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Pan H, Bakalov V, Cox L, Engle ML, Erickson SW, Feolo M, Guo Y, Huggins W, Hwang S, Kimura M, Krzyzanowski M, Levy J, Phillips M, Qin Y, Williams D, Ramos EM, Hamilton CM. Identifying Datasets for Cross-Study Analysis in dbGaP using PhenX. Sci Data 2022; 9:532. [PMID: 36050327 PMCID: PMC9434066 DOI: 10.1038/s41597-022-01660-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 08/23/2022] [Indexed: 11/09/2022] Open
Abstract
Identifying relevant studies and harmonizing datasets are major hurdles for data reuse. Common Data Elements (CDEs) can help identify comparable study datasets and reduce the burden of retrospective data harmonization, but they have not been required, historically. The collaborative team at PhenX and dbGaP developed an approach to use PhenX variables as a set of CDEs to link phenotypic data and identify comparable studies in dbGaP. Variables were identified as either comparable or related, based on the data collection mode used to harmonize data across mapped datasets. We further added a CDE data field in the dbGaP data submission packet to indicate use of PhenX and annotate linkages in the future. Some 13,653 dbGaP variables from 521 studies were linked through PhenX variable mapping. These variable linkages have been made accessible for browsing and searching in the repository through dbGaP CDE-faceted search filter and the PhenX variable search tool. New features in dbGaP and PhenX enable investigators to identify variable linkages among dbGaP studies and reveal opportunities for cross-study analysis.
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Affiliation(s)
- Huaqin Pan
- RTI International, Research Triangle Park, NC, USA.
| | | | - Lisa Cox
- RTI International, Research Triangle Park, NC, USA
| | | | | | - Michael Feolo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Yuelong Guo
- GeneCentric Therapeutics Inc., Durham, NC, USA
| | | | | | - Masato Kimura
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Josh Levy
- Levy Informatics, Chapel Hill, NC, USA
| | | | - Ying Qin
- RTI International, Research Triangle Park, NC, USA
| | | | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Role of Biobanks for Cancer Research and Precision Medicine in Hepatocellular Carcinoma. J Gastrointest Cancer 2021; 52:1232-1247. [PMID: 34807351 DOI: 10.1007/s12029-021-00759-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2021] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) is a highly complex and deadly cancer. There is an urgent need for new and effective treatment modalities. Since the primary goal in the management of cancer is to cure and improve survival, personalized therapy can increase survival, reduce mortality rates, and improve quality of life. Biobanks hold potential in leading to breakthroughs in biomedical research and precision medicine (PM). They serve as a biorepository, collecting, processing, storing, and supplying specimens and relevant data for basic, translational, and clinical research. OBJECTIVE We aimed to highlight the fundamental role of biobanks, harboring high quality, sustainable collections of patient samples in adequate size and variability, for developing diagnostic, prognostic, and predictive biomarkers to develop and PM approaches in the management of HCC. METHOD We obtained information from previously published articles and BBMRI directory. RESULTS AND CONCLUSION Biobanking of high-quality biospecimens along with patient clinical information provides a fundamental scientific infrastructure for basic, translational, and clinical research. Biobanks that control and eliminate pre-analytical variability of biospecimens, provide a platform to identify reliable biomarkers for the application of PM. We believe, establishing HCC biobanks will empower to underpin molecular mechanisms of HCC and generate strategies for PM. Thus, first, we will review current therapy approaches in HCC care. Then, we will summarize challenges in HCC management. Lastly, we will focus on the best practices for establishing HCC biobanking to support research, translational medicine in the light of new experimental research conducted with the aim of delivering PM for HCC patients.
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Speirs V. Quality Considerations When Using Tissue Samples for Biomarker Studies in Cancer Research. Biomark Insights 2021; 16:11772719211009513. [PMID: 33958852 PMCID: PMC8060748 DOI: 10.1177/11772719211009513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/13/2021] [Indexed: 12/12/2022] Open
Abstract
Tissue obtained from biobanks is frequently employed in biomarker studies. Biomarkers define objective, measurable characteristics of biological and biomedical procedures and have been used as indicators of clinical outcome. This article outlines some of the steps scientists should consider when embarking on biomarker research in cancer research using samples from biobanks and the importance and challenges of linking clinical data to biological samples.
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Affiliation(s)
- Valerie Speirs
- Institute of Medical Sciences, School of Medicine,
Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland,
UK
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4
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Fthenou E, Al Thani A, Al Marri A, Afifi N. Qatar Biobank: A Paradigm of Translating Biobank Science into Evidence-Based Health Care Interventions. Biopreserv Biobank 2019; 17:491-493. [PMID: 31833811 DOI: 10.1089/bio.2019.0051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Biobank science is progressively becoming indispensable for the development of novel diagnostic tools in health care, by pairing standardized high-quality biological samples, phenotypic, and omics data required to best characterize the underlying biological mechanisms of response to therapy and survival. Qatar Biobank (QBB), Qatar's National Repository Centre for biological samples and health information, aligning with these endeavors, has developed a strategic framework to enable biobanking science that can be transformed into tangible health care diagnostic tools. In this concept, QBB works closely with multidisciplinary stakeholders: (1) governmental authorities (n = 2), (2) health providers (n = 3), (3) academic institutions (n = 28), (4) other research institutions (n = 6), and (5) the Qatar National Research Fund, by providing data and biospecimens to research projects. The local community organizes campaigns through social media and interactive events, spreading the concept of biobanking to inform and encourage people to participate. Up to now, QBB has recruited up to 30% of the targeted population and collaborated with 35 national and international research entities contributing to more than 170 research projects. QBB is referring about 53% of its participants to the Hamad general hospital through the integrated information system, revealing the need of new health screening approaches for public health policy makers. QBB contributed to the development of a customized genetic screening microarray tailored to the Qatari population that will be used in research as well as for the screening of variants of medical relevance in Qatar, promoting precision medicine in Qatar's health care system. The QBB strategic plan is a paradigm for the optimal utilization of resources, infrastructure, and investments engaging the local authorities and the research entities, and committing them to data sharing and working together toward the discovery of evidence-based health care interventions.
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Affiliation(s)
- Eleni Fthenou
- Qatar Biobank, Qatar Foundation for Education, Science, and Community, Doha, Qatar
| | - Asma Al Thani
- Qatar Biobank, Qatar Foundation for Education, Science, and Community, Doha, Qatar.,College of Health Sciences, Qatar University, Doha, Qatar.,Biomedical Research Center, Qatar University, Doha, Qatar.,Qatar Genome Program Committee, Doha, Qatar
| | | | - Nahla Afifi
- Qatar Biobank, Qatar Foundation for Education, Science, and Community, Doha, Qatar
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Azad RK, Shulaev V. Metabolomics technology and bioinformatics for precision medicine. Brief Bioinform 2019; 20:1957-1971. [PMID: 29304189 PMCID: PMC6954408 DOI: 10.1093/bib/bbx170] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/29/2017] [Indexed: 12/14/2022] Open
Abstract
Precision medicine is rapidly emerging as a strategy to tailor medical treatment to a small group or even individual patients based on their genetics, environment and lifestyle. Precision medicine relies heavily on developments in systems biology and omics disciplines, including metabolomics. Combination of metabolomics with sophisticated bioinformatics analysis and mathematical modeling has an extreme power to provide a metabolic snapshot of the patient over the course of disease and treatment or classifying patients into subpopulations and subgroups requiring individual medical treatment. Although a powerful approach, metabolomics have certain limitations in technology and bioinformatics. We will review various aspects of metabolomics technology and bioinformatics, from data generation, bioinformatics analysis, data fusion and mathematical modeling to data management, in the context of precision medicine.
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Affiliation(s)
| | - Vladimir Shulaev
- Corresponding author: Vladimir Shulaev, Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX 76210, USA. Tel.: 940-369-5368; Fax: 940-565-3821; E-mail:
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Dickerson C, Hsu Y, Mendoza S, Osman I, Ogilvie J, Patel K, Moreira AL. Quality Assurance After a Natural Disaster: Lessons from Hurricane Sandy. Biopreserv Biobank 2018; 16:92-96. [PMID: 29298082 DOI: 10.1089/bio.2017.0104] [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: 12/26/2022] Open
Abstract
Biospecimen quality can vary depending on many pre- and post-collection variables. In this study, we consider a natural disaster as a post-collection variable that may have compromised the quality of frozen tissue specimens. To investigate this possible link, we compared the quality of nucleic acids, the level of antigenicity, and the preservation of histology from frozen specimens collected before and after the power outage caused by Hurricane Sandy. To analyze nucleic acid quality, we extracted both DNA and RNA and performed capillary electrophoresis to compare the quality and concentrations of the nucleic acids. To compare antigenicity, frozen sections were cut and immunostained for thyroid transcription factor 1 (TTF-1), a nuclear transcription protein commonly used as a diagnostic biomarker for multiple cancer types, including thyroid and lung cancers. Positive expression of TTF-1, as noted by homogenous nuclear staining, would demonstrate that the TTF-1 proteins could still bind antibodies and, therefore, that these proteins were not significantly degraded. Furthermore, representative frozen sections stained with hematoxylin and eosin were also assessed qualitatively by a trained pathologist to examine any possible histologic aberrations. Due to the similar quality of the tissue samples collected before and after the storm, Hurricane Sandy had no discernable effect on the quality of frozen specimens, and these specimens exposed to the natural disaster are still valuable research tools.
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Affiliation(s)
- Collin Dickerson
- 1 Center for Biospecimen Research and Development, New York University Langone Health , New York, New York
| | - Yanshen Hsu
- 1 Center for Biospecimen Research and Development, New York University Langone Health , New York, New York
| | - Sandra Mendoza
- 1 Center for Biospecimen Research and Development, New York University Langone Health , New York, New York
| | - Iman Osman
- 2 Department of Medicine, Center for Biospecimen Research and Development, New York University Langone Health , New York, New York
| | - Jennifer Ogilvie
- 3 Department of Surgery, New York University Langone Health , New York, New York
| | - Kepal Patel
- 3 Department of Surgery, New York University Langone Health , New York, New York
| | - Andre L Moreira
- 4 Department of Pathology, Center for Biospecimen Research and Development, New York University Langone Health , New York, New York
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