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Chen Y, Han X, Hua R, Li N, Zhang L, Hu W, Wang Y, Qian Z, Li S. Copy number variation sequencing for the products of conception: What is the optimal testing strategy. Clin Chim Acta 2024; 557:117884. [PMID: 38522821 DOI: 10.1016/j.cca.2024.117884] [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: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Copy number variation sequencing (CNV-seq) is crucial in prenatal diagnosis, but its limitations in detecting polyploidy, maternal cell contamination (MCC), and uniparental disomy (UPD) restrict its application in the analysis of products of conception (POCs). This study aimed to investigate an optimal genetic testing strategy for POCs in the era of CNV-seq. METHODS CNV-seq and quantitative fluorescent polymerase chain reaction (QF-PCR) were performed in all 4,211 spontaneous miscarriage cases. Different testing strategies were compared and the optimal testing strategies were proposed. RESULTS Of the 4,211 cases, 2561 (60.82%) exhibited clinically significant chromosomal abnormalities. CNV-seq alone, without QF-PCR, might misdiagnose 311 (7.39%) cases, including 278 polyploidy, 13 UPD, and 20 MCC. In 20 MCC cases identified by QF-PCR, CNV-seq successfully pinpointed the cause of miscarriage in 13 cases. Furthermore, in cases where QF-PCR suggested polyploidy, CNV-seq improved the diagnostic accuracy in 54 (1.28%) hypo/hypertriploidy cases. After comparing four different strategies, the sequential approach (initiating with CNV-seq followed by QF-PCR if necessary) emerged as advantageous, reducing approximately 70% of the cost associated with QF-PCR while maintaining result accuracy. CONCLUSIONS We propose an initial CNV-seq followed by QF-PCR if needed-an efficient and cost-effective strategy for the genetic analysis of POCs.
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Affiliation(s)
- Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Han
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Renyi Hua
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Niu Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lanlan Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenjing Hu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhida Qian
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China; Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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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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Yang Z, Yang X, Sun Y, Wang Y, Song L, Qiao Z, Fang Z, Wang Z, Liu L, Chen Y, Yan S, Guo X, Zhang J, Fan C, Liu F, Peng Z, Peng H, Sun J, Chen W. Test development, optimization and validation of a WGS pipeline for genetic disorders. BMC Med Genomics 2023; 16:74. [PMID: 37020281 PMCID: PMC10077614 DOI: 10.1186/s12920-023-01495-x] [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: 12/08/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND With advances in massive parallel sequencing (MPS) technology, whole-genome sequencing (WGS) has gradually evolved into the first-tier diagnostic test for genetic disorders. However, deployment practice and pipeline testing for clinical WGS are lacking. METHODS In this study, we introduced a whole WGS pipeline for genetic disorders, which included the entire process from obtaining a sample to clinical reporting. All samples that underwent WGS were constructed using polymerase chain reaction (PCR)-free library preparation protocols and sequenced on the MGISEQ-2000 platform. Bioinformatics pipelines were developed for the simultaneous detection of various types of variants, including single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs) and balanced rearrangements, mitochondrial (MT) variants, and other complex variants such as repeat expansion, pseudogenes and absence of heterozygosity (AOH). A semiautomatic pipeline was developed for the interpretation of potential SNVs and CNVs. Forty-five samples (including 14 positive commercially available samples, 23 laboratory-held positive cell lines and 8 clinical cases) with known variants were used to validate the whole pipeline. RESULTS In this study, a whole WGS pipeline for genetic disorders was developed and optimized. Forty-five samples with known variants (6 with SNVs and Indels, 3 with MT variants, 5 with aneuploidies, 1 with triploidy, 23 with CNVs, 5 with balanced rearrangements, 2 with repeat expansions, 1 with AOHs, and 1 with exon 7-8 deletion of SMN1 gene) validated the effectiveness of our pipeline. CONCLUSIONS This study has been piloted in test development, optimization, and validation of the WGS pipeline for genetic disorders. A set of best practices were recommended using our pipeline, along with a dataset of positive samples for benchmarking.
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Affiliation(s)
- Ziying Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xu Yang
- Department of Paediatrics, Pu'er People's Hospital, Pu'er, 665000, China
| | - Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lijie Song
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- DTU Bioengineering, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Zhihong Qiao
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhonghai Fang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhonghua Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lipei Liu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yunmei Chen
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Saiying Yan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xueqin Guo
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China
| | - Junqing Zhang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Chunna Fan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Fengxia Liu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huanhuan Peng
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
| | - Wei Chen
- Pu'er People's Hospital, Pu'er, 665000, China.
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Panikker P, Roy S, Ghosh A, Poornachandra B, Ghosh A. Advancing precision medicines for ocular disorders: Diagnostic genomics to tailored therapies. Front Med (Lausanne) 2022; 9:906482. [PMID: 35911417 PMCID: PMC9334564 DOI: 10.3389/fmed.2022.906482] [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] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/29/2022] [Indexed: 11/20/2022] Open
Abstract
Successful sequencing of the human genome and evolving functional knowledge of gene products has taken genomic medicine to the forefront, soon combining broadly with traditional diagnostics, therapeutics, and prognostics in patients. Recent years have witnessed an extraordinary leap in our understanding of ocular diseases and their respective genetic underpinnings. As we are entering the age of genomic medicine, rapid advances in genome sequencing, gene delivery, genome surgery, and computational genomics enable an ever-increasing capacity to provide a precise and robust diagnosis of diseases and the development of targeted treatment strategies. Inherited retinal diseases are a major source of blindness around the world where a large number of causative genes have been identified, paving the way for personalized diagnostics in the clinic. Developments in functional genetics and gene transfer techniques has also led to the first FDA approval of gene therapy for LCA, a childhood blindness. Many such retinal diseases are the focus of various clinical trials, making clinical diagnoses of retinal diseases, their underlying genetics and the studies of natural history important. Here, we review methodologies for identifying new genes and variants associated with various ocular disorders and the complexities associated with them. Thereafter we discuss briefly, various retinal diseases and the application of genomic technologies in their diagnosis. We also discuss the strategies, challenges, and potential of gene therapy for the treatment of inherited and acquired retinal diseases. Additionally, we discuss the translational aspects of gene therapy, the important vector types and considerations for human trials that may help advance personalized therapeutics in ophthalmology. Retinal disease research has led the application of precision diagnostics and precision therapies; therefore, this review provides a general understanding of the current status of precision medicine in ophthalmology.
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Affiliation(s)
| | - Shomereeta Roy
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | - Anuprita Ghosh
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | | | - Arkasubhra Ghosh
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
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5
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Soltani N, Mirzaei F, Ayatollahi H. Cytogenetic Studies of 608 Couples with Recurrent Spontaneous Abortions in Northeastern Iran. IRANIAN JOURNAL OF PATHOLOGY 2021; 16:418-425. [PMID: 34567191 PMCID: PMC8463753 DOI: 10.30699/ijp.2021.521514.2554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 06/09/2021] [Indexed: 11/22/2022]
Abstract
Background & Objective: One of the major genetic causes of recurrent spontaneous abortions is parental chromosomal abnormalities. The objectives of the study were to determine, compare and analyze the incidence and distribution of chromosomal abnormalities in couples with recurrent miscarriages from Northeastern Iran. Methods: This study was conducted at Ghaem Hospital, Mashhad, Iran. We evaluated karyotype results of 608 couples with history of recurrent spontaneous abortion. The standard method was used for culturing peripheral venous blood lymphocytes. Results: Chromosome aberrations were detected in 43 patients (3.54%), including 25 females and 18 males. Structural chromosomal abnormality was detected in 40 cases, including balanced translocations (25 cases), robertsonian translocations (4 cases), inversions (10 cases) and numerical chromosome aberrations (3 cases). Polymorphic variants were observed in 22 individuals. Conclusion: The frequency of chromosomal abnormalities in couples with Recurrent Spontaneous Abortion (RSA) in our study is 3.54%. Reciprocal translocation, pericentric inversions, robertsonian translocations, and numerical abnormality observed among couples who had experienced recurrent spontaneous abortions and that these couples might benefit from cytogenetic analysis.
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Affiliation(s)
- Narjes Soltani
- Department of Hematology and Blood Bank, Faculty of Medicine, Cancer Molecular Pathology Research Center, Ghaem Medical Center Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzaneh Mirzaei
- Medical Genetic Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hossein Ayatollahi
- Department of Hematology and Blood Bank, Faculty of Medicine, Cancer Molecular Pathology Research Center, Ghaem Medical Center Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetic Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Mantere T, Neveling K, Pebrel-Richard C, Benoist M, van der Zande G, Kater-Baats E, Baatout I, van Beek R, Yammine T, Oorsprong M, Hsoumi F, Olde-Weghuis D, Majdali W, Vermeulen S, Pauper M, Lebbar A, Stevens-Kroef M, Sanlaville D, Dupont JM, Smeets D, Hoischen A, Schluth-Bolard C, El Khattabi L. Optical genome mapping enables constitutional chromosomal aberration detection. Am J Hum Genet 2021; 108:1409-1422. [PMID: 34237280 PMCID: PMC8387289 DOI: 10.1016/j.ajhg.2021.05.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/28/2021] [Indexed: 01/02/2023] Open
Abstract
Chromosomal aberrations including structural variations (SVs) are a major cause of human genetic diseases. Their detection in clinical routine still relies on standard cytogenetics. Drawbacks of these tests are a very low resolution (karyotyping) and the inability to detect balanced SVs or indicate the genomic localization and orientation of duplicated segments or insertions (copy number variant [CNV] microarrays). Here, we investigated the ability of optical genome mapping (OGM) to detect known constitutional chromosomal aberrations. Ultra-high-molecular-weight DNA was isolated from 85 blood or cultured cells and processed via OGM. A de novo genome assembly was performed followed by structural variant and CNV calling and annotation, and results were compared to known aberrations from standard-of-care tests (karyotype, FISH, and/or CNV microarray). In total, we analyzed 99 chromosomal aberrations, including seven aneuploidies, 19 deletions, 20 duplications, 34 translocations, six inversions, two insertions, six isochromosomes, one ring chromosome, and four complex rearrangements. Several of these variants encompass complex regions of the human genome involved in repeat-mediated microdeletion/microduplication syndromes. High-resolution OGM reached 100% concordance compared to standard assays for all aberrations with non-centromeric breakpoints. This proof-of-principle study demonstrates the ability of OGM to detect nearly all types of chromosomal aberrations. We also suggest suited filtering strategies to prioritize clinically relevant aberrations and discuss future improvements. These results highlight the potential for OGM to provide a cost-effective and easy-to-use alternative that would allow comprehensive detection of chromosomal aberrations and structural variants, which could give rise to an era of "next-generation cytogenetics."
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Affiliation(s)
- Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Health Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Céline Pebrel-Richard
- Department of Chromosomal and Molecular Genetics, University Hospital of Clermont-Ferrand, 63003 Clermont-Ferrand, France
| | - Marion Benoist
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Guillaume van der Zande
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Ellen Kater-Baats
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Imane Baatout
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Ronald van Beek
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Tony Yammine
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Unit of Medical Genetics, Saint-Joseph University, 1107 2180 Beyrouth, Lebanon
| | - Michiel Oorsprong
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Faten Hsoumi
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Daniel Olde-Weghuis
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Wed Majdali
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Susan Vermeulen
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Marc Pauper
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Aziza Lebbar
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Damien Sanlaville
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Department of Genetics, Hospices Civils de Lyon, 69677 Bron, France
| | - Jean Michel Dupont
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France; Université de Paris, Cochin Institute U1016, INSERM, 75014 Paris, France
| | - Dominique Smeets
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands.
| | - Caroline Schluth-Bolard
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Department of Genetics, Hospices Civils de Lyon, 69677 Bron, France
| | - Laïla El Khattabi
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France; Université de Paris, Cochin Institute U1016, INSERM, 75014 Paris, France.
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7
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Hu ZM, Li LL, Zhang H, Zhang HG, Liu RZ, Yu Y. Clinical Application of Chromosomal Microarray Analysis in Pregnant Women with Advanced Maternal Age and Fetuses with Ultrasonographic Soft Markers. Med Sci Monit 2021; 27:e929074. [PMID: 33837172 PMCID: PMC8045481 DOI: 10.12659/msm.929074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background In pregnant women with advanced maternal age (AMA) and fetuses with ultrasonographic (USG) soft markers it is always challenging to decide whether to implement chromosomal microarray analysis (CMA) or not. It is unclear whether CMA should be used in the fetuses with isolated USG soft markers, and there is still a lack of extensive sample research. Material/Methods We enrolled 1521 cases in our research and divided them into 3 groups as follows: pregnant women with isolated AMA (group 1, n=633), pregnant women whose fetuses had isolated USG soft markers (group 2, n=750), and pregnant women with AMA whose fetuses had isolated USG soft markers (group 3, n=138). All pregnant women underwent prenatal ultrasound and amniocentesis, and fetal cells in the amniotic fluid were used for genetic analysis of CMA. All participants signed a written informed consent prior to CMA. Results Abnormal findings were detected by CMA in 330 (21.70%) fetuses, including 37 (2.43%) clinically significant copy number variations (CNVs), 52 (3.42%) benign or likely benign CNVs, and 240 (15.78%) variants of unknown significance. The frequency of clinically significant CNVs in group 1 and group 2 were significantly lower than that in group 3 (2.37% and 2.0% vs 5.07%, P<0.01). More than a half (59.46%, 22/37) of the pregnant women decided to continue their pregnancy despite having a fetus diagnosed with clinically significant CNV. Conclusions CMA can increase the diagnostic yield of fetal chromosomal abnormality for pregnant women with isolated AMA or/and their fetuses had isolated USG soft markers.
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Affiliation(s)
- Zhu-Ming Hu
- Center of Reproductive Medicine and Prenatal Diagnosis, The First Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Lei-Lei Li
- Center of Reproductive Medicine and Prenatal Diagnosis, The First Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Han Zhang
- Center of Reproductive Medicine and Prenatal Diagnosis, The First Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Hong-Guo Zhang
- Center of Reproductive Medicine and Prenatal Diagnosis, The First Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Rui-Zhi Liu
- Center of Reproductive Medicine and Prenatal Diagnosis, The First Hospital of Jilin University, Changchun, Jilin, China (mainland)
| | - Yang Yu
- Center of Reproductive Medicine and Prenatal Diagnosis, The First Hospital of Jilin University, Changchun, Jilin, China (mainland)
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8
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Chromosomal abnormality, laboratory techniques, tools and databases in molecular Cytogenetics. Mol Biol Rep 2020; 47:9055-9073. [DOI: 10.1007/s11033-020-05895-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/03/2020] [Indexed: 11/30/2022]
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9
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Wu X, An G, Xie X, Su L, Cai M, Chen X, Li Y, Lin N, He D, Wang M, Huang H, Xu L. Chromosomal microarray analysis for pregnancies with or without ultrasound abnormalities in women of advanced maternal age. J Clin Lab Anal 2020; 34:e23117. [PMID: 31762079 PMCID: PMC7171339 DOI: 10.1002/jcla.23117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/15/2019] [Accepted: 10/26/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Chromosomal microarray analysis (CMA) has been suggested to be routinely conducted for fetuses with ultrasound abnormalities (UA), especially with ultrasound structural anomalies (USA). Whether to routinely offer CMA to women of advanced maternal age (AMA) without UA when undergoing invasive prenatal testing is inconclusive. OBJECTIVE This study aimed to evaluate the efficiency of CMA in detecting clinically significant chromosomal abnormalities in fetuses, with or without UA, of women with AMA. METHODS Data from singleton pregnancies referred for prenatal CMA due to AMA, with or without UA were obtained. The enrolled cases were divided into AMA group (group A) and AMA accompanied by UA group (group B). Single nucleotide polymorphism (SNP) array technology and conventional karyotyping were performed simultaneously. RESULTS A total of 703 cases were enrolled and divided into group A (N = 437) and group B (N = 266). Clinically significant abnormalities were detected by CMA in 52 cases (7.4%, 52/703; the value in group A was significantly lower than that in group B (3.9% vs 13.2%, P < .05); no statistic difference was observed with respect to submicroscopic variants of clinical significance between the two groups (0.9% vs 2.6%, P > .05). CONCLUSIONS Chromosomal microarray analysis should be available to all women with AMA undergoing invasive prenatal testing, regardless of ultrasound findings.
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Affiliation(s)
- Xiaoqing Wu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Gang An
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Xiaorui Xie
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Linjuan Su
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Meiying Cai
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Xuemei Chen
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Ying Li
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Na Lin
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Deqin He
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Meiying Wang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Hailong Huang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Liangpu Xu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
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Méjécase C, Malka S, Guan Z, Slater A, Arno G, Moosajee M. Practical guide to genetic screening for inherited eye diseases. Ther Adv Ophthalmol 2020; 12:2515841420954592. [PMID: 33015543 PMCID: PMC7513416 DOI: 10.1177/2515841420954592] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/29/2020] [Indexed: 12/16/2022] Open
Abstract
Genetic eye diseases affect around one in 1000 people worldwide for which the molecular aetiology remains unknown in the majority. The identification of disease-causing gene variant(s) allows a better understanding of the disorder and its inheritance. There is now an approved retinal gene therapy for autosomal recessive RPE65-retinopathy, and numerous ocular gene/mutation-targeted clinical trials underway, highlighting the importance of establishing a genetic diagnosis so patients can fully access the latest research developments and treatment options. In this review, we will provide a practical guide to managing patients with these conditions including an overview of inheritance patterns, required pre- and post-test genetic counselling, different types of cytogenetic and genetic testing available, with a focus on next generation sequencing using targeted gene panels, whole exome and genome sequencing. We will expand on the pros and cons of each modality, variant interpretation and options for family planning for the patient and their family. With the advent of genomic medicine, genetic screening will soon become mainstream within all ophthalmology subspecialties for prevention of disease and provision of precision therapeutics.
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Affiliation(s)
- Cécile Méjécase
- Institute of Ophthalmology, University College
London, London, UK
| | - Samantha Malka
- Institute of Ophthalmology, University College
London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
| | - Zeyu Guan
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
| | - Amy Slater
- Royal Brompton and Harefield NHS Foundation
Trust, London, UK
| | - Gavin Arno
- Institute of Ophthalmology, University College
London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
- Great Ormond Street Hospital for Children NHS
Trust, London, UK
| | - Mariya Moosajee
- Professor, Institute of Ophthalmology,
University College London, 11-43 Bath Street, London EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
- Great Ormond Street Hospital for Children NHS
Trust, London, UK
- The Francis Crick Institute, London, UK
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11
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Chai H, DiAdamo A, Grommisch B, Xu F, Zhou Q, Wen J, Mahoney M, Bale A, McGrath J, Spencer-Manzon M, Li P, Zhang H. A Retrospective Analysis of 10-Year Data Assessed the Diagnostic Accuracy and Efficacy of Cytogenomic Abnormalities in Current Prenatal and Pediatric Settings. Front Genet 2019; 10:1162. [PMID: 31850057 PMCID: PMC6902283 DOI: 10.3389/fgene.2019.01162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/23/2019] [Indexed: 01/01/2023] Open
Abstract
Background: Array comparative genomic hybridization (aCGH), karyotyping and fluorescence in situ hybridization (FISH) analyses have been used in a clinical cytogenetic laboratory. A systematic analysis on diagnostic findings of cytogenomic abnormalities in current prenatal and pediatric settings provides approaches for future improvement. Methods: A retrospective analysis was performed on abnormal findings by aCGH, karyotyping, and FISH from 3,608 prenatal cases and 4,509 pediatric cases during 2008–2017. The diagnostic accuracy was evaluated by comparing the abnormality detection rate (ADR) and the relative frequency (RF) of different types of cytogenomic abnormalities between prenatal and pediatric cases. A linear regression correlation between known prevalence and ADR of genomic disorders was used to extrapolate the prevalence of other genomic disorders. The diagnostic efficacy was estimated as percentage of detected abnormal cases by expected abnormal cases from served population. Results: The composite ADR for numerical chromosome abnormalities, structural chromosome abnormalities, recurrent genomic disorders, and sporadic pathogenic copy number variants (pCNVs) in prenatal cases were 13.03%, 1.77%, 1.69%, and 0.9%, respectively, and were 5.13%, 2.84%, 7.08%, and 2.69% in pediatric cases, respectively. The chromosomal abnormalities detected in prenatal cases (14.80%) were significantly higher than that of pediatric cases (7.97%) (p < 0.05), while the pCNVs detected in prenatal cases (2.59%) were significantly lower than that of pediatric cases (9.77%) (p < 0.05). The prevalence of recurrent genomic disorders and total pCNVs was estimated to be 1/396 and 1/291, respectively. Approximately, 29% and 35% of cytogenomic abnormalities expected from the population served were detected in current prenatal and pediatric diagnostic practice, respectively. Conclusion: For chromosomal abnormalities, effective detection of Down syndrome (DS) and Turner syndrome (TS) and under detection of sex chromosome numerical abnormalities in both prenatal and pediatric cases were noted. For pCNVs, under detection of pCNVs in prenatal cases and effective detection of DiGeorge syndrome (DGS) and variable efficacy in detecting other pCNVs in pediatric cases were noted. Extend aCGH analysis to more prenatal cases with fetal ultrasonographic anomalies, enhanced non-invasive prenatal (NIPT) testing screening for syndromic genomic disorders, and better clinical indications for pCNVs are approaches that could improve diagnostic yield of cytogenomic abnormalities.
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Affiliation(s)
- Hongyan Chai
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Autumn DiAdamo
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Brittany Grommisch
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Fang Xu
- Prevention Genetics, Marshfield, WI, United States
| | - Qinghua Zhou
- The First Affiliated Hospital, Biomedical Translational Research Institute, Jinan University, Guangzhou, China
| | - Jiadi Wen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Maurice Mahoney
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - James McGrath
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Michele Spencer-Manzon
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Hui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
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12
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Liang S, Yang J, Wu H, Teng X, Duan T. Effects of chromosome 9 inversion on IVF/ICSI: A 7-year retrospective cohort study. Mol Genet Genomic Med 2019; 7:e856. [PMID: 31353845 PMCID: PMC6732300 DOI: 10.1002/mgg3.856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/20/2019] [Accepted: 07/01/2019] [Indexed: 11/16/2022] Open
Abstract
Background This study focused on the outcomes of patients with pericentric inversion of chromosome 9 who underwent IVF/ICSI and fresh day 2 or day 3 embryo transfer and the possible impacts of carrier gender and chromosome karyotype on pregnancy outcomes. Methods A total of 214 couples (107 couples with one pericentric inversion of chromosome 9 in one partner [Group 1], 107 couples with normal karyotypes [Group 2]) underwent their first IVF/ICSI treatment and were included in this study. Oocyte number, normal fertilization rates, abnormal fertilization rates, cleavage rates, embryo utilization rates, fresh embryo transfer rates, clinical pregnancy rates (CPR), implantation rates, miscarriage rates, and live birth rates per embryo transfer (LBR) were compared between groups. Results Group 1 did not show any disadvantage when compared with Group 2. The CPR and LBR were similar between all groups. The female carrier group had a higher normal fertilization rate and higher utilization rate than the male carrier group. Cases with inv(9)(p12;q13) had a lower utilization rate but a higher implantation rate than the remaining karyotypes. Conclusion In the first IVF or ICSI cycle, couples with one pericentric inversion of chromosome 9 in one partner had satisfactory outcomes. The subgroup analysis showed a tendency of better prognosis for the female carrier and inv(9)(p12;q13) type. This is a retrospective cohort study during 7 years period. In the first IVF or ICSI cycle, couples with one pericentric inversion of chromosome 9 in one partner had satisfactory outcomes. The subgroup analysis showed a tendency of better prognosis for the female carrier and inv(9)(p12;q13) type.
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Affiliation(s)
- Shanshan Liang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jianzhi Yang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Haixia Wu
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoming Teng
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tao Duan
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
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13
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Additive Diagnostic Yield of Homozygosity Regions Identified During Chromosomal microarray Testing in Children with Developmental Delay, Dysmorphic Features or Congenital Anomalies. Biochem Genet 2019; 58:74-101. [PMID: 31273557 DOI: 10.1007/s10528-019-09931-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
Abstract
Chromosomal microarray (CMA) has emerged as a robust tool for identifying microdeletions and microduplications, termed copy number variants (CNVs). Nevertheless, data regarding its utility in different patient populations with developmental delay (DD), dysmorphic features (DF) and congenital anomalies (CA), is a matter of dense debate. Although regions of homozygosity (ROH) are not diagnostic of a specific condition, they may have pathogenic implications. Certain CNVs and ROH have ethnically specific occurrences and frequencies. We aimed to determine whether CMA testing offers additional diagnostic information over classical cytogenetics for identifying genomic imbalances in a pediatric cohort with idiopathic DD, DF, or CA. One hundred sixty-nine patients were offered cytogenetics and CMA simultaneously for etiological diagnosis of DD (n = 67), DF (n = 52) and CA (n = 50). CMA could identify additional, clinically significant anomalies as compared with cytogenetics. CMA detected 61 CNVs [21 (34.4%) pathogenic CNVs, 37 (60.7%) variants of uncertain clinical significance and 3 (4.9%) benign CNVs] in 44 patients. CMA identified one or more ROH in 116/169 (68.6%) patients. When considering pathogenic CNVs and aneuploidies as positive findings, 9/169 (5.3%) received a genetic diagnosis from cytogenetics, while 25/169 (14.8%) could have a genetic diagnosis from CMA. The identification of ROH was clinically significant in two cases (2/169), thereby, adding 1.2% to the diagnostic yield of CMA (16% vs. 5.3%, p < 0.001). CMA uncovers additional genetic diagnoses over cytogenetics, thereby, offering a much higher diagnostic yield. Our findings convincingly demonstrate the additive diagnostic value of clinically significant ROH identified during CMA testing, highlighting the need for careful clinical interpretation of these ROH.
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14
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Currall BB, Antolik CW, Collins RL, Talkowski ME. Next Generation Sequencing of Prenatal Structural Chromosomal Rearrangements Using Large-Insert Libraries. Methods Mol Biol 2019; 1885:251-265. [PMID: 30506203 DOI: 10.1007/978-1-4939-8889-1_17] [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] [Indexed: 06/09/2023]
Abstract
Precise tests for genomic structural variation (SV) are essential for accurate diagnosis of prenatal genome abnormalities. The two most ubiquitous traditional methods for prenatal SV assessment, karyotyping and chromosomal microarrays, do not provide sufficient resolution for some clinically actionable SVs. Standard whole-genome sequencing (WGS) overcomes shortcomings of traditional techniques by providing base-pair resolution of the entire accessible genome. However, while sequencing costs have continued to decline in recent years, conventional WGS costs remain high for most routine clinical applications. Here, we describe a specialized WGS technique using large inserts (liWGS; also known as "jumping libraries") to resolve large (>5000-10,000 nucleotides) SVs at kilobase-resolution in prenatal samples, and at a fraction of the cost of standard WGS. We explicate the protocols for generating liWGS libraries and supplement with an overview for processing and analyzing liWGS data.
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Affiliation(s)
- Benjamin B Currall
- Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Harvard Medical School, Cambridge, MA, USA
| | - Caroline W Antolik
- Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Harvard Medical School, Cambridge, MA, USA
| | - Ryan L Collins
- Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Harvard Medical School, Cambridge, MA, USA
| | - Michael E Talkowski
- Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute, Harvard Medical School, Cambridge, MA, USA.
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15
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Leeming W, Barahona A. Synthesis, convergence, and differences in the entangled histories of cytogenetics in medicine: A comparative study of Canada and Mexico. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2018; 71:8-16. [PMID: 30224294 DOI: 10.1016/j.shpsc.2018.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/18/2017] [Accepted: 08/19/2018] [Indexed: 06/08/2023]
Abstract
Most historians of science and medicine agree that medical interest in genetics intensified after 1930, and interest in the relationship of radiation damage and genetics continued and expanded after World War II. Moreover, they maintain that the synthesis and convergence of human genetics and cytological techniques in European centers resulted in their dissemination to centers in the United States, resulting in a new field of expertise focused on medicine and clinical research, known as cytogenetics. In this article, we broaden the scope of the inquiry by showing how the early histories of cytogenetics in Canada and Mexico unfolded against strikingly different backgrounds in clinical research and the delivery of health care. We thus argue that the field of cytogenetics did not emerge in a straightforward manner and develop in the same way in all countries. The article provides a brief background to the history of human cytogenetics, and then outlines key developments related to the early adoption of cytogenetics in Canada and Mexico. Conclusions are then drawn using comparisons of the different ways in which local determinants affected adoption. We then propose directions for future study focused on the ways in which circuits of practices, collaborative research, and transfers of knowledge have shaped how cytogenetics has come to be organised in medicine around the world.
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Affiliation(s)
- William Leeming
- Faculty of Liberal Arts & Sciences and School of Interdisciplinary Studies, OCAD University, Canada
| | - Ana Barahona
- Department of Evolutionary Biology, School of Sciences, National Autonomous University of Mexico, UNAM, Mexico.
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16
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Wang J, Chen L, Zhou C, Wang L, Xie H, Xiao Y, Zhu H, Hu T, Zhang Z, Zhu Q, Liu Z, Liu S, Wang H, Xu M, Ren Z, Yu F, Cram DS, Liu H. Prospective chromosome analysis of 3429 amniocentesis samples in China using copy number variation sequencing. Am J Obstet Gynecol 2018; 219:287.e1-287.e18. [PMID: 29852155 DOI: 10.1016/j.ajog.2018.05.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 04/25/2018] [Accepted: 05/22/2018] [Indexed: 11/15/2022]
Abstract
BACKGROUND Next-generation sequencing is emerging as a viable alternative to chromosome microarray analysis for the diagnosis of chromosome disease syndromes. One next-generation sequencing methodology, copy number variation sequencing, has been shown to deliver high reliability, accuracy, and reproducibility for detection of fetal copy number variations in prenatal samples. However, its clinical utility as a first-tier diagnostic method has yet to be demonstrated in a large cohort of pregnant women referred for fetal chromosome testing. OBJECTIVE We sought to evaluate copy number variation sequencing as a first-tier diagnostic method for detection of fetal chromosome anomalies in a general population of pregnant women with high-risk prenatal indications. STUDY DESIGN This was a prospective analysis of 3429 pregnant women referred for amniocentesis and fetal chromosome testing for different risk indications, including advanced maternal age, high-risk maternal serum screening, and positivity for an ultrasound soft marker. Amniocentesis was performed by standard procedures. Amniocyte DNA was analyzed by copy number variation sequencing with a chromosome resolution of 0.1 Mb. Fetal chromosome anomalies including whole chromosome aneuploidy and segmental imbalances were independently confirmed by gold standard cytogenetic and molecular methods and their pathogenicity determined following guidelines of the American College of Medical Genetics for sequence variants. RESULTS Clear interpretable copy number variation sequencing results were obtained for all 3429 amniocentesis samples. Copy number variation sequencing identified 3293 samples (96%) with a normal molecular karyotype and 136 samples (4%) with an altered molecular karyotype. A total of 146 fetal chromosome anomalies were detected, comprising 46 whole chromosome aneuploidies (pathogenic), 29 submicroscopic microdeletions/microduplications with known or suspected associations with chromosome disease syndromes (pathogenic), 22 other microdeletions/microduplications (likely pathogenic), and 49 variants of uncertain significance. Overall, the cumulative frequency of pathogenic/likely pathogenic and variants of uncertain significance chromosome anomalies in the patient cohort was 2.83% and 1.43%, respectively. In the 3 high-risk advanced maternal age, high-risk maternal serum screening, and ultrasound soft marker groups, the most common whole chromosome aneuploidy detected was trisomy 21, followed by sex chromosome aneuploidies, trisomy 18, and trisomy 13. Across all clinical indications, there was a similar incidence of submicroscopic copy number variations, with approximately equal proportions of pathogenic/likely pathogenic and variants of uncertain significance copy number variations. If karyotyping had been used as an alternate cytogenetics detection method, copy number variation sequencing would have returned a 1% higher yield of pathogenic or likely pathogenic copy number variations. CONCLUSION In a large prospective clinical study, copy number variation sequencing delivered high reliability and accuracy for identifying clinically significant fetal anomalies in prenatal samples. Based on key performance criteria, copy number variation sequencing appears to be a well-suited methodology for first-tier diagnosis of pregnant women in the general population at risk of having a suspected fetal chromosome abnormality.
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Affiliation(s)
- Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Lin Chen
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Cong Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Hanbing Xie
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yuanyuan Xiao
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Hongmei Zhu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Ting Hu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Zhu Zhang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Qian Zhu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Zhiying Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Shanlin Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - He Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Mengnan Xu
- Berry Genomics Corporation, Beijing, China
| | - Zhilin Ren
- Berry Genomics Corporation, Beijing, China
| | - Fuli Yu
- Berry Genomics Corporation, Beijing, China; Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Hongqian Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University and the Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China.
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Chen M, Fu XY, Luo YQ, Qian YQ, Pan L, Wang LY, Dong MY. Detection of fetal duplication 16p11.2q12.1 by next-generation sequencing of maternal plasma and invasive diagnosis. J Matern Fetal Neonatal Med 2017; 32:38-45. [PMID: 28882078 DOI: 10.1080/14767058.2017.1369947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVE The objective of study is to report the feasibility of non-invasive prenatal screening (NIPS) combined with invasive detection by chromosomal analysis in identifying fetal duplication, providing clinical performance of NIPS on copy number variations (CNVs) detection. MATERIAL AND METHODS NIPS was offered to a 35-year-old pregnant woman. Amniocentesis was performed to confirm the positive screening result. Fetal sample was detected by karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA). Parental karyotyping was also conducted. RESULTS NIPS result was positive for chromosome 16, indicating an extra copy of chromosome 16. FISH and chromosomal karyotyping revealed that the fetus had a marker chromosome derived from chromosome 16. CMA further demonstrated an approximately 19-Mb duplication in chromosome 16. The final fetal karyotype was 47,XY,+mar. ish der (16)(D16Z3+).arr 16p11.2q12.1 (30 624 186-49 696 337 × 3). Ultrasound scan and MRI showed some structure malformations. CONCLUSIONS A protocol for CNVs detection by combining a series of genetic methods was presented in this study and a novel marker duplication 16p11.2q12.1 was reported. With the ability to identify subchromosomal deletions and duplications in fetus, NIPS could reduce the possibility of invasive diagnosis. The followed confirmation test for positive sample is necessary and ensures the accuracy of the diagnosis.
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Affiliation(s)
- Min Chen
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Xiao-Ying Fu
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Yu-Qin Luo
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Ye-Qing Qian
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Ling Pan
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Li-Ya Wang
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
| | - Min-Yue Dong
- a Women's Hospital, School of Medicine, Zhejiang University , Hangzhou , China.,b Key Laboratory of Reproductive Genetics , Zhejiang University, Ministry of Education , Hangzhou , China.,c Key Laboratory of Women's Reproductive Health of Zhejiang Province , Hangzhou , China
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Trevisan P, Rosa RFM, Koshiyama DB, Zen TD, Paskulin GA, Zen PRG. Congenital heart disease and chromossomopathies detected by the karyotype. ACTA ACUST UNITED AC 2016; 32:262-71. [PMID: 25119760 PMCID: PMC4183026 DOI: 10.1590/0103-0582201432213213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 10/17/2013] [Indexed: 02/06/2023]
Abstract
OBJECTIVE: To review the relationship between congenital heart defects and chromosomal
abnormalities detected by the karyotype. DATA SOURCES: Scientific articles were searched in MEDLINE database, using the descriptors
"karyotype" OR "chromosomal" OR "chromosome" AND "heart defects, congenital". The
research was limited to articles published in English from 1980 on. DATA SYNTHESIS: Congenital heart disease is characterized by an etiologically heterogeneous and
not well understood group of lesions. Several researchers have evaluated the
presence of chromosomal abnormalities detected by the karyotype in patients with
congenital heart disease. However, most of the articles were retrospective studies
developed in Europe and only some of the studied patients had a karyotype exam. In
this review, only one study was conducted in Latin America, in Brazil. It is known
that chromosomal abnormalities are frequent, being present in about one in every
ten patients with congenital heart disease. Among the karyotype alterations in
these patients, the most important is the trisomy 21 (Down syndrome). These
patients often have associated extra-cardiac malformations, with a higher risk of
morbidity and mortality, which makes heart surgery even more risky. CONCLUSIONS: Despite all the progress made in recent decades in the field of cytogenetic, the
karyotype remains an essential tool in order to evaluate patients with congenital
heart disease. The detailed dysmorphological physical examination is of great
importance to indicate the need of a karyotype.
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Dutta UR. The history of human cytogenetics in India-A review. Gene 2016; 589:112-7. [PMID: 26850130 DOI: 10.1016/j.gene.2016.01.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 01/13/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
Abstract
It is 60years since the discovery of the correct number of chromosomes in 1956; the field of cytogenetics had evolved. The late evolution of this field with respect to other fields is primarily due to the underdevelopment of lenses and imaging techniques. With the advent of the new technologies, especially automation and evolution of advanced compound microscopes, cytogenetics drastically leaped further to greater heights. This review describes the historic events that had led to the development of human cytogenetics with a special attention about the history of cytogenetics in India, its present status, and future. Apparently, this review provides a brief account into the insights of the early laboratory establishments, funding, and the German collaborations. The details of the Indian cytogeneticists establishing their labs, promoting the field, and offering the chromosomal diagnostic services are described. The detailed study of chromosomes helps in increasing the knowledge of the chromosome structure and function. The delineation of the chromosomal rearrangements using cytogenetics and molecular cytogenetic techniques pays way in identifying the molecular mechanisms involved in the chromosomal rearrangement. Although molecular cytogenetics is greatly developing, the conventional cytogenetics still remains the gold standard in the diagnosis of various numerical chromosomal aberrations and a few structural aberrations. The history of cytogenetics and its importance even in the era of molecular cytogenetics are discussed.
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Affiliation(s)
- Usha R Dutta
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, Tuljaguda Complex, 4-1-714, Hyderabad 500 001, Andhra-Pradesh, India.
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Liu S, Song L, Cram DS, Xiong L, Wang K, Wu R, Liu J, Deng K, Jia B, Zhong M, Yang F. Traditional karyotyping vs copy number variation sequencing for detection of chromosomal abnormalities associated with spontaneous miscarriage. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 46:472-477. [PMID: 25767059 DOI: 10.1002/uog.14849] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 02/19/2015] [Accepted: 03/10/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVES To compare the performance of traditional G-banding karyotyping with that of copy number variation sequencing (CNV-Seq) for detection of chromosomal abnormalities associated with miscarriage. METHODS Products of conception (POC) were collected from spontaneous miscarriages. Chromosomal abnormalities were detected using high-resolution G-banding karyotyping and CNV sequencing. Quantitative fluorescent polymerase chain reaction analysis of maternal and POC DNA for short tandem repeat (STR) markers was used to both monitor maternal cell contamination and confirm the chromosomal status and sex of the miscarriage tissue. RESULTS A total of 64 samples of POC, comprising 16 with an abnormal and 48 with a normal karyotype, were selected and coded for analysis by CNV-Seq. CNV-Seq results were concordant for 14 (87.5%) of the 16 gross chromosomal abnormalities identified by karyotyping, including 11 autosomal trisomies and three sex chromosomal aneuploidies (45,X). Of the two discordant results, a 69,XXX polyploidy was missed by CNV-Seq, although supporting STR marker analysis confirmed the triploidy. In contrast, CNV-Seq identified a sample with 45,X karyotype as a 45,X/46,XY mosaic. In the remaining 48 samples of POC with a normal karyotype, CNV-Seq detected a 2.58-Mb 22q deletion associated with DiGeorge syndrome and nine different smaller CNVs of no apparent clinical significance. CONCLUSIONS CNV-Seq used in parallel with STR profiling is a reliable and accurate alternative to karyotyping for identifying chromosome copy number abnormalities associated with spontaneous miscarriage.
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Affiliation(s)
- S Liu
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - L Song
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - D S Cram
- Berry Genomics, Chaoyang District, Beijing, China
| | - L Xiong
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - K Wang
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - R Wu
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - J Liu
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Guangzhou, Guangdong, China
| | - K Deng
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - B Jia
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - M Zhong
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
| | - F Yang
- Southern Medical University, Nanfang Hospital, Department of Obstetrics and Gynecology, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Guangzhou, Guangdong, China
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Lay-Son RG, León PL. [Current perspectives on genome-based diagnostic tests in Pediatrics]. REVISTA CHILENA DE PEDIATRIA 2015. [PMID: 26223391 DOI: 10.1016/j.rchipe.2015.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Etiological diagnosis is essential in the clinical management of individual patients. Some children with complex medical conditions are subjected to numerous testing, known as "diagnostic odyssey", which often gives no conclusive results. In recent years, a revolution in genomic medicine is underway with the use of technologies that promise to increase the ability to make a diagnosis and reduce the time involved. The main advantages and limitations of genomic diagnosis, as opposed to usual methodologies are reviewed with an emphasis on Pediatrics.
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Affiliation(s)
- R Guillermo Lay-Son
- Centro de Genética y Genómica, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, San Ramón, Santiago, Chile.
| | - P Luis León
- Centro de Genética y Genómica, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
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22
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Chromosomal microarrays testing in children with developmental disabilities and congenital anomalies. JORNAL DE PEDIATRIA (VERSÃO EM PORTUGUÊS) 2015. [DOI: 10.1016/j.jpedp.2014.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Lay-Son G, Espinoza K, Vial C, Rivera JC, Guzmán ML, Repetto GM. Chromosomal microarrays testing in children with developmental disabilities and congenital anomalies. J Pediatr (Rio J) 2015; 91:189-95. [PMID: 25458876 DOI: 10.1016/j.jped.2014.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/28/2014] [Accepted: 07/09/2014] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Clinical use of microarray-based techniques for the analysis of many developmental disorders has emerged during the last decade. Thus, chromosomal microarray has been positioned as a first-tier test. This study reports the first experience in a Chilean cohort. METHODS Chilean patients with developmental disabilities and congenital anomalies were studied with a high-density microarray (CytoScan™ HD Array, Affymetrix, Inc., Santa Clara, CA, USA). Patients had previous cytogenetic studies with either a normal result or a poorly characterized anomaly. RESULTS This study tested 40 patients selected by two or more criteria, including: major congenital anomalies, facial dysmorphism, developmental delay, and intellectual disability. Copy number variants (CNVs) were found in 72.5% of patients, while a pathogenic CNV was found in 25% of patients and a CNV of uncertain clinical significance was found in 2.5% of patients. CONCLUSION Chromosomal microarray analysis is a useful and powerful tool for diagnosis of developmental diseases, by allowing accurate diagnosis, improving the diagnosis rate, and discovering new etiologies. The higher cost is a limitation for widespread use in this setting.
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Affiliation(s)
- Guillermo Lay-Son
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, Santiago, Chile.
| | - Karena Espinoza
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Cecilia Vial
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Juan C Rivera
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - María L Guzmán
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, Santiago, Chile
| | - Gabriela M Repetto
- Center for Human Genetics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, Santiago, Chile
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Liang D, Peng Y, Lv W, Deng L, Zhang Y, Li H, Yang P, Zhang J, Song Z, Xu G, Cram DS, Wu L. Copy Number Variation Sequencing for Comprehensive Diagnosis of Chromosome Disease Syndromes. J Mol Diagn 2014; 16:519-526. [DOI: 10.1016/j.jmoldx.2014.05.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/18/2014] [Accepted: 05/16/2014] [Indexed: 10/25/2022] Open
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Sidonets IV, Meshkov AN. GENETICS FOR DIAGNOSTICS IN PREVENTIVE MEDICINE. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2014. [DOI: 10.15829/1728-8800-2014-4-75-80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The sequencing of first human genome followed by rapid development of technologies, that led to significant lowering of costs for genetic analyze and its fast performing, made possible a broad invention of genetic diagnostics methods into clinical practice. Contemporary methods of molecular genetics make possible to research on inherited factors on chromosome level with molecular cytogenetics methods, and on the level of local mutations with the use or polymeraze chain reaction, microchips and sequencing. Temps of the next generation sequencing methods provide the opportunity to predict soon inclusion in practice of the personalized medical analysis of large genetic data massive, that can be used for the disease outcome prediction, estimation of its course, and for the prescription and correction of pharmacotherapy. In this review, different (including novel) approaches to genetic diagnostics are explored for the rare as common diseases, their benefits and restrictions.
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Affiliation(s)
- I. V. Sidonets
- FSBI State Scientific-Research Centre for Preventive Medicine of the Ministry of Health, Moscow
| | - A. N. Meshkov
- FSBI State Scientific-Research Centre for Preventive Medicine of the Ministry of Health, Moscow
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Zaslav AL, Marino MA, Jurgens CY, Mercado T. Cytogenetic evaluation: a primer for pediatric nurse practitioners. J Pediatr Health Care 2013; 27:426-33. [PMID: 22595375 DOI: 10.1016/j.pedhc.2012.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 04/05/2012] [Accepted: 04/14/2012] [Indexed: 11/25/2022]
Abstract
Patients with genetic disorders require specific types of cytogenetic testing for accurate diagnosis and prognosis followed by prompt treatment. This primer will serve as a guide for pediatric nurse practitioners on the use of various cytogenetic testing for the diagnosis of genetic disorders. Knowledge of the latest cytogenetic technologies will facilitate diagnosis and counseling related to genetic abnormalities such as inherited disorders, mental retardation, developmental delay, and autism. This reference will enable pediatric nurse practitioners to help identify patients with various inherited genetic disorders and provide subsequent monitoring and treatment.
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Trevisan P, Zen TD, Rosa RFM, da Silva JN, Koshiyama DB, Paskulin GA, Zen PRG. Chromosomal abnormalities in patients with congenital heart disease. Arq Bras Cardiol 2013; 101:495-501. [PMID: 24145389 PMCID: PMC4106807 DOI: 10.5935/abc.20130204] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 06/24/2013] [Indexed: 01/24/2023] Open
Abstract
Background Chromosomal abnormalities (CAs) are an important cause of congenital heart disease
(CHD). Objective Determine the frequency, types and clinical characteristics of CAs identified in a
sample of prospective and consecutive patients with CHD. Method Our sample consisted of patients with CHD evaluated during their first
hospitalization in a cardiac intensive care unit of a pediatric referral hospital
in Southern Brazil. All patients underwent clinical and cytogenetic assessment
through high-resolution karyotype. CHDs were classified according to Botto et al.
Chi-square, Fisher exact test and odds ratio were used in the statistical analysis
(p < 0.05). Results Our sample consisted of 298 patients, 53.4% males, with age ranging from 1 day to
14 years. CAs were observed in 50 patients (16.8%), and 49 of them were syndromic.
As for the CAs, 44 (88%) were numeric (40 patients with +21, 2 with +18, 1 with
triple X and one with 45,X) and 6 (12%) structural [2 patients with der(14,21),
+21, 1 with i(21q), 1 with dup(17p), 1 with del(6p) and 1 with add(18p)]. The
group of CHDs more often associated with CAs was atrioventricular septal defect. Conclusions CAs detected through karyotyping are frequent in patients with CHD. Thus,
professionals, especially those working in Pediatric Cardiology Services, must be
aware of the implications that performing the karyotype can bring to the
diagnosis, treatment and prognosis and for genetic counseling of patients and
families.
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Affiliation(s)
- Patrícia Trevisan
- Programa de Pós-Graduação em Patologia da Universidade Federal e
Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS - Brazil
| | - Tatiana Diehl Zen
- Programa de Pós-Graduação em Patologia da Universidade Federal e
Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS - Brazil
| | - Rafael Fabiano Machado Rosa
- Programa de Pós-Graduação em Patologia da Universidade Federal e
Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS - Brazil
- Genética Clínica, Hospital Materno-Infantil Presidente Vargas (HMIPV),
Porto Alegre, RS - Brazil
- Genética Clínica, Universidade Federal de Ciências da Saúde de Porto
Alegre (UFCSPA) e Complexo Hospitalar Santa Casa de Porto Alegre (CHSCPA), Porto Alegre,
RS - Brazil
| | - Juliane Nascimento da Silva
- Programa de Pós-Graduação em Patologia da Universidade Federal e
Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS - Brazil
| | - Dayane Bohn Koshiyama
- Programa de Pós-Graduação em Patologia da Universidade Federal e
Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS - Brazil
| | - Giorgio Adriano Paskulin
- Programa de Pós-Graduação em Patologia da Universidade Federal e
Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS - Brazil
- Genética Clínica, Universidade Federal de Ciências da Saúde de Porto
Alegre (UFCSPA) e Complexo Hospitalar Santa Casa de Porto Alegre (CHSCPA), Porto Alegre,
RS - Brazil
| | - Paulo Ricardo Gazzola Zen
- Programa de Pós-Graduação em Patologia da Universidade Federal e
Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS - Brazil
- Genética Clínica, Universidade Federal de Ciências da Saúde de Porto
Alegre (UFCSPA) e Complexo Hospitalar Santa Casa de Porto Alegre (CHSCPA), Porto Alegre,
RS - Brazil
- Mailing Address: Paulo Ricardo Gazzola Zen, Rua Sarmento Leite, 245/403,
Centro. Postal Code 90050 170, Porto Alegre, RS - Brasil. E-mail:
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Wei Y, Xu F, Li P. Technology-Driven and Evidence-Based Genomic Analysis for Integrated Pediatric and Prenatal Genetics Evaluation. J Genet Genomics 2013; 40:1-14. [DOI: 10.1016/j.jgg.2012.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 12/14/2012] [Indexed: 10/27/2022]
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Lim LS, Hu M, Huang MC, Cheong WC, Gan ATL, Looi XL, Leong SM, Koay ESC, Li MH. Microsieve lab-chip device for rapid enumeration and fluorescence in situ hybridization of circulating tumor cells. LAB ON A CHIP 2012; 12:4388-96. [PMID: 22930096 DOI: 10.1039/c2lc20750h] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Herein we present a lab-chip device for highly efficient and rapid detection of circulating tumor cells (CTCs) from whole blood samples. The device utilizes a microfabricated silicon microsieve with a densely packed pore array (10(5) pores per device) to rapidly separate tumor cells from whole blood, utilizing the size and deformability differences between the CTCs and normal blood cells. The whole process, including tumor cell capture, antibody staining, removal of unwanted contaminants and immunofluorescence imaging, was performed directly on the microsieve within an integrated microfluidic unit, interconnected to a peristaltic pump for fluid regulation and a fluorescence microscope for cell counting. The latter was equipped with a dedicated digital image processing program which was developed to automatically categorize the captured cells based on the immunofluorescence images. A high recovery rate of >80% was achieved with defined numbers of MCF-7 and HepG2 cancer cells spiked into human whole blood and filtered at a rapid flow rate of 1 mL min(-1). The device was further validated with blood drawn from various cancer patients (8 samples). The whole process, from sample input to result, was completed in 1.5 h. In addition, we have also successfully demonstrated on-microsieve fluorescence in situ hybridization for single cell molecular analysis. This simple method has great potential to supplant existing complex CTC detection schemes for cancer metastasis analysis.
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Affiliation(s)
- Li Shi Lim
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore138669
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Helsmoortel C, Vandeweyer G, Kooy RF. On the spot: very local chromosomal rearrangements. F1000 BIOLOGY REPORTS 2012. [PMID: 23189093 PMCID: PMC3505860 DOI: 10.3410/b4-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the last decade, the detection of chromosomal abnormalities has shifted from conventional karyotyping under a light microscope to molecular detection using microarrays. The latter technology identified copy number variation as a major source of variation in the human genome; moreover, copy number variants were found responsible for 10-20% of cases of intellectual disability. Recent technological advances in microarray technology have also enabled the detection of very small local chromosomal rearrangements, sometimes affecting the function of only a single gene. Here, we illustrate how high resolution microarray analysis has led to increased insights into the contribution of specific genes in disease.
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Affiliation(s)
- Céline Helsmoortel
- Cognitive Genetics, Department of Medical Genetics, University of Antwerp Prins Boudewijnlaan 43, B-2650 Edegem, Belgium
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Gunn SR, Robetorye RS, Mohammed MS. Comparative Genomic Hybridization Arrays in Clinical Pathology. Mol Diagn Ther 2012; 11:73-7. [PMID: 17397242 DOI: 10.1007/bf03256225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Array-based comparative genomic hybridization (array CGH) genome scanning is a powerful method for the global detection of gains and losses of genetic material in both congenital and neoplastic disorders. When used as a clinical diagnostic test, array CGH combines the whole genome perspective of traditional G-banded cytogenetics with the targeted identification of cryptic chromosomal abnormalities characteristic of fluorescence in situ hybridization (FISH). However, the presence of structural variants in the human genome can complicate analysis of patient samples, and array CGH does not provide morphologic information about chromosome structure, balanced translocations, or the actual chromosomal location of segmental duplications. Identification of such anomalies has significant diagnostic and prognostic implications for the patient. We therefore propose that array CGH should be used as a guide to the presence of genomic structural rearrangements in germline and tumor genomes that can then be further characterized by FISH or G-banding, depending on the clinical scenario. In this article, we share some of our experiences with diagnostic array CGH and discuss recent progress and challenges involved with the integration of array CGH into clinical laboratory medicine.
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Affiliation(s)
- Shelly R Gunn
- Department of Pathology, University of Texas Health Science Center, San Antonio, Texas 78229-3900, USA.
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Kurz CM, Moosdijk SVD, Thielecke H, Velten T. Towards a cellular multi-parameter analysis platform: fluorescence in situ hybridization (FISH) on microhole-array chips. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2012; 2011:8408-11. [PMID: 22256298 DOI: 10.1109/iembs.2011.6092074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Highly-sensitive analysis systems based on cellular multi-parameter are needed in the diagnostics. Therefore we improved our previously developed chip platform for another additional analysis method, the fluorescence in situ hybridization. Fluorescence in situ hybridization (FISH) is a technique used in the diagnostics to determine the localization and the presence or absence of specific DNA sequence. To improve this labor- and cost-intensive method, we reduced the assay consumption by a factor of 5 compared to the standard protocol. Microhole chips were used for making the cells well addressable. The chips were fabricated by semiconductor technology on the basis of a Silicon wafer with a thin deposited silicon nitride layer (Si(3)N(4)). Human retina pigment epithelia (ARPE-19) cells were arrayed on 5-μm holes of a 35 × 35 microhole-array by a gently negative differential pressure of around 5 mbar. After 3 hours of incubation the cells were attached to the chip and the FISH protocol was applied to the positioned cells. A LabView software was developed to simplify the analysis. The software automatically counts the number of dots (positive labeled chromosome regions) as well as the distance between adjacent dots. Our developed platform reduces the assay consumption and the labor time. Furthermore, during the 3 hours of incubation non-invasive or minimal-invasive methods like Raman- and impedance-spectroscopy can be applied.
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Affiliation(s)
- Christian M Kurz
- Department Biomedical Microsystems, Fraunhofer Insitute for Biomedical Engineering
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Advanced microtechnologies for detection of chromosome abnormalities by fluorescent in situ hybridization. Biomed Microdevices 2012; 14:453-60. [DOI: 10.1007/s10544-011-9622-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Schaaf CP, Wiszniewska J, Beaudet AL. Copy number and SNP arrays in clinical diagnostics. Annu Rev Genomics Hum Genet 2011; 12:25-51. [PMID: 21801020 DOI: 10.1146/annurev-genom-092010-110715] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The ability of chromosome microarray analysis (CMA) to detect submicroscopic genetic abnormalities has revolutionized the clinical diagnostic approach to individuals with intellectual disability, neurobehavioral phenotypes, and congenital malformations. The recognition of the underlying copy number variant (CNV) in respective individuals may allow not only for better counseling and anticipatory guidance but also for more specific therapeutic interventions in some cases. The use of CMA technology in prenatal diagnosis is emerging and promises higher sensitivity for several highly penetrant, clinically severe microdeletion and microduplication syndromes. Genetic counseling complements the diagnostic testing with CMA, given the presence of CNVs of uncertain clinical significance, incomplete penetrance, and variable expressivity in some cases. While oligonucleotide arrays with high-density exonic coverage remain the gold standard for the detection of CNVs, single-nucleotide polymorphism (SNP) arrays allow for detection of consanguinity and most cases of uniparental disomy and provide a higher sensitivity to detect low-level mosaic aneuploidies.
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Affiliation(s)
- Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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de Klein A, Tibboel D. Genetics. Semin Pediatr Surg 2010; 19:234-9. [PMID: 20610197 DOI: 10.1053/j.sempedsurg.2010.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
For many years karyotyping has been a successful tool to identify chromosome aberrations in congenital malformations. It has proven to be a highly reliable technique for identifying numerical chromosome changes and structural chromosomal rearrangements, such as deletions, duplications, translocations, or inversions. However, karyotyping has limited resolution of 5-10 Mb and depends on the availability of metaphases. In the last decade, we have experienced the implementation of molecular cytogenetic techniques, resulting in the identification of chromosomal aberrations smaller than 5 Mbp. Because DNA is used as starting material also analysis of paraffin or frozen biopsies is possible. Several genes and loci have been identified, and careful genotype phenotype correlation has lead to the recognition of new syndromes. A further characterization of these new genes and loci involved in the etiology of congenital anomalies will lead to a better understanding of the underlying developmental pathways.
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Affiliation(s)
- Annelies de Klein
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands.
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Riley RS, Williams D, Ross M, Zhao S, Chesney A, Clark BD, Ben-Ezra JM. Bone marrow aspirate and biopsy: a pathologist's perspective. II. interpretation of the bone marrow aspirate and biopsy. J Clin Lab Anal 2010; 23:259-307. [PMID: 19774631 DOI: 10.1002/jcla.20305] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bone marrow examination has become increasingly important for the diagnosis and treatment of hematologic and other illnesses. Morphologic evaluation of the bone marrow aspirate and biopsy has recently been supplemented by increasingly sophisticated ancillary assays, including immunocytochemistry, cytogenetic analysis, flow cytometry, and molecular assays. With our rapidly expanding knowledge of the clinical and biologic diversity of leukemia and other hematologic neoplasms, and an increasing variety of therapeutic options, the bone marrow examination has became more critical for therapeutic monitoring and planning optimal therapy. Sensitive molecular techniques, in vitro drug sensitivity testing, and a number of other special assays are available to provide valuable data to assist these endeavors. Fortunately, improvements in bone marrow aspirate and needle technology has made the procurement of adequate specimens more reliable and efficient, while the use of conscious sedation has improved patient comfort. The procurement of bone marrow specimens was reviewed in the first part of this series. This paper specifically addresses the diagnostic interpretation of bone marrow specimens and the use of ancillary techniques.
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Affiliation(s)
- Roger S Riley
- Medical College of Virginia Hospitals of Virginia Commonwealth University, Richmond, Virginia, USA.
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Tefferi A, Sirhan S, Sun Y, Lasho T, Finke CM, Weisberger J, Bale S, Compton J, LeDuc CA, Pardanani A, Thorland EC, Shevchenko Y, Grodman M, Chung WK. Oligonucleotide array CGH studies in myeloproliferative neoplasms: Comparison with JAK2V617F mutational status and conventional chromosome analysis. Leuk Res 2009; 33:662-4. [DOI: 10.1016/j.leukres.2008.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 09/08/2008] [Accepted: 09/09/2008] [Indexed: 11/27/2022]
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Sieben VJ, Debes-Marun CS, Pilarski LM, Backhouse CJ. An integrated microfluidic chip for chromosome enumeration using fluorescence in situ hybridization. LAB ON A CHIP 2008; 8:2151-6. [PMID: 19023479 DOI: 10.1039/b812443d] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Fluorescence in situ hybridization (FISH) is a powerful technique for probing the genetic content of individual cells at the chromosomal scale. Conventional FISH techniques provide a sensitive diagnostic tool for the detection of chromosomal alterations on a cell-by-cell basis; however, the cost-per-test in terms of reagent and highly qualified labour has prevented its wide-spread utilization in clinical settings. Here, we address the inefficient use of labour with the first integrated and automated on-chip FISH implementation, one that requires only minutes of setup time from the technician. Our microfluidic chip has lowered the reagent use by 20-fold, decreased the labour time by 10-fold, and substantially reduced the amount of support equipment needed. We believe this cost-effective platform will make sensitive FISH techniques more accessible for routine clinical usage.
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Affiliation(s)
- Vincent J Sieben
- Department of Electrical and Computer Engineering, 2nd Floor ECERF, University of Alberta, Edmonton, CanadaT6G 2V4
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41
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Shao L, Shaw CA, Lu XY, Sahoo T, Bacino CA, Lalani SR, Stankiewicz P, Yatsenko SA, Li Y, Neill S, Pursley AN, Chinault AC, Patel A, Beaudet AL, Lupski JR, Cheung SW. Identification of chromosome abnormalities in subtelomeric regions by microarray analysis: a study of 5,380 cases. Am J Med Genet A 2008; 146A:2242-51. [PMID: 18663743 DOI: 10.1002/ajmg.a.32399] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Subtelomeric imbalances are a significant cause of congenital disorders. Screening for these abnormalities has traditionally utilized GTG-banding analysis, fluorescence in situ hybridization (FISH) assays, and multiplex ligation-dependent probe amplification. Microarray-based comparative genomic hybridization (array-CGH) is a relatively new technology that can identify microscopic and submicroscopic chromosomal imbalances. It has been proposed that an array with extended coverage at subtelomeric regions could characterize subtelomeric aberrations more efficiently in a single experiment. The targeted arrays for chromosome microarray analysis (CMA), developed by Baylor College of Medicine, have on average 12 BAC/PAC clones covering 10 Mb of each of the 41 subtelomeric regions. We screened 5,380 consecutive clinical patients using CMA. The most common reasons for referral included developmental delay (DD), and/or mental retardation (MR), dysmorphic features (DF), multiple congenital anomalies (MCA), seizure disorders (SD), and autistic, or other behavioral abnormalities. We found pathogenic rearrangements at subtelomeric regions in 236 patients (4.4%). Among these patients, 103 had a deletion, 58 had a duplication, 44 had an unbalanced translocation, and 31 had a complex rearrangement. The detection rates varied among patients with a normal karyotype analysis (2.98%), with an abnormal karyotype analysis (43.4%), and with an unavailable or no karyotype analysis (3.16%). Six patients out of 278 with a prior normal subtelomere-FISH analysis showed an abnormality including an interstitial deletion, two terminal deletions, two interstitial duplications, and a terminal duplication. In conclusion, genomic imbalances at subtelomeric regions contribute significantly to congenital disorders. Targeted array-CGH with extended coverage (up to 10 Mb) of subtelomeric regions will enhance the detection of subtelomeric imbalances, especially for submicroscopic imbalances.
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Affiliation(s)
- Lina Shao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Xiang B, Li A, Valentin D, Nowak NJ, Zhao H, Li P. Analytical and clinical validity of whole-genome oligonucleotide array comparative genomic hybridization for pediatric patients with mental retardation and developmental delay. Am J Med Genet A 2008; 146A:1942-54. [DOI: 10.1002/ajmg.a.32411] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Whole Genome Analysis by Array-Based Comparative Genomic Hybridization in Patients with Congenital Malformations. Balkan J Med Genet 2008. [DOI: 10.2478/v10034-008-0015-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Nassiri M, Gugic D, Olczyk J, Ramos S, Vincek V. Preservation of skin DNA for oligonucleotide array CGH studies: a feasibility study. Arch Dermatol Res 2007; 299:353-7. [PMID: 17665208 PMCID: PMC1950585 DOI: 10.1007/s00403-007-0773-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 06/27/2007] [Accepted: 07/10/2007] [Indexed: 10/25/2022]
Abstract
Array-based comparative genomic hybridization (a-CGH) is a promising tool for clinical genomic studies. However, pre-analytical sample preparation methods have not been fully evaluated for this purpose. Parallel sections of normal male human skin biopsy samples were collected and immediately immersed in saline, formalin and a molecular fixative for 8, 12 and 24 h. Genomic DNA was isolated from the samples and subjected to amplification and labeling. Labeled samples were then co-hybridized with normal reference female DNA to Agilent oligonucleotide-based a-CGH 44k slides. Pre-analytic parameters such as DNA yield, quality of genomic DNA and labeling efficacy were evaluated. Also microarray analytical variables, including the feature signal intensity, data distribution dynamic range, signal to noise ratio and background intensity levels were assessed for data quality. DNA yield and quality of genomic DNA--as evaluated by spectrophotometry and gel electrophoresis--were similar for fresh and molecular fixative-exposed samples. In addition, labeling efficacy of dye incorporation was not drastically different. There was no difference between fresh and molecular fixative material comparing scan parameters and stem plot analysis of a-CGH result. Formalin-fixed samples, on the other hand, showed various errors such as oversaturation, non-uniformity in replicates, and decreased signal to noise ratio. Overall, the a-CGH result of formalin samples was not interpretable. DNA extracted from formalin-fixed tissue samples is not suitable for oligonucleotide-based a-CGH studies. On the other hand, the molecular fixative preserves tissue DNA similar to its fresh state with no discernable analytical differences.
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Affiliation(s)
- Mehdi Nassiri
- Department of Pathology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA.
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Veltman JA, de Vries BBA. Whole-genome array comparative genome hybridization: the preferred diagnostic choice in postnatal clinical cytogenetics. J Mol Diagn 2007; 9:277. [PMID: 17384222 PMCID: PMC1885997 DOI: 10.2353/jmoldx.2007.060187] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Stanczak CM, Chen Z, Zhang YH, Nelson SF, McCabe ERB. Deletion mapping in Xp21 for patients with complex glycerol kinase deficiency using SNP mapping arrays. Hum Mutat 2007; 28:235-42. [PMID: 17089405 DOI: 10.1002/humu.20424] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Infantile or complex glycerol kinase deficiency (cGKD) is a contiguous gene deletion syndrome caused by a loss of GK (MIM# 300474), along with its neighboring genes, Duchenne muscular dystrophy (DMD; MIM# 300377) and/or Nuclear Receptor Subfamily 0, Group B, Member 1 (NR0B1; MIM# 300473). Patients with cGKD present with glyceroluria and hyperglycerolemia in association with DMD and/or adrenal hypoplasia congenita (AHC). The purpose of these investigations was to determine whether the Affymetrix GeneChip Mapping Array (SNP chip) could be utilized to detect and map breakpoints in patients with cGKD. Genomic DNAs from several primary lymphoblastoid cell lines from patients with cGKD were analyzed on the Affymetrix platform. The Affymetrix SNP chip is a high-density oligonucleotide array that allows a standardized, parallel interrogation of thousands of SNPs across the entire genome (except for the Y chromosome). Analysis of the array features' hybridization intensities enabled clear delineation of the patient deletions with a high degree of confidence. Many of these patient deletions had been mapped by PCR and their breakpoints confirmed by sequencing. This study demonstrates the utility of the Affymetrix Mapping GeneChips for molecular cytogenetic analysis, beyond the SNP genotyping for which the arrays were initially designed. With one out of 160 live births (approximately 25,000 U.S. neonates annually) reported to have cytogenetic disorders, we envision a significant need for such a standardized platform to carry out rapid, high-throughput, genomic analyses for molecular cytogenetics applications.
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Affiliation(s)
- Christopher M Stanczak
- Department of Human Genetics, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California 90095-1752, USA
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Tyson C, Harvard C, Locker R, Friedman JM, Langlois S, Lewis MES, Van Allen M, Somerville M, Arbour L, Clarke L, McGilivray B, Yong SL, Siegel-Bartel J, Rajcan-Separovic E. Submicroscopic deletions and duplications in individuals with intellectual disability detected by array-CGH. Am J Med Genet A 2006; 139:173-85. [PMID: 16283669 DOI: 10.1002/ajmg.a.31015] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intellectual disability (ID) affects about 3% of the population (IQ < 70), and in about 40% of moderate (IQ 35-49) to severe ID (IQ < 34), and 70% of cases of mild ID (IQ 50-70), the etiology of the disease remains unknown. It has long been suspected that chromosomal gains and losses undetectable by routine cytogenetic analysis (i.e., less than 5-10 Mb in size) are implicated in ID of unknown etiology. Array CGH has recently been used to perform a genome-wide screen for submicroscopic gains and losses in individuals with a normal karyotype but with features suggestive of a chromosome abnormality. In two recent studies, the technique has demonstrated a approximately 15% detection rate for de novo copy number changes of individual clones or groups of clones. Here, we describe a study of 22 individuals with mild to moderate ID and nonsyndromic pattern of dysmorphic features suspicious of an underlying chromosome abnormality, using the 3 Mb and 1 Mb commercial arrays (Spectral Genomics). Deletions and duplications of 16 clones, previously described to show copy number variability in normal individuals [Iafrate et al., 2004; Lapierre et al., 2004; Schoumans et al., 2004; Vermeesch et al., 2005] were seen in 21/22 subjects and were considered polymorphisms. In addition, three subjects showed submicroscopic deletions and duplications not previously reported as normal variants. Two of these submicroscopic changes were of de novo origin (microdeletions at 7q36.3 and a microduplication at 11q12.3-13.1) and one was of unknown origin as parental testing of origin could not be performed (microduplication of Xp22.3). The clinical description of the three subjects with submicroscopic chromosomal changes at 7q36.3, 11q12.3-13.1, Xp22.3 is provided.
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Affiliation(s)
- C Tyson
- Department of Pathology, University of British Columbia, Vancouver, Canada
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Lothaire P, de Azambuja E, Dequanter D, Lalami Y, Sotiriou C, Andry G, Castro G, Awada A. Molecular markers of head and neck squamous cell carcinoma: promising signs in need of prospective evaluation. Head Neck 2006; 28:256-69. [PMID: 16284973 DOI: 10.1002/hed.20326] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The aim of this article is to review recent developments in the biological understanding of head and neck squamous cell carcinomas. METHODS AND RESULTS We describe the markers according to their function and their prognostic or predictive roles. Some associations can be found between molecular markers and invasiveness, aggressiveness, degree of differentiation, and tumor stage, but only a few clinical studies have shown an impact on prognosis. In addition, despite an increasing number of articles relating to this topic, the small number of patients included in the studies reported reduces the clinical implications of these results. Few studies applied a more comprehensive molecular analysis approach, such as DNA microarrays or differential expression profiling by polymerase chain reaction, to identify a combination of markers that could be more informative than a single molecular marker. CONCLUSION Some progress has been made with respect to molecular markers and head and neck cancers. Translational and prospective, hypothesis-driven research must proceed with sufficient rigor to facilitate the clinical applicability of such results.
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Bayani J, Pandita A, Squire JA. Molecular cytogenetic analysis in the study of brain tumors: findings and applications. Neurosurg Focus 2005; 19:E1. [PMID: 16398459 DOI: 10.3171/foc.2005.19.5.2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Classic cytogenetics has evolved from black and white to technicolor images of chromosomes as a result of advances in fluorescence in situ hybridization (FISH) techniques, and is now called molecular cytogenetics. Improvements in the quality and diversity of probes suitable for FISH, coupled with advances in computerized image analysis, now permit the genome or tissue of interest to be analyzed in detail on a glass slide. It is evident that the growing list of options for cytogenetic analysis has improved the understanding of chromosomal changes in disease initiation, progression, and response to treatment. The contributions of classic and molecular cytogenetics to the study of brain tumors have provided scientists and clinicians alike with new avenues for investigation. In this review the authors summarize the contributions of molecular cytogenetics to the study of brain tumors, encompassing the findings of classic cytogenetics, interphase- and metaphase-based FISH studies, spectral karyotyping, and metaphase- and array-based comparative genomic hybridization. In addition, this review also details the role of molecular cytogenetic techniques in other aspects of understanding the pathogenesis of brain tumors, including xenograft, cancer stem cell, and telomere length studies.
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Affiliation(s)
- Jane Bayani
- Department of Applied Molecular Oncology, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Ontario, Canada.
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