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Brief Reports Prepared by Students and Graduates of Master of Science in Biobanking. Biopreserv Biobank 2023; 21:98-105. [PMID: 36169634 PMCID: PMC9963501 DOI: 10.1089/bio.2022.0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Du X, Aristizabal-Henao JJ, Garrett TJ, Brochhausen M, Hogan WR, Lemas DJ. A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research. Metabolites 2022; 12:87. [PMID: 35050209 PMCID: PMC8779534 DOI: 10.3390/metabo12010087] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/25/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Clinical metabolomics emerged as a novel approach for biomarker discovery with the translational potential to guide next-generation therapeutics and precision health interventions. However, reproducibility in clinical research employing metabolomics data is challenging. Checklists are a helpful tool for promoting reproducible research. Existing checklists that promote reproducible metabolomics research primarily focused on metadata and may not be sufficient to ensure reproducible metabolomics data processing. This paper provides a checklist including actions that need to be taken by researchers to make computational steps reproducible for clinical metabolomics studies. We developed an eight-item checklist that includes criteria related to reusable data sharing and reproducible computational workflow development. We also provided recommended tools and resources to complete each item, as well as a GitHub project template to guide the process. The checklist is concise and easy to follow. Studies that follow this checklist and use recommended resources may facilitate other researchers to reproduce metabolomics results easily and efficiently.
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Affiliation(s)
- Xinsong Du
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (X.D.); (W.R.H.)
| | | | - Timothy J. Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Mathias Brochhausen
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - William R. Hogan
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (X.D.); (W.R.H.)
| | - Dominick J. Lemas
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (X.D.); (W.R.H.)
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Chaaban H, Markel TA, Canvasser J, Good M. Biobanking for necrotizing enterocolitis: Needs and standards. J Pediatr Surg 2020; 55:1276-1279. [PMID: 31126684 PMCID: PMC6842670 DOI: 10.1016/j.jpedsurg.2019.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/19/2019] [Accepted: 05/04/2019] [Indexed: 01/21/2023]
Abstract
BACKGROUND Necrotizing enterocolitis (NEC) is a devastating gastrointestinal disease that primarily affects premature infants. Despite medical advances, mortality and morbidity from NEC are still unacceptably high. This is partly because of the lack of specific biomarkers and therapies for this disease. Availability of high-quality biological samples and the associated data from premature infants are key to advance our understanding of NEC, and for biomarker discovery and drug development. To that end, the NEC Society Biorepository was established with the goal of promoting studies in human infants through sharing specialized biospecimen and data procurement for NEC research. OBJECTIVE In this review, we will discuss the required infrastructure for biobanks, discuss the importance of informatics management, and emphasize the logistical requirements for sharing specimens. Finally, we will discuss the mechanism for how tissues and material will be shared between the institutions. CONCLUSION We have developed a state-of-the-art biobank for human infants to advance the field of NEC research. With the NEC Society Biorepository, we seek to facilitate and accelerate the basic and translational studies on NEC to provide hope to the infants afflicted with NEC and their families. STUDY TYPE Review article, level V.
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MESH Headings
- Biomarkers/metabolism
- Biomedical Research
- Enterocolitis, Necrotizing/diagnosis
- Enterocolitis, Necrotizing/metabolism
- Enterocolitis, Necrotizing/pathology
- Enterocolitis, Necrotizing/therapy
- Humans
- Infant
- Infant, Newborn
- Infant, Premature
- Infant, Premature, Diseases/diagnosis
- Infant, Premature, Diseases/metabolism
- Infant, Premature, Diseases/pathology
- Infant, Premature, Diseases/therapy
- Informatics
- Reference Standards
- Specimen Handling/ethics
- Specimen Handling/methods
- Specimen Handling/standards
- Tissue Banks/ethics
- Tissue Banks/organization & administration
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Affiliation(s)
- Hala Chaaban
- Department of Pediatrics, Section of Neonatal-Perinatal Medicine, University of Oklahoma, Oklahoma City, OK, USA
| | - Troy A Markel
- Department of Surgery, Section of Pediatric Surgery, The Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Misty Good
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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Luckhaus C, Roosterman D, Juckel G. [Biobanking in Psychiatry]. FORTSCHRITTE DER NEUROLOGIE-PSYCHIATRIE 2020; 88:722-729. [PMID: 32542622 DOI: 10.1055/a-0832-8766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Medical biobanking is concerned with establishing and maintaining large-scale repositories of biological specimens combined with comprehensive archives of clinical and biographical information on donors. This aims for controlled high and consistent quality of specimens for future biomedical research. One major objective is to assemble multiple blood components for various types of biochemical analysis and experimentation including different isolated cell types. With proper cryo-conservation, blood-derived cells can be conserved and revitalized after thawing and employed as in-vitro cell models carrying specific biological traits of donors. Optimizing pre-analytical methods can reduce pre-analytical variance thereby reducing imprecision of analytical data. This is particularly valuable for multivariate analyses of biological systems ("omics") and biomarker research. Introducing biobanking to psychiatry carries the challenge of making diagnostic allocation more compatible with biological entities than is achieved with current diagnostic categories of ICD-10 or DSM-V. Diagnostic or transdiagnostic subgroups can be stratified using biologically anchored clinical criteria. An important ethical issue of biobanking is the need for broad consent by the donors for specimen use in not yet defined future research projects. The organizational, logistic and financial costs of establishing and maintaining a biobank are considerable, but seem well warranted in view of the gainable advances in biomedical research quality, translations and clinical applications.
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Schwarz N, Knutti N, Rose M, Neugebauer S, Geiger J, Jahns R, Klopp N, Illig T, Mathay C, Betsou F, Scherag A, Kiehntopf M. Quality Assessment of the Preanalytical Workflow in Liquid Biobanking: Taurine as a Serum-Specific Quality Indicator for Preanalytical Process Variations. Biopreserv Biobank 2019; 17:458-467. [PMID: 31339743 DOI: 10.1089/bio.2019.0004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The scientific impact of translational biomedical research largely depends on the availability of high-quality biomaterials. However, evidence-based and robust quality indicators (QIs) covering the most relevant preanalytical variations are still lacking. The aim of this study was to identify and validate a QI suitable for assessing time-to-centrifugation (TTC) delays in human liquid biospecimens originating from both healthy and diseased individuals. Serum and plasma samples with varying TTCs were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in a pilot cohort of healthy individuals to identify a suitable QI candidate. Taurine (TAU), as a TTC QI candidate, was validated in healthy individuals and patients with rheumatologic and cardiologic diseases, considering the (1) preanalytical handling temperature, (2) platelet count, and (3) postcentrifugation delay. For discrimination of high TTC (TTC >60 minutes) from low TTC serum specimens, a probability calculation tool was developed (Triple-T-cutoff-model). TTC-dependent changes in healthy individuals were observed for amino acids, particularly TAU. Validation of the TAU levels in an independent cohort of healthy individuals revealed a time-dependent increase in serum, but not in plasma, for a TTC delay of 30-240 minutes. TAU increases were dependent on the handling temperature and platelet count and volume. By contrast, no changes in TAU concentrations were observed for additional postcentrifugation delays. Validation of TAU and the Triple-T-cutoff-model, in rheumatologic/cardiologic patient collectives, allowed the discrimination of samples with TTC ≤60 min/>60 min with estimated AUROC (area under the receiver operating characteristic curve) values of 89% [78%-100%]/86% [71%-100%] and 91% [79%-100%]/84% [68%-100%], respectively. Considering the preanalytical handling temperature and platelet count and volume, TAU and the Triple-T-cutoff-model represent reliable QIs for TTC >60 minutes in serum samples from healthy individuals and selected rheumatologic/cardiologic patients. However, further studies in larger patient collectives with various diseases are needed to assess the robustness and potential of the QIs presented in this article as biobanking quality assurance/quality control tools to support high-quality biomedical research.
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Affiliation(s)
- Nicolle Schwarz
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), Jena University Hospital, Jena, Germany
| | - Nadine Knutti
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), Jena University Hospital, Jena, Germany
| | - Michael Rose
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), Jena University Hospital, Jena, Germany
| | - Sophie Neugebauer
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), Jena University Hospital, Jena, Germany
| | - Jörg Geiger
- Interdisciplinary Bank of Biomaterials and Data Würzburg (ibdw), Würzburg, Germany
| | - Roland Jahns
- Interdisciplinary Bank of Biomaterials and Data Würzburg (ibdw), Würzburg, Germany
| | - Norman Klopp
- Hannover Unified Biobank (HUB), Hannover, Germany
| | - Thomas Illig
- Hannover Unified Biobank (HUB), Hannover, Germany
| | - Conny Mathay
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Fay Betsou
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - André Scherag
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Institute of Medical Statistics, Computer and Data Sciences, Jena University Hospital, Jena, Germany
| | - Michael Kiehntopf
- Institute of Clinical Chemistry and Laboratory Diagnostics and Integrated Biobank Jena (IBBJ), Jena University Hospital, Jena, Germany
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Paskal W, Paskal AM, Dębski T, Gryziak M, Jaworowski J. Aspects of Modern Biobank Activity - Comprehensive Review. Pathol Oncol Res 2018; 24:771-785. [PMID: 29728978 PMCID: PMC6132819 DOI: 10.1007/s12253-018-0418-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 04/27/2018] [Indexed: 12/13/2022]
Abstract
Biobanks play an increasing role in contemporary research projects. These units meet all requirements to regard them as a one of the most innovative and up-to-date in the field of biomedical research. They enable conducting wide-scale research by the professional collection of biological specimens and correlated clinical data. Pathology units may be perceived roots of biobanking. The review aims at describing the concept of biobanks, their model of function and scientific potential. It comprises the division of biobanks, sample preservation methods and IT solutions as well as guidelines and recommendations for management of a vast number of biological samples and clinical data. Therefore, appropriate standard operating procedures and protocols are outlined. Constant individualization of diagnostic process and treatment procedures creates the niche for translational units. Thus, the role of biobanks in personalized medicine was also specified. The exceptionality of biobanks poses some new ethical-legal issues which have various solutions, in each legal system, amongst the world. Finally, distribution and activity of European biobanks are mentioned.
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Affiliation(s)
- Wiktor Paskal
- The Department of Histology and Embryology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, ul. Banacha 1B, 02-097, Warsaw, Poland.
- Plastic Surgery Department, Centre of Postgraduate Medical Education, Warsaw, Poland.
- The Department of Applied Pharmacy, Medical University of Warsaw, Warsaw, Poland.
| | - Adriana M Paskal
- The Department of Histology and Embryology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, ul. Banacha 1B, 02-097, Warsaw, Poland
| | - Tomasz Dębski
- Plastic Surgery Department, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Maciej Gryziak
- The Department of Applied Pharmacy, Medical University of Warsaw, Warsaw, Poland
- Maria Sklodowska-Curie Institute of Oncology, Warsaw, Poland
| | - Janusz Jaworowski
- The Department of Applied Pharmacy, Medical University of Warsaw, Warsaw, Poland
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Abstract
Schizophrenia is a devastating disease that arises on the background of genetic predisposition and environmental risk factors, such as early life stress (ELS). In this study, we show that ELS-induced schizophrenia-like phenotypes in mice correlate with a widespread increase of histone-deacetylase 1 (Hdac1) expression that is linked to altered DNA methylation. Hdac1 overexpression in neurons of the medial prefrontal cortex, but not in the dorsal or ventral hippocampus, mimics schizophrenia-like phenotypes induced by ELS. Systemic administration of an HDAC inhibitor rescues the detrimental effects of ELS when applied after the manifestation of disease phenotypes. In addition to the hippocampus and prefrontal cortex, mice subjected to ELS exhibit increased Hdac1 expression in blood. Moreover, Hdac1 levels are increased in blood samples from patients with schizophrenia who had encountered ELS, compared with patients without ELS experience. Our data suggest that HDAC1 inhibition should be considered as a therapeutic approach to treat schizophrenia.
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Abstract
Mental disorders are among the greatest medical and social challenges facing us. They can occur at all stages of life and are among the most important commonly occurring diseases. In Germany 28 % of the population suffer from a mental disorder every year, while the lifetime risk of suffering from a mental disorder is almost 50 %. Mental disorders cause great suffering for those affected and their social network. Quantitatively speaking, they can be considered to be among those diseases creating the greatest burden for society due to reduced productivity, absence from work and premature retirement. The Federal Ministry of Education and Research is funding a new research network from 2015 to 2019 with up to 35 million euros to investigate mental disorders in order to devise and develop better therapeutic measures and strategies for this population by means of basic and translational clinical research. This is the result of a competitive call for research proposals entitled research network for mental diseases. It is a nationwide network of nine consortia with up to ten psychiatric and clinical psychology partner institutions from largely university-based research facilities for adults and/or children and adolescents. Furthermore, three cross-consortia platform projects will seek to identify shared causes of diseases and new diagnostic modalities for anxiety disorders, attention deficit hyperactivity disorders (ADHS), autism, bipolar disorders, depression, schizophrenia and psychotic disorders as well as substance-related and addictive disorders. The spectrum of therapeutic approaches to be examined ranges from innovative pharmacological and psychotherapeutic treatment to novel brain stimulation procedures. In light of the enormous burden such diseases represent for society as a whole, a sustainable improvement in the financial support for those researching mental disorders seems essential. This network aims to become a nucleus for long overdue and sustained support for a German center for mental disorders.
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Neoadjuvant Therapy in Rectal Cancer - Biobanking of Preoperative Tumor Biopsies. Sci Rep 2016; 6:35589. [PMID: 27752113 PMCID: PMC5067705 DOI: 10.1038/srep35589] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/03/2016] [Indexed: 12/27/2022] Open
Abstract
Translational research relies on high-quality biospecimens. In patients with rectal cancer treated preoperatively with radiochemotherapy tissue based analyses are challenging. To assess quality challenges we analyzed tissue samples taken over the last years in a multicenter setting. We retrospectively evaluated overall 197 patients of the CAO/ARO/AIO-94- and 04-trial with locally advanced rectal cancer that were biopsied preoperatively at the University Medical Center Goettingen as well as in 10 cooperating hospitals in Germany. The cellular content of tumor, mucosa, stroma, necrosis and the amount of isolated DNA and RNA as well as the RNA integrity number (RIN) as quality parameters were evaluated. A high RNA yield (p = 2.75e–07) and the content of tumor (p = 0.004) is significantly associated to high RIN-values, whereas a high content of mucosa (p = 0.07) shows a trend and a high amount of necrosis (p = 0.01) is significantly associated with RNA of poor quality. Correlating biopsies from Goettingen and the cooperating centers showed comparable tumor content results. By taking small sized biopsies we could assess a clear correlation between a good RNA quality and a high amount of RNA and tumor cells. These results also indicate that specimens collected at different centers are of comparable quality.
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Zhang L, Wu X, Hu Y, Wang X, He Z, Xie Y, Pan K, Wang N, Dong Z, Zhang L, Ji J. Establishment of a network-based intra-hospital virtual cancer biobank. Biopreserv Biobank 2015; 13:43-8. [PMID: 25686047 DOI: 10.1089/bio.2014.0086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is a growing interest in integrating biomaterial repositories into larger infrastructures in order to meet research demands. However, even for a single hospital or institute, where both population-based and multiple disease-based biobanks have existed for a long time, the integration of existing separate biobanks into a virtual cancer biobank is still challenging. The guidelines and procedures for biobanking are varied and not universally enforced or followed in separate biobanks. Within the last 2 years, we initiated a project to establish a centralized biobank facility in a common storage environment. Analyzing the challenges and interests of stakeholders for the biobanks, a working group comprised of representatives from the central and separate banks, ethic committees, and research administration offices reached an agreement to implement a central facility by following the ISBER best practices for biobanking, and including regular project reviews by the ethical and scientific boards. Furthermore, by implementing a modified minimum information system with biobank data sharing, a network based intra-hospital virtual cancer bank was established to facilitate sharing information of samples held by separate banks. Meanwhile, this virtual biobank network, which has integrated patient information from hospital health care systems, will gradually integrate follow-up information from the cancer registry office and data from epidemiology studies, providing controlled access for sample providers and resource users. In the future, this infrastructure designed for a single hospital may be helpful for building a broader virtual network for data and specimen exchanges.
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Affiliation(s)
- Lianhai Zhang
- 1 Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Cancer Biobank, Peking University Cancer Hospital and Institute , Beijing, China
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Rush A, Christiansen JH, Farrell JP, Goode SM, Scott RJ, Spring KJ, Byrne JA. Biobank Classification in an Australian Setting. Biopreserv Biobank 2015; 13:212-8. [DOI: 10.1089/bio.2015.0007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Amanda Rush
- Children's Cancer Research Unit, Kids Research Institute, NSW, Australia
| | | | | | - Susan M. Goode
- Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Rodney J. Scott
- Hunter Medical Research Institute, New Lambton, NSW, Australia
| | - Kevin J. Spring
- Ingham Institute, Liverpool, NSW, Australia
- University of Western Sydney, Liverpool Clinical School, Liverpool, NSW, Australia
| | - Jennifer A. Byrne
- Children's Cancer Research Unit, Kids Research Institute, NSW, Australia
- University of Sydney Discipline of Paediatrics and Child Health, The Children's Hospital at Westmead, Westmead, NSW, Australia
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Gao Z, Gu Y, Lv Z, Yu G, Zhou J. Practical electronic information system and printed recording promote management accuracy in an early-stage small-scale non-automatic biobank. Biopreserv Biobank 2015; 13:61-6. [PMID: 25686050 DOI: 10.1089/bio.2014.0102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
It is particularly necessary for biomedical researchers to obtain applicable biosamples accurately and efficiently, especially from a biobank with multiple-disease catalogs. To optimize the retrieval procedure, especially in the early stages of a non-automatic biobank, we developed a procedure that combined the electronic information system with a graphically designed printed recording system, which assisted in retrieving the samples quickly in a visualized way. In this procedure, we designed tables depending on the structure of equipment and registered the corresponding information in the tables layer by layer. Different samples from different types of diseases were first registered in the electronic system with the specific pre-allocation and barcodes. Then they were stored in the allocated position using their respective barcodes. In this way, the sample number and the location information in the electronic database were completely matched with the printed record. When the samples are needed, it is convenient to check the electronic information with the printed record. This procedure provides a convenient way to record the sample information during its lifecycle, and helps the administrator to double check information about the sample. The current solution offers an easy way for the transformation of a non-automatic biobank from the small-scale early-stage to the large-scale highly-automated level.
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Affiliation(s)
- Zhimei Gao
- Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University , Shanghai, China
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