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Cho YD, Cho ES, Song JS, Kim YY, Hwang I, Kim SY. Standard operating procedures for the collection, processing, and storage of oral biospecimens at the Korea Oral Biobank Network. J Periodontal Implant Sci 2023; 53:336-346. [PMID: 36919006 PMCID: PMC10627733 DOI: 10.5051/jpis.2203680184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/02/2022] [Accepted: 12/12/2022] [Indexed: 02/10/2023] Open
Abstract
PURPOSE The Korea Oral Biobank Network (KOBN) was established in 2021 as a branch of the Korea Biobank Network under the Korea Centers for Disease Control and Prevention to provide infrastructure for the collection, management, storage, and utilization of human bioresources from the oral cavity and associated clinical data for basic research and clinical studies. METHODS To address the need for the unification of the biobanking process, the KOBN organized the concept review for all the processes. RESULTS The KOBN established standard operating procedures for the collection, processing, and storage of oral samples. CONCLUSIONS The importance of collecting high-quality bioresources to generate accurate and reproducible research results has always been emphasized. A standardized procedure is a basic prerequisite for implementing comprehensive quality management of biological resources and accurate data production.
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Affiliation(s)
- Young-Dan Cho
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Seoul, Korea
| | - Eunae Sandra Cho
- Department of Oral Pathology, Oral Cancer Research Institute, Yonsei University College of Dentistry, Seoul, Korea
| | - Je Seon Song
- Department of Pediatric Dentistry, Yonsei University College of Dentistry, Seoul, Korea
| | - Young-Youn Kim
- Department of Oral and Maxillofacial Surgery, Apple Tree Institute of Biomedical Science, Apple Tree Dental Hospital, Seoul, Korea
| | | | - Sun-Young Kim
- Department of Conservative Dentistry, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Seoul, Korea.
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Meza MS, Michel IM, Rivas RA, Benítez GB, Solaeche SM, Salas-de la Cruz D, Moran KS. Obtaining human teeth for dental education: A cross-sectional study to create ethical and transparent processes. J Dent Educ 2023; 87:50-59. [PMID: 36044346 DOI: 10.1002/jdd.13094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 07/22/2022] [Accepted: 08/11/2022] [Indexed: 01/11/2023]
Abstract
OBJECTIVES This study explores the practices of obtaining human teeth for teaching and research in Paraguay. The goal of this research is to understand whether the data supports the need to improve ethical training within dental education, including the creation of a human tooth bank (HTB) METHODS: An observational cross-sectional study was conducted. Three semi-structured questionnaires were developed, one for each target population: dental students, dentists in practice, and the general population. The questionnaires were distributed between February and April 2021, using Google Forms RESULTS: The main places where human teeth were obtained by a student are dental clinics, followed by cemeteries. 94% of students and 91% of dentists paid for teeth on at least one occasion. There is a willingness on the part of students and dentists to donate collections of teeth, and among the general population to donate their teeth if they are extracted, for both teaching and research use. Note that, 31% of students and 6% of the population are aware of what an HTB is, at the same time only 16% of dentists know how it functions CONCLUSION: The number of respondents who obtain teeth from cemeteries and who pay for their acquisition is high. Both of these practices raise ethical concerns. The implementation of informed consent for the donation of extracted teeth is practically nil; although there is a positive attitude towards its implementation. Also, there is a lack of knowledge about the role of an HTB; although the population expressed a willingness to donate extracted teeth.
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Affiliation(s)
- María S Meza
- Research Directorate, Faculty of Dentistry of the National University of Asunción, Asunción, Paraguay
| | - Ingrid M Michel
- Research Directorate, Faculty of Dentistry of the National University of Asunción, Asunción, Paraguay
| | - Ronald A Rivas
- Health Sciences Research Institute, National University of Asunción, San Lorenzo, Paraguay
| | - Gloria B Benítez
- Research Directorate, Faculty of Dentistry of the National University of Asunción, Asunción, Paraguay
| | - Sandra M Solaeche
- Research Directorate, Faculty of Dentistry of the National University of Asunción, Asunción, Paraguay
| | | | - Kimberlee S Moran
- Department of Chemistry, Rutgers University, Camden, New Jersey, USA
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Nobile H, Borry P, Pischon T, Steinbrecher A, Boeing H, Vigl M, Bergmann MM. Participants' decision to enroll in cohort studies with biobanks: quantitative insights from two German studies. Per Med 2018; 14:477-485. [PMID: 29749857 DOI: 10.2217/pme-2017-0049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
AIM To understand participants' actual motivations to enroll in cohort studies with biobanks. METHODS Participants of two such studies currently ongoing in Germany were invited to fill in a questionnaire about their decision to enroll. RESULTS From the 623 questionnaires completed, contributing to scientific knowledge appeared as a main motive for enrollment, followed by learning about personal health status and receiving personal medical advice. CONCLUSION Motivating participation as a way to contribute to the common good rather than as a way to obtain personal benefits appears to be particularly appropriate to ensure participants' long-term commitment and should therefore be further investigated in this setting.
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Affiliation(s)
- Hélène Nobile
- Department of Epidemiology, German Institute for Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany.,Center for Biomedical Ethics & Law, Department of Public Health & Primary Care, KU Leuven, Leuven, Belgium
| | - Pascal Borry
- Center for Biomedical Ethics & Law, Department of Public Health & Primary Care, KU Leuven, Leuven, Belgium
| | - Tobias Pischon
- Molecular Epidemiology Research Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Astrid Steinbrecher
- Molecular Epidemiology Research Group, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Heiner Boeing
- Department of Epidemiology, German Institute for Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
| | - Matthäus Vigl
- Department of Epidemiology, German Institute for Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
| | - Manuela M Bergmann
- Department of Epidemiology, German Institute for Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
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Lee JE, Kim YY. How Should Biobanks Prioritize and Diversify Biosample Collections? A 40-Year Scientific Publication Trend Analysis by the Type of Biosample. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 22:255-263. [PMID: 29584577 DOI: 10.1089/omi.2017.0197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Biobanks are infrastructures for large-scale biology innovation. Governance of biobanks can be usefully informed by studies of publication trends, for example, on the types of biosamples employed in scientific publications. We examined trends in each of the serum, plasma, peripheral blood mononuclear cell (PBMC), buffy coat, tissue, and gut microbiome biosample-related scientific publications over the past 40 years, using data between 1977 and 2016 from the Scopus database. We found that the number of tissue-related publications was the highest in each year of our analysis than other biosamples, but was generally less than the sum of serum- and plasma-related publications. Importantly, the microbiome publications increased greatly starting in the 2010s, and currently overtook the number of publications on PBMC and buffy coat. Among serum-, plasma-, and tissue-related publications, the number of protein- and RNA-related publications was generally higher than cell-free DNA-, DNA-, and metabolite-related publications for the past 40 years. Mass spectrometry- and next-generation sequencing-related publications have increased dramatically since the 2000s and 2010s, respectively. Microbiome- and metabolite-related biosamples can help diversify future biosample collections, while tissue collections appear to maintain their importance in scientific publications. We also report here our observations on the countries that use biosample research (e.g., China, United Kingdom, United States, and others). These publication trends by the type of biosamples illuminate roadmaps by which biobanks might establish and diversify their biosample collections in the future. In addition, we note that biobanks need to secure biosamples appropriate for integrated analysis of multi-omics research data.
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Affiliation(s)
- Jae-Eun Lee
- Division of Biobank for Health Sciences, Center for Genome Science, Korea National Institute of Health , Korea Centers for Disease Control and Prevention, Cheongju-si, Korea
| | - Young-Youl Kim
- Division of Biobank for Health Sciences, Center for Genome Science, Korea National Institute of Health , Korea Centers for Disease Control and Prevention, Cheongju-si, Korea
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Hoosain N, Pearce B, Jacobs C, Benjeddou M. Mapping SLCO1B1 Genetic Variation for Global Precision Medicine in Understudied Regions in Africa: A Focus on Zulu and Cape Admixed Populations. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 20:546-54. [PMID: 27631194 DOI: 10.1089/omi.2016.0115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The U.S. President Barack Obama has announced, in his State of the Union address on January 20, 2015, the Precision Medicine Initiative, a US$215-million program. For global precision medicine to become a reality, however, biological and environmental "variome" in previously understudied populations ought to be mapped and catalogued. Chief among the molecular targets that warrant global mapping is the organic anion-transporting polypeptide 1B1 (OATP1B1), encoded by solute carrier organic anion transporter family member 1B1 (SLCO1B1), a hepatic uptake transporter predominantly expressed in the basolateral side of hepatocytes. Human OATP1B1 plays a crucial role in the transport of a wide variety of substrates. This includes endogenous compounds such as bile salts as well as medicines, including benzylpenicillin, methotrexate, pravastatin, and rifampicin, and natural toxins microcystin and phalloidin. Genetic variations observed in the SLCO1B1 gene have been associated with altered in vitro and in vivo OATP1B1 transport activity, and consequently influencing patients' response to medicines, toxins, and susceptibility to common complex diseases. Well-characterized haplotypes, *5 (RS4149056C) and *15 (RS4149056T), have been associated with a strikingly reduced uptake of multiple OATP1B1 substrates, including estrone-3-sulfate, estradiol-17β-d-glucuronide, atorvastatin, cerivastatin, pravastatin, and rifampicin. In particular, RS4149056C is observed in 60% of the Cape admixed (CA) population and is associated with increased plasma concentrations of many statins as well as fexofenadine and repaglinide. We designed and optimized a SNaPshot minisequencing panel to characterize the variants of relevance for precision medicine in the clinic. We report here the first study on allele and genotype frequencies for 10 nonsynonymous, 4 synonymous, and 6 intronic single-nucleotide polymorphisms of SLCO1B1 in the Zulu and CA populations of South Africa. These variants are further contextualized here, in relation to their potential clinical relevance. These observations collectively contribute to current efforts to advance global precision medicine in understudied populations and resource-limited regions of the world.
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Affiliation(s)
- Nisreen Hoosain
- Pharmacogenetics Laboratory, Department of Biotechnology, Faculty of Natural Science, University of the Western Cape , Bellville, South Africa
| | - Brendon Pearce
- Pharmacogenetics Laboratory, Department of Biotechnology, Faculty of Natural Science, University of the Western Cape , Bellville, South Africa
| | - Clifford Jacobs
- Pharmacogenetics Laboratory, Department of Biotechnology, Faculty of Natural Science, University of the Western Cape , Bellville, South Africa
| | - Mongi Benjeddou
- Pharmacogenetics Laboratory, Department of Biotechnology, Faculty of Natural Science, University of the Western Cape , Bellville, South Africa
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Jin P, Lan J, Wang K, Baker MS, Huang C, Nice EC. Pathology, proteomics and the pathway to personalised medicine. Expert Rev Proteomics 2018; 15:231-243. [PMID: 29310484 DOI: 10.1080/14789450.2018.1425618] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ping Jin
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology, The Affiliated Hospital of Hainan Medical College, Haikou, P.R. China
| | - Jiang Lan
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology, The Affiliated Hospital of Hainan Medical College, Haikou, P.R. China
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Kui Wang
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, Australia
| | - Canhua Huang
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology, The Affiliated Hospital of Hainan Medical College, Haikou, P.R. China
- West China School of Basic Medical Sciences & Forensic Medicine, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia and Visiting Professor, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P.R. China
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Balasopoulou A, Mooy FM, Baker DJ, Mitropoulou C, Skoufas E, Bulgiba A, Katsila T, Patrinos GP. Advancing Global Precision Medicine: An Overview of Genomic Testing and Counseling Services in Malaysia. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:733-740. [PMID: 29173101 DOI: 10.1089/omi.2017.0136] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Precision medicine, genomic and diagnostic services are no longer limited to developed countries. This broadening in geography of biomarker applications and omics diagnostics also demands empirical study of implementation, diagnostic testing, and counseling practices in the field. For example, the Malaysian population has large ethnic diversity and high prevalence of genetic disorders such as hemoglobinopathies and metabolic disorders. Increased morbidity and mortality from such diseases have a direct impact on society and health system sustainability and for this, decision-making becomes of outmost importance. We report here on our findings on the landscape of genomic testing and genetic counseling services in Malaysia. We first defined the framework of all Malaysian stakeholders that offer genomics services and next, we identified the related information gaps, as depicted through the service providers' online websites. Our research framework revealed that there is a very diverse spectrum of genomics services in Malaysia, in which wet- and dry-laboratory services integrate. Moreover, we identify the current gaps and possible remedies to improve the quality of genomic and predictive analytics, not to mention considerations to ensure robust ethics and responsible innovation. To our knowledge, this is the first such study to be performed for a Southeast Asian country. Our genomics and precision medicine services mapping strategy presented in this study may serve as a model for field assessment at regional, national, and international levels as precision medicine is expanding globally and new governance challenges and opportunities continue to emerge for smart implementation science.
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Affiliation(s)
- Angeliki Balasopoulou
- 1 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece
| | - Foong-Ming Mooy
- 2 Department of Social and Preventive Medicine, Faculty of Medicine, Julius Centre University of Malaya , Kuala Lumpur, Malaysia
| | | | | | - Efthymios Skoufas
- 1 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece
| | - Awang Bulgiba
- 2 Department of Social and Preventive Medicine, Faculty of Medicine, Julius Centre University of Malaya , Kuala Lumpur, Malaysia
| | - Theodora Katsila
- 1 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece
| | - George P Patrinos
- 1 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece .,4 Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University , Al Ain, United Arab Emirates .,5 Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University , Al Ain, United Arab Emirates
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Lee JE, Kim YY. Impact of Preanalytical Variations in Blood-Derived Biospecimens on Omics Studies: Toward Precision Biobanking? OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:499-508. [PMID: 28873014 DOI: 10.1089/omi.2017.0109] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Research data and outcomes do vary across populations and persons, but this is not always due to experimental or true biological variation. Preanalytical components of experiments, be they biospecimen acquisition, preparation, storage, or transportation to the laboratory, may all contribute to apparent variability in research data, outcomes, and interpretation. The present review article and biobanking innovation analysis offer new insights with a summary of such preanalytical variables, for example, the type of blood collection tube, centrifugation conditions, long-term sample storage temperature, and duration, on output of omics analyses of blood-derived biospecimens: whole blood, serum, plasma, buffy coat, and peripheral blood mononuclear cells. Furthermore, we draw parallels from the field of precision medicine in this study, with a view to the future of "precision biobanking" wherein such preanalytical variations are carefully taken into consideration so as to minimize their influence on outcomes of omics data, analyses, and sensemaking, particularly in clinical omics applications. We underscore the need for using broadly framed, critical, independent, social and political science, and humanities research so as to understand the multiple possible future trajectories of, and the motivations and values embedded in, precision biobanking that is increasingly relevant in the current age of Big Data.
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Affiliation(s)
- Jae-Eun Lee
- Division of Biobank for Health Sciences, Center for Genome Science, Korea National Institute of Health , Korea Centers for Disease Control and Prevention, Cheongju-si, Korea
| | - Young-Youl Kim
- Division of Biobank for Health Sciences, Center for Genome Science, Korea National Institute of Health , Korea Centers for Disease Control and Prevention, Cheongju-si, Korea
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