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Yin Z, Qu S, Huang C, Chen F, Li J, Chen S, Ye J, Yang Y, Zheng Y, Zhang X, Yang X, Xie L, Wei J, Wei F, Guo J, Huang J. Development of a genomic DNA reference material panel for thalassemia genetic testing. Int J Lab Hematol 2020; 42:510-517. [PMID: 32297451 DOI: 10.1111/ijlh.13213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/20/2020] [Accepted: 03/27/2020] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Thalassemia is one of the most common autosomal recessive inherited diseases worldwide, and it is also highly prevalent and variable in southern China. Various types of genetic testing technologies have been developed for diagnosis and screening of thalassemia. Characterized genomic DNA reference materials (RMs) are necessary for assay development, validation, proficiency testing, and quality assurance. However, there are no publicly available RMs for thalassemia genetic testing as yet. METHODS To address the need for the publicly available DNA RMs for thalassemia genetic testing, the National Institutes for Food and Drug Control and the China National GeneBank established 32 new cell lines with three wild-type genotypes and 29 distinct genotypes of thalassemia which account for approximately 90% thalassemia carriers in China. The genomic DNA of 32 cell lines was characterized by four clinical genetic testing laboratories using different genetic testing methods and technology platforms. RESULTS The genotyping results are concordant among four laboratories. In addition, the results of stability test demonstrated that the genotypes of these DNA samples are not influenced by preanalytical conditions such as long-term exposure to high-temperature (37°C) environment and repeated freeze-thawing. CONCLUSION We developed the first national panel of 32 genomic DNA RMs which are renewable and publicly available for the quality assurance of various genetic testing methods and will facilitate research and development in thalassemia genetic testing.
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Affiliation(s)
- Zhenzhen Yin
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Shoufang Qu
- Division of In Vitro Diagnostics for Non-Infectious Diseases, National Institutes for Food and Drug Control, Beijing, China
| | - Chuanfeng Huang
- Division of In Vitro Diagnostics for Non-Infectious Diseases, National Institutes for Food and Drug Control, Beijing, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,MGI-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Jianbiao Li
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Shiping Chen
- BGI-Shenzhen, Shenzhen, China.,Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Jingyu Ye
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Ying Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yu Zheng
- BGI-Shenzhen, Shenzhen, China.,Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Xi Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xuexi Yang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Longxu Xie
- Hybribio Limited, Sino-Singapore Guangzhou Knowledge City, Guangzhou, China
| | - Jitao Wei
- Research and Development Department, Yaneng BIOscience (Shenzhen) Co. Ltd, Shenzhen, China
| | - Fengxiang Wei
- The Genetics Laboratory, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Jian Guo
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jie Huang
- Division of In Vitro Diagnostics for Non-Infectious Diseases, National Institutes for Food and Drug Control, Beijing, China
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Kalman LV, Datta V, Williams M, Zook JM, Salit ML, Han JY. Development and Characterization of Reference Materials for Genetic Testing: Focus on Public Partnerships. Ann Lab Med 2017; 36:513-20. [PMID: 27578503 PMCID: PMC5011103 DOI: 10.3343/alm.2016.36.6.513] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/08/2016] [Accepted: 07/18/2016] [Indexed: 01/29/2023] Open
Abstract
Characterized reference materials (RMs) are needed for clinical laboratory test development and validation, quality control procedures, and proficiency testing to assure their quality. In this article, we review the development and characterization of RMs for clinical molecular genetic tests. We describe various types of RMs and how to access and utilize them, especially focusing on the Genetic Testing Reference Materials Coordination Program (Get-RM) and the Genome in a Bottle (GIAB) Consortium. This review also reinforces the need for collaborative efforts in the clinical genetic testing community to develop additional RMs.
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Affiliation(s)
- Lisa V Kalman
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Vivekananda Datta
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Gaithersburg, MD, USA
| | - Mickey Williams
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Gaithersburg, MD, USA
| | - Justin M Zook
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Marc L Salit
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jin Yeong Han
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea.
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Sernheim ÅS, Hemmingsson H, Witt Engerström I, Liedberg G. Activities that girls and women with Rett syndrome liked or did not like to do. Scand J Occup Ther 2016; 25:267-277. [DOI: 10.1080/11038128.2016.1250812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Åsa-Sara Sernheim
- Department of Social and Welfare Studies, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
- Swedish National Rett Center, Östersund, Sweden
| | - Helena Hemmingsson
- Department of Social and Welfare Studies, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | | | - Gunilla Liedberg
- Department of Social and Welfare Studies, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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Simmons DBD, Benskin JP, Cosgrove JR, Duncker BP, Ekman DR, Martyniuk CJ, Sherry JP. Omics for aquatic ecotoxicology: control of extraneous variability to enhance the analysis of environmental effects. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2015; 34:1693-1704. [PMID: 25827364 DOI: 10.1002/etc.3002] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/09/2015] [Accepted: 03/30/2015] [Indexed: 06/04/2023]
Abstract
There are multiple sources of biological and technical variation in a typical ecotoxicology study that may not be revealed by traditional endpoints but that become apparent in an omics dataset. As researchers increasingly apply omics technologies to environmental studies, it will be necessary to understand and control the main source(s) of variability to facilitate meaningful interpretation of such data. For instance, can variability in omics studies be addressed by changing the approach to study design and data analysis? Are there statistical methods that can be employed to correctly interpret omics data and make use of unattributed, inherent variability? The present study presents a review of experimental design and statistical considerations applicable to the use of omics methods in systems toxicology studies. In addition to highlighting potential sources that contribute to experimental variability, this review suggests strategies with which to reduce and/or control such variability so as to improve reliability, reproducibility, and ultimately the application of omics data for systems toxicology.
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Affiliation(s)
- Denina B D Simmons
- Emerging Methods Section, Aquatic Contaminants Research Division, Water Science & Technology Directorate, Environment Canada, Ontario, Canada
| | | | | | | | - Drew R Ekman
- Ecosystems Research Division, National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency, Athens, Georgia, USA
| | - Christopher J Martyniuk
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, University of Florida, Gainesville, Florida, USA
| | - James P Sherry
- Emerging Methods Section, Aquatic Contaminants Research Division, Water Science & Technology Directorate, Environment Canada, Ontario, Canada
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