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Xie M, Zheng ZJ, Zhou Y, Zhang YX, Li Q, Tian LY, Cao J, Xu YT, Ren J, Yu Q, Wu SS, Fang S, Zhuang DY, Geng J, Chen CS, Li HB. Prospective Investigation of Optical Genome Mapping for Prenatal Genetic Diagnosis. Clin Chem 2024; 70:820-829. [PMID: 38517460 DOI: 10.1093/clinchem/hvae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Optical genome mapping (OGM) is a novel assay for detecting structural variants (SVs) and has been retrospectively evaluated for its performance. However, its prospective evaluation in prenatal diagnosis remains unreported. This study aimed to prospectively assess the technical concordance of OGM with standard of care (SOC) testing in prenatal diagnosis. METHODS A prospective cohort of 204 pregnant women was enrolled in this study. Amniotic fluid samples from these women were subjected to OGM and SOC testing, which included chromosomal microarray analysis (CMA) and karyotyping (KT) in parallel. The diagnostic yield of OGM was evaluated, and the technical concordance between OGM and SOC testing was assessed. RESULTS OGM successfully analyzed 204 cultured amniocyte samples, even with a cell count as low as 0.24 million. In total, 60 reportable SVs were identified through combined OGM and SOC testing, with 22 SVs detected by all 3 techniques. The diagnostic yield for OGM, CMA, and KT was 25% (51/204), 22.06% (45/204), and 18.14% (37/204), respectively. The highest diagnostic yield (29.41%, 60/204) was achieved when OGM and KT were used together. OGM demonstrated a concordance of 95.56% with CMA and 75.68% with KT in this cohort study. CONCLUSIONS Our findings suggest that OGM can be effectively applied in prenatal diagnosis using cultured amniocytes and exhibits high concordance with SOC testing. The combined use of OGM and KT appears to yield the most promising diagnostic outcomes.
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Affiliation(s)
- Min Xie
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, China
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Ningbo Women and Children's Hospital, Ningbo, China
| | - Zhao-Jing Zheng
- Laboratory of Cytogenetics & Cytogenomics, Hangzhou Juno Genomics Inc., Hangzhou, China
| | - Ying Zhou
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, China
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Ningbo Women and Children's Hospital, Ningbo, China
| | - Yu-Xin Zhang
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, China
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Ningbo Women and Children's Hospital, Ningbo, China
| | - Qiong Li
- Prenatal and Neonatal Screening Center, Ningbo Women and Children's Hospital, Ningbo, China
| | - Li-Yun Tian
- Fetal Medicine Centre, Ningbo Women and Children's Hospital, Ningbo, China
| | - Juan Cao
- Fetal Medicine Centre, Ningbo Women and Children's Hospital, Ningbo, China
| | - Yan-Ting Xu
- Laboratory of Cytogenetics & Cytogenomics, Hangzhou Juno Genomics Inc., Hangzhou, China
| | - Jie Ren
- Laboratory of Cytogenetics & Cytogenomics, Hangzhou Juno Genomics Inc., Hangzhou, China
| | - Qi Yu
- Prenatal and Neonatal Screening Center, Ningbo Women and Children's Hospital, Ningbo, China
| | - Shan-Shan Wu
- Paediatric Surgery Centre, Ningbo Women and Children's Hospital, Ningbo, China
| | - Shu Fang
- Laboratory of Cytogenetics & Cytogenomics, Hangzhou Juno Genomics Inc., Hangzhou, China
| | - Dan-Yan Zhuang
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, China
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Ningbo Women and Children's Hospital, Ningbo, China
| | - Juan Geng
- Laboratory of Cytogenetics & Cytogenomics, Hangzhou Juno Genomics Inc., Hangzhou, China
| | - Chang-Shui Chen
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Ningbo Women and Children's Hospital, Ningbo, China
| | - Hai-Bo Li
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children's Hospital, Ningbo, China
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Ningbo Women and Children's Hospital, Ningbo, China
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2
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Baelen J, Dewaele B, Debiec-Rychter M, Sciot R, Schöffski P, Hompes D, Sinnaeve F, Wafa H, Vanden Bempt I. Optical Genome Mapping for Comprehensive Cytogenetic Analysis of Soft-Tissue and Bone Tumors for Diagnostic Purposes. J Mol Diagn 2024; 26:374-386. [PMID: 38395407 DOI: 10.1016/j.jmoldx.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/21/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Soft-tissue and bone tumors represent a heterogeneous group of tumors encompassing more than 100 histologic subtypes today. Identifying genetic aberrations increasingly is important in these tumors for accurate diagnosis. Although gene mutations typically are detected by second-generation sequencing, the identification of structural variants (SVs) and copy number alterations (CNAs) remains challenging and requires various cytogenetic techniques including karyotyping, fluorescence in situ hybridization, and arrays, each with important limitations. Optical Genome Mapping (OGM), a non-sequencing-based technique for high-resolution detection of SVs and CNAs, was applied in a retrospective series of diagnostic soft-tissue and bone tumor samples. Sample preparation was successful in 38 of 53 cases, with the highest success rate in nonadipocytic soft-tissue tumors (24 of 27 cases; 89%). In 32 of 35 cases carrying a diagnostic SV or CNA, OGM identified the aberration (91%), including a POU2AF3::EWSR1 fusion in a round cell sarcoma and a translocation t(1;5)(p22;p15) in a myxoinflammatory fibroblastic sarcoma. Interestingly, OGM shed light on the genomic complexity underlying the various aberrations. In five samples, OGM showed that chains of rearrangements generated the diagnostic fusion, three of which involved chromoplexy. In addition, in nine samples, chromothripsis was causal to the formation of giant marker/ring/double-minute chromosomes. Finally, compared with standard-of-care cytogenetics, OGM revealed additional aberrations, requiring further investigation of their potential clinical relevance.
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Affiliation(s)
- Jef Baelen
- Department of Human Genetics, KU Leuven, University Hospitals Leuven, Leuven, Belgium.
| | - Barbara Dewaele
- Department of Human Genetics, KU Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Maria Debiec-Rychter
- Department of Human Genetics, KU Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Raphael Sciot
- Department of Imaging and Pathology, KU Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Patrick Schöffski
- Department of General Medical Oncology, University Hospitals Leuven, Leuven, Belgium; Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Daphne Hompes
- Department of Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Friedl Sinnaeve
- Department of Orthopaedic Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Hazem Wafa
- Department of Orthopaedic Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Isabelle Vanden Bempt
- Department of Human Genetics, KU Leuven, University Hospitals Leuven, Leuven, Belgium
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3
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Hu P, Xu Y, Zhang Q, Zhou R, Ji X, Wang Y, Xu Z. Prenatal diagnosis of chromosomal abnormalities using optical genome mapping vs chromosomal microarray. Am J Obstet Gynecol 2024; 230:e82-e83. [PMID: 38097028 DOI: 10.1016/j.ajog.2023.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 01/07/2024]
Affiliation(s)
- Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei St, Nanjing, China 210029.
| | - Yiyun Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei St, Nanjing, China 210029
| | - Qinxin Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei St, Nanjing, China 210029
| | - Ran Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei St, Nanjing, China 210029
| | - Xiuqing Ji
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei St, Nanjing, China 210029
| | - Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei St, Nanjing, China 210029.
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfei St, Nanjing, China 210029.
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4
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El‐Wahsh S, Fellner A, Hobbs M, Copty J, Deveson I, Stevanovski I, Stoll M, Zhu D, Narayanan RK, Grosz B, Worgan L, Cheong PL, Yeow D, Rudaks L, Hasan MM, Hayes VM, Kennerson M, Kumar KR, Hayes M. An Inversion Affecting the GCH1 Gene as a Novel Finding in Dopa-Responsive Dystonia. Mov Disord Clin Pract 2024; 11:582-585. [PMID: 38497520 PMCID: PMC11078477 DOI: 10.1002/mdc3.14023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/23/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Affiliation(s)
- Shadi El‐Wahsh
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
| | - Avi Fellner
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
- The Neurogenetics Clinic, Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson HospitalPetah TikvaIsrael
| | - Matthew Hobbs
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Joe Copty
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Ira Deveson
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Igor Stevanovski
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
| | - Marion Stoll
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
| | - Danqing Zhu
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
| | - Ramesh K. Narayanan
- Northcott Neuroscience LaboratoryANZAC Research Institute—Sydney Local Health DistrictConcordNew South WalesAustralia
| | - Bianca Grosz
- Northcott Neuroscience LaboratoryANZAC Research Institute—Sydney Local Health DistrictConcordNew South WalesAustralia
| | - Lisa Worgan
- Clinical Genetics ServiceRoyal Prince Alfred HospitalSydneyNew South WalesAustralia
- Department of Medical GenomicsRoyal Prince Alfred HospitalSydneyNew South WalesAustralia
| | - Pak Leng Cheong
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Concord Clinical School, Sydney Medical School, Faculty of Health and MedicineUniversity of SydneySydneyNew South WalesAustralia
- Royal Prince Alfred Hospital, New South Wales Health PathologySydneyNew South WalesAustralia
- Institute of Precision Medicine and Bioinformatics, Sydney Local Health DistrictSydneyNew South WalesAustralia
| | - Dennis Yeow
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Concord Clinical School, Sydney Medical School, Faculty of Health and MedicineUniversity of SydneySydneyNew South WalesAustralia
- Neuroscience Research AustraliaSydneyNew South WalesAustralia
| | - Laura Rudaks
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Concord Clinical School, Sydney Medical School, Faculty of Health and MedicineUniversity of SydneySydneyNew South WalesAustralia
| | - Md Mehedi Hasan
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneySydneyNew South WalesAustralia
| | - Vanessa M. Hayes
- Ancestry and Health Genomics Laboratory, Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and HealthUniversity of SydneySydneyNew South WalesAustralia
- School of Health Systems & Public HealthUniversity of PretoriaPretoriaSouth Africa
- Manchester Cancer Research CentreUniversity of ManchesterManchesterUK
| | - Marina Kennerson
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Northcott Neuroscience LaboratoryANZAC Research Institute—Sydney Local Health DistrictConcordNew South WalesAustralia
- Institute of Precision Medicine and Bioinformatics, Sydney Local Health DistrictSydneyNew South WalesAustralia
| | - Kishore R. Kumar
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Faculty of MedicineUniversity of New South WalesSydneyNew South WalesAustralia
- Garvan Institute of Medical ResearchSydneyNew South WalesAustralia
- Molecular Medicine LaboratoryConcord Repatriation General HospitalSydneyNew South WalesAustralia
- Concord Clinical School, Sydney Medical School, Faculty of Health and MedicineUniversity of SydneySydneyNew South WalesAustralia
- Institute of Precision Medicine and Bioinformatics, Sydney Local Health DistrictSydneyNew South WalesAustralia
| | - Michael Hayes
- Neurology DepartmentConcord Repatriation General HospitalSydneyNew South WalesAustralia
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5
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Yang Q, Huang X, Lin Y, Chen K, Lu Q, Lin W, Wang X, Teng Y, Jiang P, Patil S, Zheng Y. Exploring the Multifaceted Landscape of Pediatric Obstructive Sleep Apnea: Insights into Prevalence, Severity, and Coexisting Conditions. Nat Sci Sleep 2024; 16:359-368. [PMID: 38617037 PMCID: PMC11012695 DOI: 10.2147/nss.s452221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/03/2024] [Indexed: 04/16/2024] Open
Abstract
Background Pediatric obstructive sleep apnea (OSA) is a multifaceted disorder marked by recurrent upper airway obstruction during sleep, often coexisting with various medical conditions. This study, aimed to comprehensively analyze the Multifaceted Landscape of Pediatric Insights into Prevalence, Severity, and Coexisting Conditions. With a sample of 1928 participants, our study sought to determine the prevalence, severity, and associations between OSA and diverse conditions. Methods Conducted retrospectively from February 2019 to April 2023, the study included pediatric patients. Data were collected through electronic health records, involving clinical assessments, medical histories, and diagnostic tests to establish OSA and coexisting condition diagnoses. Relationships between sleep parameters, apnea types, and severity indices were evaluated. Results High OSA prevalence was evident across age groups, with severity peaking between 3 to 12 years. Among the participants, coexisting conditions included allergic rhinitis (59.6%), tonsillar hypertrophy (49.7%), adenoid hypertrophy (28.4%), and obesity (15.3%). Analysis revealed intriguing relationships between different sleep parameters and apnea types. Notable associations were observed between Obstructive Apnea (OA) and Central Apnea (CA), and Mixed Apnea (MA) displayed associations with both OA and CA. Hypopnea correlated directly with the Apnea-Hypopnea Index (AHI), reflecting its role in OSA severity. Conclusion This study provides a comprehensive understanding of the intricate dynamics between pediatric OSA and coexisting conditions. The prevalence of OSA and its coexistence with various conditions underscore the need for comprehensive evaluation and management strategies. By revealing associations between different sleep parameters and apnea types, the study emphasizes the complexity of OSA diagnosis and management. These findings hold the potential to enhance clinical approaches, ultimately leading to improved care and outcomes for affected children.
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Affiliation(s)
- Qin Yang
- Department of Respiratory Medicine, Shenzhen Children’s Hospital, Shenzhen, Guangdong Province, People’s Republic of China
- Department of Sleep Centre, Shenzhen Children’s Hospital, Shenzhen, Guangdong Province, People’s Republic of China
| | - Xiao Huang
- Department of Sleep Centre, Shenzhen Children’s Hospital, Shenzhen, Guangdong Province, People’s Republic of China
| | - Yanhong Lin
- Department of Respiratory Medicine, Shenzhen Children’s Hospital, Shenzhen, Guangdong Province, People’s Republic of China
| | - Ke Chen
- Department of Respiratory Medicine, Shenzhen Children’s Hospital, Shenzhen, Guangdong Province, People’s Republic of China
| | - Qinghua Lu
- Department of Respiratory Medicine, Shenzhen Children’s Hospital, Shenzhen, Guangdong Province, People’s Republic of China
| | - Weinan Lin
- Department of Respiratory Medicine, Shenzhen Children’s Hospital, Shenzhen, Guangdong Province, People’s Republic of China
| | - Xing Wang
- Department of Sleep Centre, Shenzhen Children’s Hospital, Shenzhen, Guangdong Province, People’s Republic of China
| | - Yishu Teng
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong Province, People’s Republic of China
| | - Peng Jiang
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong Province, People’s Republic of China
| | - Sandip Patil
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong Province, People’s Republic of China
| | - Yuejie Zheng
- Department of Respiratory Medicine, Shenzhen Children’s Hospital, Shenzhen, Guangdong Province, People’s Republic of China
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6
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Bouassida M, Molina‐Gomes D, Koraichi F, Hervé B, Lhuilier M, Duvillier C, Le Gall J, Gauthier‐Villars M, Serazin V, Quibel T, Dard R, Vialard F. The clinical value of optical genome mapping in the rapid characterization of RB1 duplication and 15q23q24.2 triplication, for more appropriate prenatal genetic counselling. Mol Genet Genomic Med 2024; 12:e2437. [PMID: 38588252 PMCID: PMC11000809 DOI: 10.1002/mgg3.2437] [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: 01/07/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Despite recent advances in prenatal genetic diagnosis, medical geneticists still face considerable difficulty in interpreting the clinical outcome of copy-number-variant duplications and defining the mechanisms underlying the formation of certain chromosomal rearrangements. Optical genome mapping (OGM) is an emerging cytogenomic tool with proved ability to identify the full spectrum of cytogenetic aberrations. METHODS Here, we report on the use of OGM in a prenatal diagnosis setting. Detailed breakpoint mapping was used to determine the relative orientations of triplicated and duplicated segments in two unrelated foetuses harbouring chromosomal aberrations: a de novo 15q23q24.2 triplication and a paternally inherited 13q14.2 duplication that overlapped partially with the RB1 gene. RESULTS OGM enabled us to suggest a plausible mechanism for the triplication and confirmed that the RB1 duplication was direct oriented and in tandem. This enabled us to predict the pathogenic consequences, refine the prognosis and adapt the follow-up and familial screening appropriately. CONCLUSION Along with an increase in diagnostic rates, OGM can rapidly highlight genotype-phenotype correlations, improve genetic counselling and significantly influence prenatal management.
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Affiliation(s)
- Malek Bouassida
- Genetics DepartmentCHI de Poissy‐St Germain en LayePoissyFrance
| | | | | | - Bérénice Hervé
- Genetics DepartmentCHI de Poissy‐St Germain en LayePoissyFrance
| | | | | | | | | | - Valérie Serazin
- Genetics DepartmentCHI de Poissy‐St Germain en LayePoissyFrance
| | - Thibaud Quibel
- Obstetrics DepartmentCHI de Poissy‐St Germain en LayePoissyFrance
| | - Rodolphe Dard
- Genetics DepartmentCHI de Poissy‐St Germain en LayePoissyFrance
- RHuMA TeamUMR‐BREED, UVSQ, INRAE, ENVAMontigny le BretonneuxFrance
| | - François Vialard
- Genetics DepartmentCHI de Poissy‐St Germain en LayePoissyFrance
- RHuMA TeamUMR‐BREED, UVSQ, INRAE, ENVAMontigny le BretonneuxFrance
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7
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Yan X, Mischel P, Chang H. Extrachromosomal DNA in cancer. Nat Rev Cancer 2024; 24:261-273. [PMID: 38409389 DOI: 10.1038/s41568-024-00669-8] [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] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Extrachromosomal DNA (ecDNA) has recently been recognized as a major contributor to cancer pathogenesis that is identified in most cancer types and is associated with poor outcomes. When it was discovered over 60 years ago, ecDNA was considered to be rare, and its impact on tumour biology was not well understood. The application of modern imaging and computational techniques has yielded powerful new insights into the importance of ecDNA in cancer. The non-chromosomal inheritance of ecDNA during cell division results in high oncogene copy number, intra-tumoural genetic heterogeneity and rapid tumour evolution that contributes to treatment resistance and shorter patient survival. In addition, the circular architecture of ecDNA results in altered patterns of gene regulation that drive elevated oncogene expression, potentially enabling the remodelling of tumour genomes. The generation of clusters of ecDNAs, termed ecDNA hubs, results in interactions between enhancers and promoters in trans, yielding a new paradigm in oncogenic transcription. In this Review, we highlight the rapid advancements in ecDNA research, providing new insights into ecDNA biogenesis, maintenance and transcription and its role in promoting tumour heterogeneity. To conclude, we delve into a set of unanswered questions whose answers will pave the way for the development of ecDNA targeted therapeutic approaches.
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Affiliation(s)
- Xiaowei Yan
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Howard Chang
- Department of Dermatology, Stanford University, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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8
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Broeckel U, Iqbal MA, Levy B, Sahajpal N, Nagy PL, Scharer G, Rodriguez V, Bossler A, Stence A, Skinner C, Skinner SA, Kolhe R, Stevenson R. Detection of Constitutional Structural Variants by Optical Genome Mapping: A Multisite Study of Postnatal Samples. J Mol Diagn 2024; 26:213-226. [PMID: 38211722 DOI: 10.1016/j.jmoldx.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/26/2023] [Accepted: 12/14/2023] [Indexed: 01/13/2024] Open
Abstract
Optical genome mapping is a high-resolution technology that can detect all types of structural variations in the genome. This second phase of a multisite study compares the performance of optical genome mapping and current standard-of-care methods for diagnostic testing of individuals with constitutional disorders, including neurodevelopmental impairments and congenital anomalies. Among the 627 analyses in phase 2, 405 were of retrospective samples supplied by five diagnostic centers in the United States and 94 were prospective samples collected over 18 months by two diagnostic centers (June 2021 to October 2022). Additional samples represented a family cohort to determine inheritance (n = 119) and controls (n = 9). Full concordance of results between optical genome mapping and one or more standard-of-care diagnostic tests was 98.6% (618/627), with partial concordance in an additional 1.1% (7/627).
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Affiliation(s)
- Ulrich Broeckel
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - M Anwar Iqbal
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Brynn Levy
- Columbia University Medical Center, New York, New York
| | | | - Peter L Nagy
- Columbia University Medical Center, New York, New York
| | - Gunter Scharer
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | | | - Aaron Stence
- University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | | | | | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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9
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Mackinnon AC, Chandrashekar DS, Suster DI. Molecular pathology as basis for timely cancer diagnosis and therapy. Virchows Arch 2024; 484:155-168. [PMID: 38012424 DOI: 10.1007/s00428-023-03707-2] [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: 08/21/2023] [Revised: 10/16/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023]
Abstract
Precision and personalized therapeutics have witnessed significant advancements in technology, revolutionizing the capabilities of laboratories to generate vast amounts of genetic data. Coupled with computational resources for analysis and interpretation, and integrated with various other types of data, including genomic data, electronic medical health (EMH) data, and clinical knowledge, these advancements support optimized health decisions. Among these technologies, next-generation sequencing (NGS) stands out as a transformative tool in the field of cancer treatment, playing a crucial role in precision oncology. NGS-based workflows are employed across a range of applications, including gene panels, exome sequencing, and whole-genome sequencing, supporting comprehensive analysis of the entire cancer genome, including mutations, copy number variations, gene expression profiles, and epigenetic modifications. By utilizing the power of NGS, these workflows contribute to enhancing our understanding of disease mechanisms, diagnosis confirmation, identifying therapeutic targets, and guiding personalized treatment decisions. This manuscript explores the diverse applications of NGS in cancer treatment, highlighting its significance in guiding diagnosis and treatment decisions, identifying therapeutic targets, monitoring disease progression, and improving patient outcomes.
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Affiliation(s)
- A Craig Mackinnon
- Department of Pathology, University of Alabama at Birmingham, 619 19Th Street South, Birmingham, AL, 35249, USA.
| | | | - David I Suster
- Department of Pathology, Rutgers University New Jersey Medical School, 150 Bergen Street, Newark, NJ, 07103, USA.
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10
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Li Y, Yang X, Zhang Y, Lou H, Wu M, Liu F, Chang W, Zhao X. The detection efficacy of noninvasive prenatal genetic testing (NIPT) for sex chromosome abnormalities and copy number variation and its differentiation in pregnant women of different ages. Heliyon 2024; 10:e24155. [PMID: 38293423 PMCID: PMC10826137 DOI: 10.1016/j.heliyon.2024.e24155] [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: 08/26/2023] [Revised: 11/15/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Objective To analyze the efficacy of noninvasive prenatal genetic testing (NIPT) in detecting fetal sex chromosome abnormalities and copy number variation (CNV), compare the efficacy between NIPT and serological screening alone, and further analyze the fetal sex chromosome abnormalities and CNV differentiation in pregnant women of different ages, so as to provide a reference for the prevention and control of fetal birth defects. Methods Clinical data from 22,692 pregnant women admitted to our hospital from January 2013 to December 2022 were retrospectively analyzed. All participants underwent serological screening and NIPT screening to compare fetal chromosomal abnormalities between the two screening modalities. 145 women whose fetus were diagnosed as sex chromosome abnormalities and 36 women whose fetus were diagnosed as CNV abnormalities based on NIPT screening were selected for prenatal diagnosis by amniocentesis or karyotyping. Taking prenatal diagnosis as the standard, the four-grid table method was used to detect the positive predictive value of NIPT screening for fetal sex chromosomal abnormalities and CNV. According to the age, pregnant women were divided into 18-30 years old (n = 9844), 31-35 years old (n = 7612), >35 years old (n = 5236), and then the detection rates of sexual fetal chromosomal abnormalities, CNV and total chromosomal abnormalities were compared in pregnant women. Results Among the 22,692 pregnant women in this study, the high-risk proportion of serologic screening with 4.38% was higher than that of NIPT screening with 1.93% (P < 0.05). Among the 145 women with fetal sex chromosome abnormalities screened by NIPT, 122 cases of fetal sex chromosome abnormalities were diagnosed prenatally, including 45, X/47, XXX/47, XYY/47, XXY. The positive predictive values of NIPT screening were 25.00%, 58.82%, 85.71%, and 85.71%, respectively, with an overall predictive value of 44.26%. The positive predictive value of fetal sex chromosome abnormalities in NIPT screening was higher than that of serological screening (P < 0.05). Among the 36 pregnant women with fetal CNV, NIPT screening showed that CNVs≤10 Mb and CNVs>10 Mb were 33.33% and 66.67%, respectively. There were 12 cases of prenatal diagnosis of fetal CNV, among which the NIPT-screened positive predictive values of fetal copy number deletion, duplicate, deletion and duplicate were 50.00%, 57.14% and 100.00%, respectively, with an overall predictive value of 58.33%. The positive predictive value of CNV in NIPT screening was higher than that of serological screening without statistically significant difference (P > 0.05). The results of NIPT screening showed that the detection rate of fetal sex chromosome abnormalities and total abnormalities of pregnant women over 35 years of age was significantly higher than that of pregnant women aged 18-30 and 31-35 years (P < 0.05). Conclusion NIPT screening could greatly improve the detection efficacy of fetal sex chromosome abnormalities, CNV and other chromosome abnormalities, and decline the false positive rate. However, the positive predictive value of NIPT screening was relatively low, and further prenatal testing and genetic counseling are still required. In addition, NIPT screening for fetal sex chromosome abnormalities, and the detection rate of total abnormalities in pregnant women older than 35 years old were increased significantly, and pregnancy at an advanced age may be one of the risk factors for fetal chromosomal abnormalities.
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Affiliation(s)
- Yimei Li
- Department of Gynecology and Obstetrics, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450000, Henan, PR China
| | - Xiaofeng Yang
- Department of Gynecology and Obstetrics, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450000, Henan, PR China
| | - Ying Zhang
- Department of Gynecology and Obstetrics, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450000, Henan, PR China
| | - Huan Lou
- Department of Gynecology and Obstetrics, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450000, Henan, PR China
| | - Mingli Wu
- Department of Gynecology and Obstetrics, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450000, Henan, PR China
| | - Fang Liu
- Department of Gynecology and Obstetrics, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450000, Henan, PR China
| | - Wenjing Chang
- Department of Gynecology and Obstetrics, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450000, Henan, PR China
| | - Xueling Zhao
- Department of Gynecology and Obstetrics, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450000, Henan, PR China
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11
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Joksic I, Toljic M, Milacic I, Stankovic A, Karadzov Orlic N, Mikovic Z. Small supernumerary marker chromosomes in prenatal diagnosis-molecular characterization and clinical outcomes. Front Genet 2024; 14:1326985. [PMID: 38259626 PMCID: PMC10800731 DOI: 10.3389/fgene.2023.1326985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Small supernumerary marker chromosomes (sSMCs) are infrequent findings in prenatal diagnostics, however they pose a great challenge for prenatal genetic counseling. Methods: We report prenatal 12 sSMC cases detected in a single center during 10 years period, their molecular characterization by fluorescence in situ hybridization (FISH) or chromosomal microarray (CMA). Those cases were found among 9620 prenatal diagnostic analyzes by GTG-banding technique. In selected cases, additional UPD testing was also done. Results: Incidence of sSMCs in our study was 0.12%. sSMC characterization was done by FISH in 9 cases, in the remainder of three CMA was employed. The most common sSMC shape was centric minute, followed by inverted duplication and one case with ring conformation. sSMCs originating from acrocentric chromosomes (chromosomes 14, 21 and 22), sex chromosomes (X, Y) and non-acrocentric autosomal chromosomes (chromosome 4 and 18) were confirmed in 3 cases each; no result could be obtained in 3 further cases. Discussion: No anomalies were detected by prenatal ultrasound in any of the cases. In 58% of the cases, outcome was reported as normal at birth, while anomalies at birth were described in one case. Only two patients opted for pregnancy termination. Preterm labor occurred in case of twin pregnancy resulting in stillbirth and early neonatal death of twins. Overall, our study highlights the importance of a sSMC characterization by molecular cytogenomic methods in order to make appropriate genotype-phenotype correlations and ensure adequate genetic counseling.
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Affiliation(s)
- Ivana Joksic
- Laboratory for Medical Genetics, Gynecology and Obstetrics Clinic “Narodni Front”, Belgrade, Serbia
| | - Mina Toljic
- Laboratory for Medical Genetics, Gynecology and Obstetrics Clinic “Narodni Front”, Belgrade, Serbia
| | - Iva Milacic
- Laboratory for Medical Genetics, Gynecology and Obstetrics Clinic “Narodni Front”, Belgrade, Serbia
| | - Andjela Stankovic
- Laboratory for Medical Genetics, Gynecology and Obstetrics Clinic “Narodni Front”, Belgrade, Serbia
| | - Natasa Karadzov Orlic
- High-Risk Pregnancy Department, Gynecology and Obstetrics Clinic “Narodni Front”, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Zeljko Mikovic
- High-Risk Pregnancy Department, Gynecology and Obstetrics Clinic “Narodni Front”, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
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12
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Hao N, Lou H, Li M, Zhang H, Chang J, Qi Q, Zhou X, Bai J, Guo J, Wang Y, Zhang Y, Jiang Y. Analysis of complex chromosomal rearrangement involving chromosome 6 via the integration of optical genomic mapping and molecular cytogenetic methodologies. J Hum Genet 2024; 69:3-11. [PMID: 37821671 DOI: 10.1038/s10038-023-01197-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
Complex chromosomal rearrangements (CCRs) can result in spontaneous abortions, infertility, and malformations in newborns. In this study, we explored a familial CCR involving chromosome 6 by combining optical genomic mapping (OGM) and molecular cytogenetic methodologies. Within this family, the father and the paternal grandfather were both asymptomatic carriers of an identical balanced CCR, while the two offspring with an unbalanced paternal-origin CCR and two microdeletions presented with clinical manifestation. The first affected child, a 5-year-old boy, exhibited neurodevelopmental delay, while the second, a fetus, presented with hydrops fetalis. SNP-genotype analysis revealed a recombination event during gamete formation in the father that may have contributed to the deletion in his offspring. Meanwhile, the couple's haplotypes will facilitate the selection of normal gametes in the setting of assisted reproduction. Our study demonstrated the potential of OGM in identifying CCRs and its ability to work with current methodologies to refine precise breakpoints and construct accurate haplotypes for couples with a CCR.
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Affiliation(s)
- Na Hao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | | | - Mengmeng Li
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hanzhe Zhang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiazhen Chang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qingwei Qi
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiya Zhou
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | | | | | - Yaru Wang
- Ecobono (Beijing) Biotech Co., Ltd, Beijing, China
| | - Yanli Zhang
- Peking Jabrehoo Med Tech Co., Ltd, Beijing, China
| | - Yulin Jiang
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetric & Gynecologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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Goumy C, Guy Ouedraogo Z, Soler G, Eymard-Pierre E, Laurichesse H, Delabaere A, Gallot D, Bouchet P, Perthus I, Pebrel-Richard C, Gouas L, Salaun G, Salse J, Véronèse L, Tchirkov A. Optical genome mapping for prenatal diagnosis: A prospective study. Clin Chim Acta 2023; 551:117594. [PMID: 37832906 DOI: 10.1016/j.cca.2023.117594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
PURPOSE Cytogenetic analysis provides important information for prenatal decision-making and genetic counseling. Optical genome mapping (OGM) has demonstrated its performances in retrospective studies. In our prospective study, we assessed the quality of DNA obtained from cultures of amniotic fluid (AF) and chorionic villi (CV) and evaluated the ability of OGM to detect all clinically relevant aberrations identified by standard methods. METHODS A total of 37 prenatal samples from pregnancies with a fetal anomaly on ultrasound were analyzed prospectively by OGM between January 1, 2021 and June 31, 2022. OGM results were interpreted blindly and compared to the results obtained by standard techniques. RESULTS OGM results were interpretable in 92% of samples. We observed 100% concordance between OGM and karyotype and/or chromosomal microarray results. In addition, OGM identified a median of 30 small (<100 kb) structural variations per case with the involvement of 12 OMIM genes, of which 3 were OMIM morbid genes. CONCLUSION This prospective study showed OGM performed well in detecting genomic alterations in cell cultures from prenatal samples. The place of OGM in relation to CMA or exome sequencing remains to be defined in order to optimize the prenatal diagnostic procedure.
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Affiliation(s)
- Carole Goumy
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; INSERM U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont Ferrand, France.
| | - Zangbéwendé Guy Ouedraogo
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; Service de Biochimie et Génétique Moléculaire, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Inserm, GReD, 63001 Clermont-Ferrand, France
| | - Gwendoline Soler
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France
| | - Eleonore Eymard-Pierre
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; INSERM U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont Ferrand, France
| | - Hélène Laurichesse
- Unité de Médecine Fœtale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Amélie Delabaere
- Unité de Médecine Fœtale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Denis Gallot
- Unité de Médecine Fœtale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France; Université Clermont Auvergne, CNRS, Inserm, GReD, 63001 Clermont-Ferrand, France
| | - Pamela Bouchet
- Unité de Médecine Fœtale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Isabelle Perthus
- Service de Génétique Médicale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Céline Pebrel-Richard
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France
| | - Laetitia Gouas
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; INSERM U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont Ferrand, France
| | - Gaëlle Salaun
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France
| | - Jérôme Salse
- UMR 1095 INRAE/UCA Génétique, Diversité et Ecophysiologie des Céréales (GDEC), Genotyping and Sequencing Plateform Gentyane, Clermont-Ferrand, France
| | - Lauren Véronèse
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; EA7453 CHELTER « Clonal Heterogeneity, Leukemic Environment, Therapy Resistance of Chronic Leukemias », Université Clermont Auvergne, Clermont-Ferrand, France
| | - Andrei Tchirkov
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; EA7453 CHELTER « Clonal Heterogeneity, Leukemic Environment, Therapy Resistance of Chronic Leukemias », Université Clermont Auvergne, Clermont-Ferrand, France
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Si L, Wang Z, Li XY, Song Y, Yao T, Xu E, Wang X, Wang C. Novel mutations and molecular pathways identified in patients with brain iron accumulation disorders. Neurogenetics 2023; 24:231-241. [PMID: 37453004 DOI: 10.1007/s10048-023-00725-9] [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: 04/04/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
Brain iron accumulation disorders (BIADs) are a group of diseases characterized by iron overload in deep gray matter nuclei, which is a common feature of neurodegenerative diseases. Although genetic factors have been reported to be one of the etiologies, much more details about the genetic background and molecular mechanism of BIADs remain unclear. This study aimed to illustrate the genetic characteristics of BIADs and clarify their molecular mechanisms. A total of 84 patients with BIADs were recruited from April 2018 to October 2022 at Xuanwu Hospital. Clinical characteristics including family history, consanguineous marriage history, and age at onset (AAO) were collected and assessed by two senior neurologists. Neuroimaging data were conducted for all the patients, including cranial magnetic resonance imaging (MRI) and susceptibility-weighted imaging (SWI). Whole-exome sequencing (WES) and capillary electrophoresis for detecting sequence mutation and trinucleotide repeat expansion, respectively, were conducted on all patients and part of their parents (whose samples were available). Variant pathogenicity was assessed according to the American College of Medical Genetics and Association for Molecular Pathology (ACMG/AMP). The NBIA and NBIA-like genes with mutations were included for bioinformatic analysis, using Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genome (KEGG). GO annotation and KEGG pathway analysis were performed on Metascape platform. In the 84 patients, 30 (35.7%) were found to carry mutations, among which 20 carried non-dynamic mutations (missense, stop-gained, frameshift, inframe, and exonic deletion) and 10 carried repeat expansion mutations. Compared with sporadic cases, familial cases had more genetic variants (non-dynamic mutation: P=0.025, dynamic mutation: P=0.003). AAO was 27.85±10.42 years in cases with non-dynamic mutations, which was significantly younger than those without mutations (43.13±17.17, t=3.724, P<0.001) and those with repeated expansions (45.40±8.90, t=4.550, P<0.001). Bioinformatic analysis suggested that genes in lipid metabolism, autophagy, mitochondria regulation, and ferroptosis pathways are more likely to be involved in the pathogenesis of BIADs. This study broadens the genetic spectrum of BIADs and has important implications in genetic counselling and clinical diagnosis. Patients diagnosed as BIADs with early AAO and family history are more likely to carry mutations. Bioinformatic analysis provides new insights into the molecular pathogenesis of BIADs, which may shed lights on the therapeutic strategy for neurodegenerative diseases.
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Affiliation(s)
- Lianghao Si
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Zhanjun Wang
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Xu-Ying Li
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Yang Song
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Tingyan Yao
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Erhe Xu
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Xianling Wang
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China
| | - Chaodong Wang
- Department of Neurology & Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, 100053, China.
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Xie M, Xue J, Zhang Y, Zhou Y, Yu Q, Li H, Li Q. Combination of trio-based whole exome sequencing and optical genome mapping reveals a cryptic balanced translocation that causes unbalanced chromosomal rearrangements in a family with multiple anomalies. Front Genet 2023; 14:1248544. [PMID: 37745854 PMCID: PMC10512417 DOI: 10.3389/fgene.2023.1248544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Background: Balanced translocation (BT) carriers can produce imbalanced gametes and experience recurrent spontaneous abortions (RSAs) and even give birth to a child with complex chromosomal disorders. Here, we report a cryptic BT, t(5; 6) (p15.31; p25.1), in the proband's grandmother, which caused unbalanced chromosomal rearrangements and various anomalies in the two subsequent generations. We also provide a thorough overview of the application of optical genome mapping (OGM) to identify chromosomal structural variants (SVs). Methods: Trio-based whole exome sequencing (Trio-WES) was conducted to explore the genetic basis of the phenotype of the proband and her mother. High-resolution karyotype analysis and OGM detection were performed on the proband's grandparents to trace the origin of the unbalanced rearrangements between chromosomes 5 and 6. A PubMed search was conducted with the following keywords: "OGM" and "SVs." Then, relevant studies were collected and systematically reviewed. Results: The proband and her mother presented with various anomalies, whereas the grandmother was healthy but had a history of four abnormal pregnancies. Trio-WES revealed a heterozygous duplication on the terminal region of chromosome 5p and a heterozygous deletion on the proximal end of chromosome 6p in the proband and her mother. High-resolution karyotype analysis revealed no aberrant karyotypes in either grandparent, whereas OGM detection revealed a cryptic BT, t(5; 6)(p15.31; p25.1), in the proband's grandmother. An overwhelming majority of research publications have verified the clinical utility of OGM in detecting SVs. Conclusion: The results of this study revealed that the unbalanced chromosomal rearrangements and many anomalies observed in multiple members of the family were attributable to the cryptic BT carried by the proband's grandmother. This study supports that OGM has a unique advantage for detecting cryptic BTs, and can be used as a first-tier genetic test for the etiological diagnosis of infertility, RSAs, and other complex genetic disorders.
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Affiliation(s)
- Min Xie
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
| | - Jiangyang Xue
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
| | - Yuxin Zhang
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
| | - Ying Zhou
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
| | - Qi Yu
- Neonatal Screening Center, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
| | - Haibo Li
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
| | - Qiong Li
- Neonatal Screening Center, Ningbo Women and Children’s Hospital, Ningbo, Zhejiang, China
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Rao H, Zhang H, Zou Y, Ma P, Huang T, Yuan H, Zhou J, Lu W, Li Q, Huang S, Liu Y, Yang B. Analysis of chromosomal structural variations in patients with recurrent spontaneous abortion using optical genome mapping. Front Genet 2023; 14:1248755. [PMID: 37732322 PMCID: PMC10507169 DOI: 10.3389/fgene.2023.1248755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023] Open
Abstract
Background and aims: Certain chromosomal structural variations (SVs) in biological parents can lead to recurrent spontaneous abortions (RSAs). Unequal crossing over during meiosis can result in the unbalanced rearrangement of gamete chromosomes such as duplication or deletion. Unfortunately, routine techniques such as karyotyping, fluorescence in situ hybridization (FISH), chromosomal microarray analysis (CMA), and copy number variation sequencing (CNV-seq) cannot detect all types of SVs. In this study, we show that optical genome mapping (OGM) quickly and accurately detects SVs for RSA patients with a high resolution and provides more information about the breakpoint regions at gene level. Methods: Seven couples who had suffered RSA with unbalanced chromosomal rearrangements of aborted embryos were recruited, and ultra-high molecular weight (UHMW) DNA was isolated from their peripheral blood. The consensus genome map was created by de novo assembly on the Bionano Solve data analysis software. SVs and breakpoints were identified via alignments of the reference genome GRCh38/hg38. The exact breakpoint sequences were verified using either Oxford Nanopore sequencing or Sanger sequencing. Results: Various SVs in the recruited couples were successfully detected by OGM. Also, additional complex chromosomal rearrangement (CCRs) and four cryptic balanced reciprocal translocations (BRTs) were revealed, further refining the underlying genetic causes of RSA. Two of the disrupted genes identified in this study, FOXK2 [46,XY,t(7; 17)(q31.3; q25)] and PLXDC2 [46,XX,t(10; 16)(p12.31; q23.1)], had been previously shown to be associated with male fertility and embryo transit. Conclusion: OGM accurately detects chromosomal SVs, especially cryptic BRTs and CCRs. It is a useful complement to routine human genetic diagnostics, such as karyotyping, and detects cryptic BRTs and CCRs more accurately than routine genetic diagnostics.
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Affiliation(s)
- Huihua Rao
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Haoyi Zhang
- School of Public Health, Nanchang University, Nanchang, Jiangxi, China
| | - Yongyi Zou
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Pengpeng Ma
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Tingting Huang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Huizhen Yuan
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Jihui Zhou
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Wan Lu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Qiao Li
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Shuhui Huang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Yanqiu Liu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Bicheng Yang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
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Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
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Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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18
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Lloveras E, Pérez C, Mendez B, Martin S, Alves C, Reis-Lima M. Tandem Triplication 11p15.5-ICR1 (H19/IGF2) Detected by Microarray and Optical Genome Mapping in a Prenatal Beckwith-Wiedemann Case. Cytogenet Genome Res 2023; 163:32-35. [PMID: 37369188 DOI: 10.1159/000531703] [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: 04/21/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023] Open
Abstract
Optical genome mapping (OGM) appears as a new tool for matching standard cytogenetic methods (karyotype and microarray) into a single assay. The chromosomal region 11p15.5 harbours two differentially methylated regions, the imprinting centre regions 1 and 2 (ICR1, ICR2). Disturbances in both regions alter human growth and are associated with two imprinting disorders, Beckwith-Wiedemann (BWS) and Silver-Russell syndromes. Herein, we present a prenatal case with a triplication in 11p15.5, including the H19/IGF2 imprinted region, detected by microarray and OGM. A 30-year-old pregnant woman of 17 weeks of gestation was referred for prenatal karyotype and microarray study because of increased nuchal translucency, short femur, megabladder, hyperechogenic bowel, and renal ectasia. Microarray, OGM, and MS-MLPA were performed, and a tandem cis-triplication in 11p15.5 and hypermethylation of the ICR1 region, compatible with BWS was detected. OGM, with its power to detect all classes of structural variants, including copy number variants, at a higher resolution than traditional cytogenetic methods can play a significant role in prenatal care and management as a next-generation cytogenomic tool. This study further supports the hypotheses that the amplification/duplication-triplication of the H19/IGF2 region could be related to BWS if it is of paternal origin.
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Affiliation(s)
- Elisabet Lloveras
- Departamento de Genética, Laboratorio Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Cristina Pérez
- Departamento de Genética, Laboratorio Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Begoña Mendez
- Departamento de Genética, Laboratorio Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Susana Martin
- Departamento de Genética, Laboratorio Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Claudia Alves
- Laboratório de Genética Médica, SYNLAB International Group, Porto, Portugal
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Ogiwara Y, Hattori A, Ikegawa K, Hasegawa Y, Kuroki Y, Miyado M, Fukami M. Optical Genome Mapping for a Patient with a Congenital Disorder and Chromosomal Translocation. Cytogenet Genome Res 2023; 162:617-624. [PMID: 37231804 DOI: 10.1159/000531103] [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: 10/19/2022] [Accepted: 05/11/2023] [Indexed: 05/27/2023] Open
Abstract
We performed optical genome mapping (OGM), a newly developed cytogenetic technique, for a patient with a disorder of sex development (DSD) and a 46,XX,t(9;11)(p22;p13) karyotype. The results of OGM were validated using other methods. OGM detected a 9;11 reciprocal translocation and successfully mapped its breakpoints to small regions of 0.9-12.3 kb. OGM identified 46 additional small structural variants, only three of which were detected by array-based comparative genomic hybridization. OGM suggested the presence of complex rearrangements on chromosome 10; however, these variants appeared to be artifacts. The 9;11 translocation was unlikely to be associated with DSD, while the pathogenicity of the other structural variants remained unknown. These results indicate that OGM is a powerful tool for detecting and characterizing chromosomal structural variations, although the current methods of OGM data analyses need to be improved.
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Affiliation(s)
- Yasuko Ogiwara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Endocrinology and Metabolism, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan
| | - Atsushi Hattori
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kento Ikegawa
- Division of Endocrinology and Metabolism, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Yukihiro Hasegawa
- Division of Endocrinology and Metabolism, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Yoko Kuroki
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Genome Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Mami Miyado
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
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20
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Nifker G, Grunwald A, Margalit S, Tulpova Z, Michaeli Y, Har-Gil H, Maimon N, Roichman E, Schütz L, Weinhold E, Ebenstein Y. Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays. ACS NANO 2023; 17:9178-9187. [PMID: 37154345 DOI: 10.1021/acsnano.2c12755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in order to perform genomic tasks such as gene activation and transcription. Hence, chromatin accessibility is a central regulator of gene expression, and its genomic profile holds essential information on the cell type and state. We utilized the E. coli Dam methyltransferase in combination with a fluorescent cofactor analogue to generate fluorescent tags in accessible DNA regions within the cell nucleus. The accessible portions of the genome are then detected by single-molecule optical genome mapping in nanochannel arrays. This method allowed us to characterize long-range structural variations and their associated chromatin structure. We show the ability to create whole-genome, allele-specific chromatin accessibility maps composed of long DNA molecules extended in silicon nanochannels.
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Affiliation(s)
- Gil Nifker
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Assaf Grunwald
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Sapir Margalit
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Zuzana Tulpova
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Yael Michaeli
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Hagai Har-Gil
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Noy Maimon
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Elad Roichman
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Leonie Schütz
- Institute of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Yuval Ebenstein
- Department of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801 Tel Aviv, Israel
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, 6997801 Tel Aviv, Israel
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21
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Shi S, Huang P, Yan R, Li R. Identification of complex and cryptic chromosomal rearrangements by optical genome mapping. Mol Cytogenet 2023; 16:5. [PMID: 37101225 PMCID: PMC10134526 DOI: 10.1186/s13039-023-00636-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Optical genome mapping (OGM) has developed into a highly promising method for detecting structural variants (SVs) in human genomes. Complex chromosomal rearrangements (CCRs) and cryptic translocations are rare events that are considered difficult to detect by routine cytogenetic methods. In this study, OGM was applied to delineate the precise chromosomal rearrangements in three cases with uncertain or unconfirmed CCRs detected by conventional karyotyping and one case with a cryptic translocation suggested by fetal chromosomal microarray analysis (CMA). RESULTS In the three cases with CCRs, OGM not only confirmed or revised the original karyotyping results but also refined the precise chromosomal structures. In the case with a suspected translocation not detected by karyotyping, OGM efficiently identified the cryptic translocation and defined the genomic breakpoints with relatively high accuracy. CONCLUSIONS Our study confirmed OGM as a robust alternative approach to karyotyping for the detection of chromosomal structural rearrangements, including CCRs and cryptic translocations.
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Affiliation(s)
- Shanshan Shi
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Jinan University, No. 613 Huangpu West Road, Guangzhou, 510630, People's Republic of China
| | - Peizhi Huang
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ruiling Yan
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Jinan University, No. 613 Huangpu West Road, Guangzhou, 510630, People's Republic of China.
| | - Ruiman Li
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Jinan University, No. 613 Huangpu West Road, Guangzhou, 510630, People's Republic of China.
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22
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Sahajpal NS, Mondal AK, Fee T, Hilton B, Layman L, Hastie AR, Chaubey A, DuPont BR, Kolhe R. Clinical Validation and Diagnostic Utility of Optical Genome Mapping in Prenatal Diagnostic Testing. J Mol Diagn 2023; 25:234-246. [PMID: 36758723 DOI: 10.1016/j.jmoldx.2023.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/23/2022] [Accepted: 01/12/2023] [Indexed: 02/11/2023] Open
Abstract
The standard-of-care diagnostic prenatal testing includes a combination of cytogenetic methods, such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), using either direct or cultured amniocytes or chorionic villi sampling. However, each technology has its limitations: karyotyping has a low resolution (>5 Mb), FISH is targeted, and CMA does not detect balanced structural variations (SVs). These limitations necessitate the use of multiple tests, either simultaneously or sequentially, to reach a genetic diagnosis. Optical genome mapping (OGM) is an emerging technology that can detect several classes of SVs in a single assay, but it has not been evaluated in the prenatal setting. This validation study analyzed 114 samples that were received in our laboratory for traditional cytogenetic analysis with karyotyping, FISH, and/or CMA. OGM was 100% concordant in identifying the 101 aberrations that included 29 interstitial/terminal deletions, 28 duplications, 26 aneuploidies, 6 absence of heterozygosity regions, 3 triploid genomes, 4 isochromosomes, and 1 translocation; and the method revealed the identity of 3 marker chromosomes and 1 chromosome with additional material not determined by karyotyping. In addition, OGM detected 64 additional clinically reportable SVs in 43 samples. OGM has a standardized laboratory workflow and reporting solution that can be adopted in routine clinical laboratories and demonstrates the potential to replace the current standard-of-care methods for prenatal diagnostic testing.
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Affiliation(s)
- Nikhil S Sahajpal
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Timothy Fee
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Benjamin Hilton
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Lawrence Layman
- Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | | | | | - Barbara R DuPont
- Cytogenetics Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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23
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Iqbal MA, Broeckel U, Levy B, Skinner S, Sahajpal NS, Rodriguez V, Stence A, Awayda K, Scharer G, Skinner C, Stevenson R, Bossler A, Nagy PL, Kolhe R. Multisite Assessment of Optical Genome Mapping for Analysis of Structural Variants in Constitutional Postnatal Cases. J Mol Diagn 2023; 25:175-188. [PMID: 36828597 PMCID: PMC10851778 DOI: 10.1016/j.jmoldx.2022.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/13/2022] [Accepted: 12/06/2022] [Indexed: 02/24/2023] Open
Abstract
This study compares optical genome mapping (OGM) performed at multiple sites with current standard-of-care (SOC) methods used in clinical cytogenetics. This study included 50 negative controls and 359 samples from individuals (patients) with suspected genetic conditions referred for cytogenetic testing. OGM was performed using the Saphyr system and Bionano Access software version 1.7. Structural variants, including copy number variants, aneuploidy, and regions of homozygosity, were detected and classified according to American College of Medical Genetics and Genomics guidelines. Repeated expansions in FMR1 and contractions in facioscapulohumeral dystrophy 1 were also analyzed. OGM results were compared with SOC for technical concordance, clinical classification concordance, intrasite and intersite reproducibility, and ability to provide additional, clinically relevant information. Across five testing sites, 98.8% (404/409) of samples yielded successful OGM data for analysis and interpretation. Overall, technical concordance for OGM to detect previously reported SOC results was 99.5% (399/401). The blinded analysis and variant classification agreement between SOC and OGM was 97.6% (364/373). Replicate analysis of 130 structural variations was 100% concordant. On the basis of this demonstration of the analytic validity and clinical utility of OGM by this multisite assessment, the authors recommend this technology as an alternative to existing SOC tests for rapid detection and diagnosis in postnatal constitutional disorders.
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Affiliation(s)
- M Anwar Iqbal
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Ulrich Broeckel
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Brynn Levy
- Columbia University Medical Center, New York, New York
| | | | - Nikhil S Sahajpal
- Greenwood Genetic Center, Greenwood, South Carolina; Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | | | - Aaron Stence
- Department of Pathology, Carver College of Medicine, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Kamel Awayda
- DNA Microarray CGH Laboratory, Department of Pathology, University of Rochester Medical Center, Rochester, New York
| | - Gunter Scharer
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | | | | | | | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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24
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Zhang S, Pei Z, Lei C, Zhu S, Deng K, Zhou J, Yang J, Lu D, Sun X, Xu C, Xu C. Detection of cryptic balanced chromosomal rearrangements using high-resolution optical genome mapping. J Med Genet 2023; 60:274-284. [PMID: 35710108 DOI: 10.1136/jmedgenet-2022-108553] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/28/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Chromosomal rearrangements have profound consequences in diverse human genetic diseases. Currently, the detection of balanced chromosomal rearrangements (BCRs) mainly relies on routine cytogenetic G-banded karyotyping. However, cryptic BCRs are hard to detect by karyotyping, and the risk of miscarriage or delivering abnormal offspring with congenital malformations in carrier couples is significantly increased. In the present study, we aimed to investigate the potential of single-molecule optical genome mapping (OGM) in unravelling cryptic chromosomal rearrangements. METHODS Eleven couples with normal karyotypes that had abortions/affected offspring with unbalanced rearrangements were enrolled. Ultra-high-molecular-weight DNA was isolated from peripheral blood cells and processed via OGM. The genome assembly was performed followed by variant calling and annotation. Meanwhile, multiple detection strategies, including FISH, long-range-PCR amplicon-based next-generation sequencing and Sanger sequencing were implemented to confirm the results obtained from OGM. RESULTS High-resolution OGM successfully detected cryptic reciprocal translocation in all recruited couples, which was consistent with the results of FISH and sequencing. All high-confidence cryptic chromosomal translocations detected by OGM were confirmed by sequencing analysis of rearrangement breakpoints. Moreover, OGM revealed additional complex rearrangement events such as inverted aberrations, further refining potential genetic interpretation. CONCLUSION To the best of our knowledge, this is the first study wherein OGM facilitate the rapid and robust detection of cryptic chromosomal reciprocal translocations in clinical practice. With the excellent performance, our findings suggest that OGM is well qualified as an accurate, comprehensive and first-line method for detecting cryptic BCRs in routine clinical testing.
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Affiliation(s)
- Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Zhenle Pei
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Saijuan Zhu
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Ke Deng
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jing Zhou
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jingmin Yang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning, Science and Technology Research Institute, Chongqing, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning, Science and Technology Research Institute, Chongqing, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chenming Xu
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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25
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Brakta S, Hawkins ZA, Sahajpal N, Seman N, Kira D, Chorich LP, Kim HG, Xu H, Phillips JA, Kolhe R, Layman LC. Rare structural variants, aneuploidies, and mosaicism in individuals with Mullerian aplasia detected by optical genome mapping. Hum Genet 2023; 142:483-494. [PMID: 36797380 DOI: 10.1007/s00439-023-02522-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/06/2023] [Indexed: 02/18/2023]
Abstract
The molecular basis of Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome remains largely unknown. Pathogenic variants in WNT4 and HNF1B have been confirmed in a small percent of individuals. A variety of copy number variants have been reported, but causal gene(s) remain to be identified. We hypothesized that rare structural variants (SVs) would be present in some individuals with MRKH, which could explain the genetic basis of the syndrome. Large molecular weight DNA was extracted from lymphoblastoid cells from 87 individuals with MRKH and available parents. Optical genome mapping (OGM) was performed to identify SVs, which were confirmed by another method (quantitative PCR, chromosomal microarray, karyotype, or fluorescent in situ hybridization) when possible. Thirty-four SVs that overlapped coding regions of genes with potential involvement in MRKH were identified, 14 of which were confirmed by a second method. These 14 SVs were present in 17/87 (19.5%) of probands with MRKH and included seven deletions, three duplications, one new translocation in 5/50 cells-t(7;14)(q32;q32), confirmation of a previously identified translocation-t(3;16)(p22.3;p13.3), and two aneuploidies. Of interest, three cases of mosaicism (3.4% of probands) were identified-25% mosaicism for trisomy 12, 45,X(75%)/46,XX (25%), and 10% mosaicism for a 7;14 translocation. Our study constitutes the first systematic investigation of SVs by OGM in individuals with MRKH. We propose that OGM is a promising method that enables a comprehensive investigation of a variety of SVs in a single assay including cryptic translocations and mosaic aneuploidies. These observations suggest that mosaicism could play a role in the genesis of MRKH.
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Affiliation(s)
- Soumia Brakta
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia.
| | - Zoe A Hawkins
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Nikhil Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Department of Genetics, Greenwood Genetics Center, Greenwood, SC, USA
| | - Natalie Seman
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Dina Kira
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Lynn P Chorich
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Hongyan Xu
- Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - John A Phillips
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia. .,Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia. .,Department of Physiology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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26
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Points to consider in the detection of germline structural variants using next-generation sequencing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100316. [PMID: 36507974 DOI: 10.1016/j.gim.2022.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
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27
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Koppikar P, Shenoy S, Guruju N, Hegde M. Testing for Facioscapulohumeral Muscular Dystrophy with Optical Genome Mapping. Curr Protoc 2023; 3:e629. [PMID: 36648278 DOI: 10.1002/cpz1.629] [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: 01/18/2023]
Abstract
The introduction of optical genome mapping has improved time constraints and a lack of specificity from previous methodologies when performing genome-wide analyses of samples. Optical genome mapping allows for the detection of structural variations, aberrations, and functionality traits from a single stained molecule of DNA. Though the preparation time is increased compared to previously utilized visualization techniques, optical genome mapping significantly reduces the time needed for analysis. Specifically, individual disease pipelines have been developed to rapidly analyze prepared samples. One of these diseases, Facioscapulohumeral Muscular Dystrophy (FSHD), is detected through quantification of the D4Z4 repeat array on chromosome 4q35. Optical genome mapping, with the ability to enumerate the repeats of the D4Z4 array, has demonstrated the capability to precisely diagnose FSHD. In this protocol, the preparation of samples and subsequent loading and analysis in an optical genome mapping system is discussed for the detection and analysis of FSHD. These methods should prove highly useful in FSHD analyses and beyond with the development of further disease analysis pipelines within the instrument. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Genomic DNA isolation, labeling, and staining Basic Protocol 2: Mapping and analysis with the Bionano Saphyr® system.
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Affiliation(s)
| | | | - Naga Guruju
- PerkinElmer Genomics, Pittsburgh, Pennsylvania, USA
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28
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Andrews PW, Barbaric I, Benvenisty N, Draper JS, Ludwig T, Merkle FT, Sato Y, Spits C, Stacey GN, Wang H, Pera MF. The consequences of recurrent genetic and epigenetic variants in human pluripotent stem cells. Cell Stem Cell 2022; 29:1624-1636. [PMID: 36459966 DOI: 10.1016/j.stem.2022.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022]
Abstract
It is well established that human pluripotent stem cells (hPSCs) can acquire genetic and epigenetic changes during culture in vitro. Given the increasing use of hPSCs in research and therapy and the vast expansion in the number of hPSC lines available for researchers, the International Society for Stem Cell Research has recognized the need to reassess quality control standards for ensuring the genetic integrity of hPSCs. Here, we summarize current knowledge of the nature of recurrent genetic and epigenetic variants in hPSC culture, the methods for their detection, and what is known concerning their effects on cell behavior in vitro or in vivo. We argue that the potential consequences of low-level contamination of cell therapy products with cells bearing oncogenic variants are essentially unknown at present. We highlight the key challenges facing the field with particular reference to safety assessment of hPSC-derived cellular therapeutics.
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Affiliation(s)
- Peter W Andrews
- Centre for Stem Cell Biology, School of Biological Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Steering Committee, International Stem Cell Initiative
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biological Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Steering Committee, International Stem Cell Initiative
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel; Steering Committee, International Stem Cell Initiative
| | - Jonathan S Draper
- Stem Cell Network, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada; Steering Committee, International Stem Cell Initiative
| | - Tenneille Ludwig
- WiCell Research Institute, Madison, WI, USA; University of Wisconsin-Madison, Madison, WI 53719, USA; Steering Committee, International Stem Cell Initiative
| | - Florian T Merkle
- Wellcome Trust-Medical Research Council Institute of Metabolic Science, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0QQ, UK; Steering Committee, International Stem Cell Initiative
| | - Yoji Sato
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki Ward, Kawasaki City, Kanagawa 210-9501, Japan; Steering Committee, International Stem Cell Initiative
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; Steering Committee, International Stem Cell Initiative
| | - Glyn N Stacey
- International Stem Cell Banking Initiative, 2 High Street, Barley, UK; National Stem Cell Resource Centre, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100190, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China; Steering Committee, International Stem Cell Initiative
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China; Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China; Steering Committee, International Stem Cell Initiative
| | - Martin F Pera
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; Steering Committee, International Stem Cell Initiative.
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Sahajpal NS, Mondal AK, Tvrdik T, Hauenstein J, Shi H, Deeb KK, Saxe D, Hastie AR, Chaubey A, Savage NM, Kota V, Kolhe R. Clinical Validation and Diagnostic Utility of Optical Genome Mapping for Enhanced Cytogenomic Analysis of Hematological Neoplasms. J Mol Diagn 2022; 24:1279-1291. [PMID: 36265723 DOI: 10.1016/j.jmoldx.2022.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/29/2022] [Accepted: 09/12/2022] [Indexed: 11/07/2022] Open
Abstract
The current standard-of-care cytogenetic techniques for the analysis of hematological malignancies include karyotyping, fluorescence in situ hybridization, and chromosomal microarray, which are labor intensive and time and cost prohibitive, and they often do not reveal the genetic complexity of the tumor, demonstrating the need for alternative technology for better characterization of these tumors. Herein, we report the results from our clinical validation study and demonstrate the utility of optical genome mapping (OGM), evaluated using 92 sample runs (including replicates) that included 69 well-characterized unique samples (59 hematological neoplasms and 10 controls). The technical performance (quality control metrics) resulted in 100% first-pass rate, with analytical performance (concordance) showing a sensitivity of 98.7%, a specificity of 100%, and an accuracy of 99.2%. OGM demonstrated robust technical, analytical performance, and interrun, intrarun, and interinstrument reproducibility. The limit of detection was determined to be at 5% allele fraction for aneuploidy, translocation, interstitial deletion, and duplication. OGM identified several additional structural variations, revealing the genomic architecture in these neoplasms that provides an opportunity for better tumor classification, prognostication, risk stratification, and therapy selection. Overall, OGM has outperformed the standard-of-care tests in this study and demonstrated its potential as a first-tier cytogenomic test for hematologic malignancies.
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Affiliation(s)
- Nikhil S Sahajpal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Tatiana Tvrdik
- Department of Pathology, Emory University, Atlanta, Georgia
| | | | - Huidong Shi
- Georgia Cancer Center, Augusta University, Augusta, Georgia
| | - Kristin K Deeb
- Department of Pathology, Emory University, Atlanta, Georgia
| | - Debra Saxe
- Department of Pathology, Emory University, Atlanta, Georgia
| | | | | | - Natasha M Savage
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Vamsi Kota
- Department of Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, Georgia.
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30
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Senaratne TN, Saitta SC. Evaluating Genetic Disorders in the Neonate: The Role of Exome Sequencing in the NICU. Neoreviews 2022; 23:e829-e840. [PMID: 36450644 DOI: 10.1542/neo.23-12-e829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
With recent advances in the technologies used for genetic diagnosis as well as our understanding of the genetic basis of disease, a growing list of options is available for providers when caring for a newborn with features suggesting an underlying genetic etiology. The choice of the most appropriate genetic test for a specific situation includes clinical considerations such as the phenotypic features and type of genetic abnormality suspected, as well as practical considerations such as cost and turnaround time. In this review, we discuss clinical exome sequencing in the context of genetic evaluation of newborns, including technical considerations, variant interpretation, and incidental/secondary findings. Strengths and limitations of exome sequencing are discussed and compared with those of other commonly known tests such as karyotype analysis, fluorescence in situ hybridization, chromosomal microarray, and sequencing panels, along with integration of results from prenatal testing if available. We also review future directions including genome sequencing and other emerging technologies that are starting to be used in clinical settings.
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Affiliation(s)
- T Niroshi Senaratne
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Sulagna C Saitta
- Division of Clinical Genetics, Department of Pediatrics, Division of Reproductive Genetics, Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA
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31
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van der Laan L, Rooney K, Trooster TM, Mannens MM, Sadikovic B, Henneman P. DNA methylation episignatures: insight into copy number variation. Epigenomics 2022; 14:1373-1388. [PMID: 36537268 DOI: 10.2217/epi-2022-0287] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In this review we discuss epigenetic disorders that result from aberrations in genes linked to epigenetic regulation. We describe current testing methods for the detection of copy number variants (CNVs) in Mendelian disorders, dosage sensitivity, reciprocal phenotypes and the challenges of test selection and overlapping clinical features in genetic diagnosis. We discuss aberrations of DNA methylation and propose a role for episignatures as a novel clinical testing method in CNV disorders. Finally, we postulate that episignature mapping in CNV disorders may provide novel insights into the molecular mechanisms of disease and unlock key findings of the genome-wide impact on disease gene networks.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Kathleen Rooney
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, N5A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, N6A 5W9, Canada
| | - Tessa Ma Trooster
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Marcel Mam Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, N5A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, N6A 5W9, Canada
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
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32
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Spence T, Dubuc AM. Copy Number Analysis in Cancer Diagnostic Testing. Clin Lab Med 2022; 42:451-468. [DOI: 10.1016/j.cll.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Chu G, Li P, Wen J, Zheng G, Zhao Y, He R. Copy Number Variation Analysis of 5p Deletion Provides Accurate Prenatal Diagnosis and Reveals Candidate Pathogenic Genes. Front Med (Lausanne) 2022; 9:883565. [PMID: 35911393 PMCID: PMC9329539 DOI: 10.3389/fmed.2022.883565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/21/2022] [Indexed: 11/19/2022] Open
Abstract
Objective 5p deletion syndrome, that characterized by cat-like cry and peculiar timbre of voice, is believed to be one of the most common pathogenic copy number variations (CNVs). Variable critical regions on 5p involving a variety of genes contribute to the phenotypic heterogeneity without specific correlation. The objective of this study was to examine the genotype–phenotype correlation of 5p deletion syndrome, and to redefine 5p deletion syndrome relevant regions. In addition, we demonstrate the potential use of whole genome sequencing (WGS) to identify chromosomal breakpoints in prenatal diagnosis. Methods Three families with women undergoing prenatal diagnosis and two children were recruited. Karyotyping, CNV-seq, fluorescence in situ hybridization, WGS, and Sanger sequencing were performed to identify the chromosomal disorder. Results We reported three families and two children with CNVs of 5p deletion or combined 6p duplication. Five different sizes of 5p deletion were detected and their pathogenicity was determined, including 5p15.33-p15.31 [1–7,700,000, family1-variant of uncertain significance (VUS)], 5p15.33 (1–3,220,000, family 2-VUS), 5p15.33-p15.31 (1–7,040,000, family 3-VUS), 5p15.33-p15.31 (1–8,740,000, child 1-pathogenic) and 5p15.31-p15.1 (8,520,001–18,080,000, child 2-pathogenic). One duplication at 6p25.3-p24.3 (1–10,420,000) was detected and determined as likely pathogenic. The chromosomal breakpoints in family 3 were successfully identified by WGS. Conclusion Some critical genes that were supposed to be causative of the symptoms were identified. Relevant region in 5p deletion syndrome was redefined, and the chr5:7,700,000–8,740,000 region was supposed to be responsible for the cat-like cry. The great potential of WGS in detecting chromosomal translocations was demonstrated. Our findings may pave the way for further research on the prevention, diagnosis, and treatment of related diseases.
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Affiliation(s)
- Guoming Chu
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Pingping Li
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Juan Wen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Gaoyan Zheng
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yanyan Zhao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Rong He
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Rong He,
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Gerding WM, Tembrink M, Nilius‐Eliliwi V, Mika T, Dimopoulos F, Ladigan‐Badura S, Eckhardt M, Pohl M, Wünnenberg M, Farshi P, Reimer P, Schroers R, Nguyen HP, Vangala DB. Optical genome mapping reveals additional prognostic information compared to conventional cytogenetics in
AML
/
MDS
patients. Int J Cancer 2022; 150:1998-2011. [DOI: 10.1002/ijc.33942] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/27/2021] [Accepted: 01/13/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Wanda M. Gerding
- Department for Human Genetics Ruhr‐University Bochum Bochum Germany
| | - Marco Tembrink
- Department for Human Genetics Ruhr‐University Bochum Bochum Germany
| | - Verena Nilius‐Eliliwi
- Department for Human Genetics Ruhr‐University Bochum Bochum Germany
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Thomas Mika
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Fotios Dimopoulos
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Swetlana Ladigan‐Badura
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Matthias Eckhardt
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Michael Pohl
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Max Wünnenberg
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Pakhshan Farshi
- Department of Hematology and Oncology Kliniken Essen‐Mitte Essen Germany
| | - Peter Reimer
- Department of Hematology and Oncology Kliniken Essen‐Mitte Essen Germany
| | - Roland Schroers
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
| | - Huu Phuc Nguyen
- Department for Human Genetics Ruhr‐University Bochum Bochum Germany
| | - Deepak B. Vangala
- Department of Medicine, Hematology and Oncology Knappschaftskrankenhaus, Ruhr‐University Bochum Bochum Germany
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35
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Yang H, Garcia-Manero G, Sasaki K, Montalban-Bravo G, Tang Z, Wei Y, Kadia T, Chien K, Rush D, Nguyen H, Kalia A, Nimmakayalu M, Bueso-Ramos C, Kantarjian H, Medeiros LJ, Luthra R, Kanagal-Shamanna R. High-resolution structural variant profiling of myelodysplastic syndromes by optical genome mapping uncovers cryptic aberrations of prognostic and therapeutic significance. Leukemia 2022; 36:2306-2316. [PMID: 35915143 PMCID: PMC9417987 DOI: 10.1038/s41375-022-01652-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/17/2022]
Abstract
Chromosome banding analysis (CBA) remains the standard-of-care for structural variant (SV) assessment in MDS. Optical genome mapping (OGM) is a novel, non-sequencing-based technique for high-resolution genome-wide SV profiling (SVP). We explored the clinical value of SVP by OGM in 101 consecutive, newly diagnosed MDS patients from a single-center, who underwent standard-of-care cytogenetic and targeted NGS studies. OGM detected 383 clinically significant, recurrent and novel SVs. Of these, 224 (51%) SVs, seen across 34% of patients, were cryptic by CBA (included rearrangements involving MECOM, NUP98::PRRX2, KMT2A partial tandem duplications among others). SVP decreased the proportion of normal karyotype by 16%, identified complex genomes (17%), chromothripsis (6%) and generated informative results in both patients with insufficient metaphases. Precise gene/exon-level mapping allowed assessment of clinically relevant biomarkers (TP53 allele status, KMT2A-PTD) without additional testing. SV data was complementary to NGS. When applied in retrospect, OGM results changed the comprehensive cytogenetic scoring system (CCSS) and R-IPSS risk-groups in 21% and 17% patients respectively with an improved prediction of prognosis. By multivariate analysis, CCSS by OGM only (not CBA), TP53 mutation and BM blasts independently predicted survival. This is the first and largest study reporting the value of combined SVP and NGS for MDS prognostication.
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Affiliation(s)
- Hui Yang
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Guillermo Garcia-Manero
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Koji Sasaki
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Guillermo Montalban-Bravo
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Zhenya Tang
- grid.240145.60000 0001 2291 4776Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Yue Wei
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Tapan Kadia
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Kelly Chien
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Diana Rush
- grid.240145.60000 0001 2291 4776School of Health Professions, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Ha Nguyen
- grid.240145.60000 0001 2291 4776School of Health Professions, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Awdesh Kalia
- grid.240145.60000 0001 2291 4776School of Health Professions, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Manjunath Nimmakayalu
- grid.240145.60000 0001 2291 4776School of Health Professions, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Carlos Bueso-Ramos
- grid.240145.60000 0001 2291 4776Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Hagop Kantarjian
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - L. Jeffrey Medeiros
- grid.240145.60000 0001 2291 4776Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Rajyalakshmi Luthra
- grid.240145.60000 0001 2291 4776Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
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Dremsek P, Schwarz T, Weil B, Malashka A, Laccone F, Neesen J. Optical Genome Mapping in Routine Human Genetic Diagnostics-Its Advantages and Limitations. Genes (Basel) 2021; 12:1958. [PMID: 34946907 PMCID: PMC8701374 DOI: 10.3390/genes12121958] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/01/2022] Open
Abstract
In recent years, optical genome mapping (OGM) has developed into a highly promising method of detecting large-scale structural variants in human genomes. It is capable of detecting structural variants considered difficult to detect by other current methods. Hence, it promises to be feasible as a first-line diagnostic tool, permitting insight into a new realm of previously unknown variants. However, due to its novelty, little experience with OGM is available to infer best practices for its application or to clarify which features cannot be detected. In this study, we used the Saphyr system (Bionano Genomics, San Diego, CA, USA), to explore its capabilities in human genetic diagnostics. To this end, we tested 14 DNA samples to confirm a total of 14 different structural or numerical chromosomal variants originally detected by other means, namely, deletions, duplications, inversions, trisomies, and a translocation. Overall, 12 variants could be confirmed; one deletion and one inversion could not. The prerequisites for detection of similar variants were explored by reviewing the OGM data of 54 samples analyzed in our laboratory. Limitations, some owing to the novelty of the method and some inherent to it, were described. Finally, we tested the successful application of OGM in routine diagnostics and described some of the challenges that merit consideration when utilizing OGM as a diagnostic tool.
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Affiliation(s)
- Paul Dremsek
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, 1090 Vienna, Austria; (T.S.); (B.W.); (A.M.); (F.L.); (J.N.)
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Marfan Syndrome Caused by Disruption of the FBN1 Gene due to A Reciprocal Chromosome Translocation. Genes (Basel) 2021; 12:genes12111836. [PMID: 34828442 PMCID: PMC8618173 DOI: 10.3390/genes12111836] [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] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022] Open
Abstract
Marfan syndrome (MFS) is a hereditary connective tissue disease caused by heterozygous mutations in the fibrillin-1 gene (FBN1) located on chromosome 15q21.1. A complex chromosomal rearrangement leading to MFS has only been reported in one case so far. We report on a mother and daughter with marfanoid habitus and no pathogenic variant in the FBN1 gene after next generation sequencing (NGS) analysis, both showing a cytogenetically reciprocal balanced translocation between chromosomes 2 and 15. By means of fluorescence in situ hybridization of Bacterial artificial chromosome (BAC) clones from the breakpoint area on chromosome 15 the breakpoint was narrowed down to a region of approximately 110 kb in FBN1. With the help of optical genome mapping (OGM), the translocation breakpoints were further refined on chromosomes 2 and 15. Sequencing of the regions affected by the translocation identified the breakpoint of chromosome 2 as well as the breakpoint of chromosome 15 in the FBN1 gene leading to its disruption. To our knowledge, this is the first report of patients with typical clinical features of MFS showing a cytogenetically reciprocal translocation involving the FBN1 gene. Our case highlights the importance of structural genome variants as an underlying cause of monogenic diseases and the useful clinical application of OGM in the elucidation of structural variants.
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Filges I, Miny P, Holzgreve W, Tercanli S. How genomics is changing the practice of prenatal testing. J Perinat Med 2021; 49:1003-1010. [PMID: 34214293 DOI: 10.1515/jpm-2021-0220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 05/20/2021] [Indexed: 11/15/2022]
Abstract
New genomic laboratory technology namely microarrays and high throughput sequencing (HTS) as well as a steady progress in sonographic image capture and processing have changed the practice of prenatal diagnosis during the last decade fundamentally. Pregnancies at high risk for common trisomies are reliably identified by non-invasive prenatal testing (NIPT) and expert sonography has greatly improved the assessment of the fetal phenotype. Preconceptional comprehensive carrier screening using HTS is available for all parents, if they should wish to do so. A definite fetal diagnosis, however, will still require invasive testing for most conditions. Chromosomal microarrays (CMA) have greatly enhanced the resolution in the detection of chromosome anomalies and other causal copy number variations (CNV). Gene panel or whole exome sequencing (WES) is becoming the routine follow up of many anomalies detected by ultrasound after CNVs have been excluded. The benefits and limitations of the various screening as well as diagnostic options are perceived as complex by many who find it challenging to cope with the need for immediate choices. The communication of facts to ensure an informed decision making is obviously a growing challenge with the advent of the new genomic testing options. This contribution provides an overview of the current practice and policies in Switzerland.
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Affiliation(s)
- Isabel Filges
- Institut für Medizinische Genetik und Pathologie and Departement Klinische Forschung, Universitätsspital Basel, Basel, Switzerland
| | - Peter Miny
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Basel, Switzerland
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39
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Wu H, Huang Q, Zhang X, Yu Z, Zhong Z. Analysis of Genomic Copy Number Variation in Miscarriages During Early and Middle Pregnancy. Front Genet 2021; 12:732419. [PMID: 34603391 PMCID: PMC8484914 DOI: 10.3389/fgene.2021.732419] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022] Open
Abstract
The purpose of this study was to explore the copy number variations (CNVs) associated with miscarriage during early and middle pregnancy and provide useful genetic guidance for pregnancy and prenatal diagnosis. A total of 505 fetal specimens were collected and CNV sequencing (CNV-seq) analysis was performed to determine the types and clinical significance of CNVs, and relevant medical records were collected. The chromosomal abnormality rate was 54.3% (274/505), among which the numerical chromosomal abnormality rate was 40.0% (202/505) and structural chromosomal abnormality rate was 14.3% (72/505). Chromosomal monosomy mainly occurred on sex chromosomes, and chromosomal trisomy mainly occurred on chromosomes 16, 22, 21, 15, 13, and 9. The incidence of numerical chromosomal abnormalities in ≥35 year-old age pregnant women was significantly higher than <35 year-old age group. The highest incidence of pathogenic CNV (pCNV) was found in fetuses at ≤6 weeks of pregnancy (5.26%), and the incidence of variants of unknown significance (VOUS) CNVs decreased gradually with the increase of gestational age. The rate of chromosomal abnormalities of fetuses in early pregnancy (59.5%) was higher than that of fetuses in middle pregnancy (27.2%) (p < 0.001). There were 168 genes in VOUS + pCNV regions. 41 functions and 12 pathways (p < 0.05) were enriched of these genes by Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Some meaningful genetic etiology information such as genes and pathways has been obtained, it may provide useful genetic guidance for pregnancy and prenatal diagnosis.
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Affiliation(s)
- Heming Wu
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Qingyan Huang
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Xia Zhang
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Center for Prenatal Diagnosis, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Zhikang Yu
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Zhixiong Zhong
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
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40
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CNV Detection from Exome Sequencing Data in Routine Diagnostics of Rare Genetic Disorders: Opportunities and Limitations. Genes (Basel) 2021; 12:genes12091427. [PMID: 34573409 PMCID: PMC8472439 DOI: 10.3390/genes12091427] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022] Open
Abstract
To assess the potential of detecting copy number variations (CNVs) directly from exome sequencing (ES) data in diagnostic settings, we developed a CNV-detection pipeline based on ExomeDepth software and applied it to ES data of 450 individuals. Initially, only CNVs affecting genes in the requested diagnostic gene panels were scored and tested against arrayCGH results. Pathogenic CNVs were detected in 18 individuals. Most detected CNVs were larger than 400 kb (11/18), but three individuals had small CNVs impacting one or a few exons only and were thus not detectable by arrayCGH. Conversely, two pathogenic CNVs were initially missed, as they impacted genes not included in the original gene panel analysed, and a third one was missed as it was in a poorly covered region. The overall combined diagnostic rate (SNVs + CNVs) in our cohort was 36%, with wide differences between clinical domains. We conclude that (1) the ES-based CNV pipeline detects efficiently large and small pathogenic CNVs, (2) the detection of CNV relies on uniformity of sequencing and good coverage, and (3) in patients who remain unsolved by the gene panel analysis, CNV analysis should be extended to all captured genes, as diagnostically relevant CNVs may occur everywhere in the genome.
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41
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Szczerbal I, Switonski M. Clinical Cytogenetics of the Dog: A Review. Animals (Basel) 2021; 11:947. [PMID: 33801756 PMCID: PMC8066086 DOI: 10.3390/ani11040947] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/15/2022] Open
Abstract
The dog is an important companion animal and has been recognized as a model in biomedical research. Its karyotype is characterized by a high chromosome number (2n = 78) and by the presence of one-arm autosomes, which are mostly small in size. This makes the dog a difficult subject for cytogenetic studies. However, there are some chromosome abnormalities that can be easily identified, such as sex chromosome aneuploidies, XX/XY leukocyte chimerism, and centric fusions (Robertsonian translocations). Fluorescence in situ hybridization (FISH) with the use of whole-chromosome painting or locus-specific probes has improved our ability to identify and characterize chromosomal abnormalities, including reciprocal translocations. The evaluation of sex chromosome complement is an important diagnostic step in dogs with disorders of sex development (DSD). In such cases, FISH can detect the copy number variants (CNVs) associated with the DSD phenotype. Since cancers are frequently diagnosed in dogs, cytogenetic evaluation of tumors has also been undertaken and specific chromosome mutations for some cancers have been reported. However, the study of meiotic, gamete, and embryo chromosomes is not very advanced. Knowledge of canine genome organization and new molecular tools, such as aCGH (array comparative genome hybridization), SNP (single nucleotide polymorphism) microarray, and ddPCR (droplet digital PCR) allow the identification of chromosomal rearrangements. It is anticipated that the comprehensive use of chromosome banding, FISH, and molecular techniques will substantially improve the diagnosis of chromosome abnormalities in dogs.
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Affiliation(s)
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637 Poznan, Poland;
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