features and differences. The most important mechanisms of constitutional chromosomal alterations are discussed, including Non-Allelic Homologous Recombination (NAHR), Non-Homologous End-Joining (NHEJ), Fork Stalling and Template Switching (FoSTeS), and Microhomology-Mediated Break-Induced Replication (MMBIR). Their involvement in chromoanagenesis and in the formation of complex chromosomal rearrangements, inverted duplications associated with terminal deletions, and ring chromosomes is also outlined. We reinforce the importance of high-resolution analysis to determine the DNA sequence at, and near, their breakpoints in order to infer the mechanisms of formation of structural rearrangements and to reveal how cells respond to DNA damage and repair broken ends.
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Affiliation(s)
- Bruna Burssed
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Fernanda Teixeira Bellucco
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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Maya I, Kahana S, Agmon-Fishman I, Klein C, Matar R, Berger R, Josefsberg SBY, Shohat M, Marom D, Basel-Salmon L, Sagi-Dain L. The phenotype of 15 cases with rare 8q24.13-q24.3 deletions-A new syndrome or still an enigma? Am J Med Genet A 2021; 185:1461-1467. [PMID: 33619900 DOI: 10.1002/ajmg.a.62131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/26/2021] [Accepted: 02/06/2021] [Indexed: 11/10/2022]
Abstract
Diagnosis of rare copy number variants (CNVs) with scarce literature evidence poses a major challenge for interpretation of the clinical significance of chromosomal microarray analysis (CMA) results, especially in the prenatal setting. Bioinformatic tools can be used to assist in this issue; however, this prediction can be imprecise. Our objective was to describe the phenotype of the rare copy number losses encompassing the 8q24.13-q24.3 locus, and to find common features in terms of genomic coordinates, gene content, and clinical phenotypic characteristics. Appropriate cases were retrieved using local databases of two largest Israeli centers performing CMA analysis. In addition, literature and public databases search was performed. Local database search yielded seven new patients with del (8)(q24.13q24.3) (one of these with an additional copy number variant). Literature and public databases search yielded eight additional patients. The cases showed high phenotypic variability, ranging from asymptomatic adults and fetuses with normal ultrasound to patients with autism/developmental delay (6/11 postnatal cases, 54.5%). No clear association was noted between the specific disease-causing/high-pLI gene content of the described del (8)(q24.13q24.3) to neurodevelopmental disorders, except for a possibly relevant locus encompassing the KCNQ3 gene. We present the challenges in classification of rare variants with limited clinical information. In such cases, genotype-phenotype correlation must be assessed with extra-caution and possibly using additional methods to assist the classification, especially in the prenatal setting.
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Affiliation(s)
- Idit Maya
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sarit Kahana
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Ifaat Agmon-Fishman
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Cochava Klein
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Reut Matar
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Racheli Berger
- Genetics Laboratory, Maccabi Health Services, Rehovot, Israel
| | | | - Mordechai Shohat
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Genetics Laboratory, Maccabi Health Services, Rehovot, Israel.,Bioinformatics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Daphna Marom
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Lina Basel-Salmon
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Lena Sagi-Dain
- Genetics Institute, Carmel Medical Center, affiliated to the Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
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