1
|
Kang JU. Medical Implementation of Microarray Technology. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2020. [DOI: 10.15324/kjcls.2020.52.4.310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Ji Un Kang
- Department of Biomedical Laboratory Science, Korea Nazarene University, Cheonan, Korea
| |
Collapse
|
2
|
Low-pass whole-genome sequencing in clinical cytogenetics: a validated approach. Genet Med 2016; 18:940-8. [PMID: 26820068 DOI: 10.1038/gim.2015.199] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/19/2015] [Indexed: 01/12/2023] Open
Abstract
PURPOSE Chromosomal microarray analysis is the gold standard for copy-number variant (CNV) detection in prenatal and postnatal diagnosis. We aimed to determine whether next-generation sequencing (NGS) technology could be an alternative method for CNV detection in routine clinical application. METHODS Genome-wide CNV analysis (>50 kb) was performed on a multicenter group of 570 patients using a low-coverage whole-genome sequencing pipeline. These samples were referred for chromosomal analysis; CNVs (i.e., pathogenic CNVs, pCNVs) were classified according to the American College of Medical Genetics and Genomics guidelines. RESULTS Overall, a total of 198 abortuses, 37 stillbirths, 149 prenatal, and 186 postnatal samples were tested. Our approach yielded results in 549 samples (96.3%). In addition to 119 subjects with aneuploidies, 103 pCNVs (74 losses and 29 gains) were identified in 82 samples, giving diagnostic yields of 53.2% (95% confidence interval: 45.8, 60.5), 14.7% (5.0, 31.1), 28.5% (21.1, 36.6), and 30.1% (23.6, 37.3) in each group, respectively. Mosaicism was observed at a level as low as 25%. CONCLUSIONS Patients with chromosomal diseases or microdeletion/microduplication syndromes were diagnosed using a high-resolution genome-wide method. Our study revealed the potential of NGS to facilitate genetic diagnoses that were not evident in the prenatal and postnatal groups.Genet Med 18 9, 940-948.
Collapse
|
3
|
Noninvasive detection of fetal subchromosomal abnormalities by semiconductor sequencing of maternal plasma DNA. Proc Natl Acad Sci U S A 2015; 112:14670-5. [PMID: 26554006 DOI: 10.1073/pnas.1518151112] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Noninvasive prenatal testing (NIPT) using sequencing of fetal cell-free DNA from maternal plasma has enabled accurate prenatal diagnosis of aneuploidy and become increasingly accepted in clinical practice. We investigated whether NIPT using semiconductor sequencing platform (SSP) could reliably detect subchromosomal deletions/duplications in women carrying high-risk fetuses. We first showed that increasing concentration of abnormal DNA and sequencing depth improved detection. Subsequently, we analyzed plasma from 1,456 pregnant women to develop a method for estimating fetal DNA concentration based on the size distribution of DNA fragments. Finally, we collected plasma from 1,476 pregnant women with fetal structural abnormalities detected on ultrasound who also underwent an invasive diagnostic procedure. We used SSP of maternal plasma DNA to detect subchromosomal abnormalities and validated our results with array comparative genomic hybridization (aCGH). With 3.5 million reads, SSP detected 56 of 78 (71.8%) subchromosomal abnormalities detected by aCGH. With increased sequencing depth up to 10 million reads and restriction of the size of abnormalities to more than 1 Mb, sensitivity improved to 69 of 73 (94.5%). Of 55 false-positive samples, 35 were caused by deletions/duplications present in maternal DNA, indicating the necessity of a validation test to exclude maternal karyotype abnormalities. This study shows that detection of fetal subchromosomal abnormalities is a viable extension of NIPT based on SSP. Although we focused on the application of cell-free DNA sequencing for NIPT, we believe that this method has broader applications for genetic diagnosis, such as analysis of circulating tumor DNA for detection of cancer.
Collapse
|
4
|
Hayeems RZ, Hoang N, Chenier S, Stavropoulos DJ, Pu S, Weksberg R, Shuman C. Capturing the clinical utility of genomic testing: medical recommendations following pediatric microarray. Eur J Hum Genet 2014; 23:1135-41. [PMID: 25491637 PMCID: PMC4538218 DOI: 10.1038/ejhg.2014.260] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 10/01/2014] [Accepted: 10/21/2014] [Indexed: 01/08/2023] Open
Abstract
Interpretation of pediatric chromosome microarray (CMA) results presents diagnostic and medical management challenges. Understanding management practices triggered by CMA will inform clinical utility and resource planning. Using a retrospective cohort design, we extracted clinical and management-related data from the records of 752 children with congenital anomalies and/or developmental delay who underwent CMA in an academic pediatric genetics clinic (2009–2011). Frequency distributions and relative rates (RR) of post-CMA medical recommendations in children with reportable and benign CMA results were calculated. Medical recommendations were provided for 79.6% of children with reportable results and 62.0% of children with benign results. Overall, recommendations included specialist consultation (40.8%), imaging (32.5%), laboratory investigations (17.2%), surveillance (4.6%), and family investigations (4.9%). Clinically significant variants and variants of uncertain clinical significance were associated with higher and slightly higher rates of management recommendations, respectively, compared with benign/no variants (RR=1.34; 95% CI (1.22–1.47); RR=1.23; 95% CI (1.09–1.38)). Recommendation rates for clinically significant versus uncertain results depended upon how uncertainty was classified (RRbroad=1.09; 95% CI (0.99–1.2); RRnarrow=1.12; 95% CI (1.02–1.24)). Recommendation rates also varied by the child's age and provider type. In conclusion, medical recommendations follow CMA for the majority of children. Compared with benign CMA results, clinically significant CMA variants are a significant driver of pediatric medical recommendations. Variants of uncertain clinical significance drive recommendations, but to a lesser extent. As a broadening range of specialists will need to respond to CMA results, targeted capacity building is warranted.
Collapse
Affiliation(s)
- Robin Z Hayeems
- 1] Program in Child Health Evaluative, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada [2] Institute of Health Policy Management and Evaluation, The University of Toronto, Toronto, ON, Canada
| | - Ny Hoang
- 1] Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada [2] Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sebastien Chenier
- Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - Dimitri J Stavropoulos
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children and The University of Toronto, Toronto, ON, Canada
| | - Shuye Pu
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Rosanna Weksberg
- 1] Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada [2] Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada [3] Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada [4] Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Cheryl Shuman
- 1] Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada [2] Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada [3] Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
5
|
Günel T, Hosseini MK, Gümüşoğlu E, Zeybek G, Dölekçap İ, Kalelioğlu İ, Benian A, Ermiş H, Aydınlı K. Current approaches on non-invasive prenatal diagnosis: Prenatal genomics, transcriptomics, personalized fetal diagnosis. Turk J Obstet Gynecol 2014; 11:233-241. [PMID: 28913027 PMCID: PMC5558368 DOI: 10.4274/tjod.26817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 07/26/2014] [Indexed: 12/27/2022] Open
Abstract
Recent developments in molecular genetics improved our knowledge on fetal genome and physiology. Novel scientific innovations in prenatal diagnosis have accelerated in the last decade changing our vision immensely. Data obtained from fetal genomic studies brought new insights to fetal medicine and by the advances in fetal DNA and RNA sequencing technology novel treatment strategies has evolved. Non-invasive prenatal diagnosis found ground in genetics and the results are widely studied in scientific arena. When Lo and colleges proved fetal genetic material can be extracted from maternal plasma and fetal DNA can be isolated from maternal serum, the gate to many exciting discoveries was open. Microarray technology and advances in sequencing helped fetal diagnosis as well as other areas of medicine. Today it is a very crucial prerequisite for physicians practicing prenatal diagnosis to have a profound knowledge in genetics. Prevailing practical use and application of fetal genomic tests in maternal and fetal medicine mandates obstetricians to update their knowledge in genetics. The purpose of this review is to assist physicians to understand and update their knowledge in fetal genetic testing from maternal blood, individualized prenatal counseling and advancements on the subject by sharing our experiences as İstanbul University Fetal Nucleic Acid Research Group.
Collapse
Affiliation(s)
- Tuba Günel
- İstanbul University, Faculty of Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Mohammad Kazem Hosseini
- İstanbul University, Faculty of Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Ece Gümüşoğlu
- İstanbul University, Faculty of Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Görkem Zeybek
- Çanakkale Provincial State Hospital, Clinic of General Obstetrics and Gynecology, Çanakkale, Turkey
| | - İsmail Dölekçap
- İstanbul University, Faculty of Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - İbrahim Kalelioğlu
- İstanbul University İstanbul Faculty of Medicine, Department of Gynecology, İstanbul, Turkey
| | - Ali Benian
- İstanbul University Cerrahpaşa Faculty of Medicine, Department of Gynecology, İstanbul, Turkey
| | - Hayri Ermiş
- İstanbul University İstanbul Faculty of Medicine, Department of Gynecology, İstanbul, Turkey
| | | |
Collapse
|
6
|
Yin A, Lu J, Liu C, Guo L, Wu J, Mai M, Zhong Y, Zhang X. A prenatal missed diagnosed case of submicroscopic chromosomal abnormalities by karyotyping: the clinical utility of array-based CGH in prenatal diagnostics. Mol Cytogenet 2014; 7:26. [PMID: 24735551 PMCID: PMC4005634 DOI: 10.1186/1755-8166-7-26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/26/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Array-based comparative genomic hybridization possesses a number of significant advantages over conventional cytogenetic and other molecular cytogenetic techniques, providing a sensitive and comprehensive detection platform for unexpected imbalances in the genome wide. CASE PRESENTATION The newborn proband, demonstrated with craniofacial dysmorphism and multiple malformations, was born to a family with spontaneous abortions. This pregnancy was uneventful, except the prenatal ultrasound examination showed an increased nuchal translucency at 12(+) weeks of gestation. Cytogenetics revealed an apparently normal karyotype, and the couple decided to continue the pregnancy. Array-based CGH analysis was applied to the affected infant, identified a combination of 18p deletion and 7q duplication. Further study indicates that the unbalanced translocation was inherited from a balanced translocation carrier parent. CONCLUSIONS In review of the case, several overlooked points leading to the missed diagnosis should be discussed and certain quality control strategies should be adopted to avoid similar problems in the future. Array-based CGH and karyotyping techniques are complemented by diverse detection spectrum and resolutions, and a combination of these methods could help providing optimal genetic diagnosis. Given that the array-CGH analysis will not introduce additional risk to patients, it is reasonable to recommend those already undergoing invasive testing should take array-based CGH as an adjunct to conventional cytogenetic tests and other molecular cytogenetic analysis.
Collapse
Affiliation(s)
- Aihua Yin
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Jian Lu
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Chang Liu
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Li Guo
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Jing Wu
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Mingqin Mai
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Yanfang Zhong
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Xiaozhuang Zhang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| |
Collapse
|