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Sukumar S, Krishnan A, Banerjee S. An Overview of Bioinformatics Resources for SNP Analysis. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Viennas E, Komianou A, Mizzi C, Stojiljkovic M, Mitropoulou C, Muilu J, Vihinen M, Grypioti P, Papadaki S, Pavlidis C, Zukic B, Katsila T, van der Spek PJ, Pavlovic S, Tzimas G, Patrinos GP. Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies. Nucleic Acids Res 2016; 45:D846-D853. [PMID: 27924022 PMCID: PMC5210643 DOI: 10.1093/nar/gkw949] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/12/2016] [Indexed: 01/20/2023] Open
Abstract
FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnic mutation databases, all built around Microsoft's PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The abovementioned updates further enhance the impact of FINDbase, as a key resource for Genomic Medicine applications.
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Affiliation(s)
- Emmanouil Viennas
- University of Patras, Faculty of Engineering, Department of Computer Engineering and Informatics, GR-26504, Patras, Greece
| | - Angeliki Komianou
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Clint Mizzi
- Erasmus University Medical Center, Faculty of Medicine and Health Sciences, Department of Bioinformatics, NL-3015 CN, Rotterdam, The Netherlands.,University of Malta, Faculty of Medicine and Surgery, Department of Physiology and Biochemistry, MSD 2090, Malta
| | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Laboratory of Molecular Biomedicine, 11010, Belgrade, Serbia
| | | | - Juha Muilu
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, SE-22100, Lund, Sweden
| | - Panagiota Grypioti
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Styliani Papadaki
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Cristiana Pavlidis
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Branka Zukic
- University of Malta, Faculty of Medicine and Surgery, Department of Physiology and Biochemistry, MSD 2090, Malta
| | - Theodora Katsila
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece
| | - Peter J van der Spek
- Erasmus University Medical Center, Faculty of Medicine and Health Sciences, Department of Bioinformatics, NL-3015 CN, Rotterdam, The Netherlands
| | - Sonja Pavlovic
- University of Malta, Faculty of Medicine and Surgery, Department of Physiology and Biochemistry, MSD 2090, Malta
| | - Giannis Tzimas
- Department of Computer and Informatics Engineering, Technological Educational Institute of Western Greece, GR-30020, Patras, Greece
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece .,Erasmus University Medical Center, Faculty of Medicine and Health Sciences, Department of Bioinformatics, NL-3015 CN, Rotterdam, The Netherlands
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4
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Kambouris ME. Population Screening for Hemoglobinopathy Profiling: Is the Development of a Microarray Worthwhile? Hemoglobin 2016; 40:240-6. [DOI: 10.1080/03630269.2016.1186686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Niroula A, Vihinen M. Variation Interpretation Predictors: Principles, Types, Performance, and Choice. Hum Mutat 2016; 37:579-97. [DOI: 10.1002/humu.22987] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/07/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Abhishek Niroula
- Department of Experimental Medical Science; Lund University; BMC B13 Lund SE-22184 Sweden
| | - Mauno Vihinen
- Department of Experimental Medical Science; Lund University; BMC B13 Lund SE-22184 Sweden
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Cooper DN, Brand A, Dolzan V, Fortina P, Innocenti F, Michael Lee MT, Macek M, Al-Mulla F, Prainsack B, Squassina A, Vayena E, Vozikis A, Williams MS, Patrinos GP. Bridging genomics research between developed and developing countries: the Genomic Medicine Alliance. Per Med 2014; 11:615-623. [PMID: 29764053 DOI: 10.2217/pme.14.59] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Genomic Medicine Alliance is a global academic research network that aims to establish and strengthen collaborative ties between the various genomic medicine stakeholders. Its focus lies on the translation of scientific research findings into clinical practice. It brings together experts from disciplines including genome informatics, pharmacogenomics, public health genomics, ethics in genomics and health economics, and it is supervised by a 14-member International Scientific Advisory Committee comprising internationally renowned scientists. The Alliance's official journal, Public Health Genomics, offers members a highly respected publication forum for their original research findings. In the short-to-medium term, the Genomic Medicine Alliance hopes to harmonize research activities between developed and developing countries and to organize educational activities in the field of genomic medicine.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Angela Brand
- University of Maastricht, Institute of Public Health Genomics, Maastricht, The Netherlands
| | - Vita Dolzan
- University of Ljubljana, School of Medicine, Ljubljana, Slovenia
| | - Paolo Fortina
- Thomas Jefferson University, Kimmel Cancer Center, Philadelphia, PA, USA
| | - Federico Innocenti
- Institute of Pharmacogenomics & Individualized Therapy, University of North Carolina, Chapel Hill, NC, USA
| | - Ming Ta Michael Lee
- Laboratory for International Alliance on Genomic Research, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Milan Macek
- Charles University Prague & Faculty Hospital Motol, Institute of Biology & Medical Genetics, Prague, Czech Republic
| | - Fahd Al-Mulla
- University of Kuwait, Molecular Pathology Unit, Safat, Kuwait
| | - Barbara Prainsack
- King's College London, Department of Social Science, Health & Medicine, London, UK
| | - Alessio Squassina
- University of Cagliari, School of Medicine, Department of Biomedical Sciences, Cagliari, Italy
| | - Effy Vayena
- University of Zurich, Institute of Biomedical Ethics, Zurich, Switzerland
| | | | - Marc S Williams
- Geisinger Health System, Genomic Medicine Institute, Danville, PA, USA
| | - George P Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, GR-26504, Patras, Greece
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7
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Vihinen M. Variation ontology: annotator guide. J Biomed Semantics 2014; 5:9. [PMID: 24533660 PMCID: PMC3931275 DOI: 10.1186/2041-1480-5-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 01/29/2014] [Indexed: 02/02/2023] Open
Abstract
Background Systematic representation of information related to genetic and non-genetic variations is required to allow large scale studies, data mining and data integration, and to make it possible to reveal novel relationships between genotype and phenotype. Although lots of variation data is available it is often difficult to use due to lack of systematics. Results A novel ontology, Variation Ontology (VariO http://variationontology.org), was developed for annotation of effects, consequences and mechanisms of variations. In this article instructions are provided on how VariO annotations are made. The major levels for description are the three molecules, namely DNA, RNA and protein. They are further divided to four major sublevels: variation type, function, structure, and property, and further up to eight sublevels. VariO annotation summarizes existing knowledge about a variation and its effects and formalizes it so that computational analyses are efficient. The annotations should be made on as many levels as possible. VariO annotations are made in reference to normal states, which vary for each data item including e.g. reference sequences, wild type properties, and activities. Conclusions Detailed instructions together with examples are provided to indicate how VariO can be used for annotation of variations and their effects. A dedicated tool has been developed for annotation and will be further developed to cover also evidence for the annotations. VariO is suitable for annotation of data in many types of databases. As several different kinds of databases are in a process of adapting VariO annotations it is important to have guidelines to guarantee consistent annotation.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, Lund University, BMC D10, SE-22184 Lund, Sweden.
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8
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Papadopoulos P, Viennas E, Gkantouna V, Pavlidis C, Bartsakoulia M, Ioannou ZM, Ratbi I, Sefiani A, Tsaknakis J, Poulas K, Tzimas G, Patrinos GP. Developments in FINDbase worldwide database for clinically relevant genomic variation allele frequencies. Nucleic Acids Res 2013; 42:D1020-6. [PMID: 24234438 PMCID: PMC3964978 DOI: 10.1093/nar/gkt1125] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
FINDbase (http://www.findbase.org) aims to document frequencies of clinically relevant genomic variations, namely causative mutations and pharmacogenomic markers, worldwide. Each database record includes the population, ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related databases and the genetic variation together with its frequency in that population. Here, we report, in addition to the regular data content updates, significant developments in FINDbase, related to data visualization and querying, data submission, interrelation with other resources and a new module for genetic disease summaries. In particular, (i) we have developed new data visualization tools that facilitate data querying and comparison among different populations, (ii) we have generated a new FINDbase module, built around Microsoft’s PivotViewer (http://www.getpivot.com) software, based on Microsoft Silverlight technology (http://www.silverlight.net), that includes 259 genetic disease summaries from five populations, systematically collected from the literature representing the documented genetic makeup of these populations and (iii) the implementation of a generic data submission tool for every module currently available in FINDbase.
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Affiliation(s)
- Petros Papadopoulos
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece, Department of Computer Engineering and Informatics, Faculty of Engineering, University of Patras, GR-26504, Patras, Greece, Faculty of Medicine and Pharmacy, Human Genomic Center, University Mohammed V Souissi, 11400, Rabat, Morocco and Department of Computer and Informatics Engineering, Technological Educational Institute of Western Greece, GR-26334, Patras, Greece
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Abstract
Adherents to the Jewish faith have resided in numerous geographic locations over the course of three millennia. Progressively more detailed population genetic analysis carried out independently by multiple research groups over the past two decades has revealed a pattern for the population genetic architecture of contemporary Jews descendant from globally dispersed Diaspora communities. This pattern is consistent with a major, but variable component of shared Near East ancestry, together with variable degrees of admixture and introgression from the corresponding host Diaspora populations. By combining analysis of monoallelic markers with recent genome-wide variation analysis of simple tandem repeats, copy number variations, and single-nucleotide polymorphisms at high density, it has been possible to determine the relative contribution of sex-specific migration and introgression to map founder events and to suggest demographic histories corresponding to western and eastern Diaspora migrations, as well as subsequent microevolutionary events. These patterns have been congruous with the inferences of many, but not of all historians using more traditional tools such as archeology, archival records, linguistics, comparative analysis of religious narrative, liturgy and practices. Importantly, the population genetic architecture of Jews helps to explain the observed patterns of health and disease-relevant mutations and phenotypes which continue to be carefully studied and catalogued, and represent an important resource for human medical genetics research. The current review attempts to provide a succinct update of the more recent developments in a historical and human health context.
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Mitropoulos K, Innocenti F, van Schaik RH, Lezhava A, Tzimas G, Kollia P, Macek M, Fortina P, Patrinos GP. Institutional Profile: Golden Helix Institute of Biomedical Research: interdisciplinary research and educational activities in pharmacogenomics and personalized medicine. Pharmacogenomics 2012; 13:387-92. [PMID: 22379996 DOI: 10.2217/pgs.12.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Golden Helix Institute of Biomedical Research is an international nonprofit scientific organization with interdisciplinary research and educational activities in the field of genome medicine in Europe, Asia and Latin America. These activities are supervised by an international scientific advisory council, consisting of world leaders in the field of genomics and translational medicine. Research activities include the regional coordination of the Pharmacogenomics for Every Nation Initiative in Europe, in an effort to integrate pharmacogenomics in developing countries, the development of several national/ethnic genetic databases and related web services and the critical assessment of the impact of genetics and genomic medicine on society in various countries. Educational activities also include the organization of the Golden Helix Symposia(®), which are high-profile scientific research symposia in the field of personalized medicine and the Golden Helix Pharmacogenomics Days, an international educational activity focused on pharmacogenomics, as part of its international pharmacogenomics education and outreach efforts.
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Patrinos GP, Smith TD, Howard H, Al-Mulla F, Chouchane L, Hadjisavvas A, Hamed SA, Li XT, Marafie M, Ramesar RS, Ramos FJ, de Ravel T, El-Ruby MO, Shrestha TR, Sobrido MJ, Tadmouri G, Witsch-Baumgartner M, Zilfalil BA, Auerbach AD, Carpenter K, Cutting GR, Dung VC, Grody W, Hasler J, Jorde L, Kaput J, Macek M, Matsubara Y, Padilla C, Robinson H, Rojas-Martinez A, Taylor GR, Vihinen M, Weber T, Burn J, Qi M, Cotton RGH, Rimoin D. Human Variome Project country nodes: documenting genetic information within a country. Hum Mutat 2012; 33:1513-9. [PMID: 22753370 DOI: 10.1002/humu.22147] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/04/2012] [Indexed: 11/09/2022]
Abstract
The Human Variome Project (http://www.humanvariomeproject.org) is an international effort aiming to systematically collect and share information on all human genetic variation. The two main pillars of this effort are gene/disease-specific databases and a network of Human Variome Project Country Nodes. The latter are nationwide efforts to document the genomic variation reported within a specific population. The development and successful operation of the Human Variome Project Country Nodes are of utmost importance to the success of Human Variome Project's aims and goals because they not only allow the genetic burden of disease to be quantified in different countries, but also provide diagnosticians and researchers access to an up-to-date resource that will assist them in their daily clinical practice and biomedical research, respectively. Here, we report the discussions and recommendations that resulted from the inaugural meeting of the International Confederation of Countries Advisory Council, held on 12th December 2011, during the 2011 Human Variome Project Beijing Meeting. We discuss the steps necessary to maximize the impact of the Country Node effort for developing regional and country-specific clinical genetics resources and summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects.
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Affiliation(s)
- George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
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12
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Viennas E, Gkantouna V, Ioannou M, Georgitsi M, Rigou M, Poulas K, Patrinos GP, Tzimas G. Population-ethnic group specific genome variation allele frequency data: a querying and visualization journey. Genomics 2012; 100:93-101. [PMID: 22659238 DOI: 10.1016/j.ygeno.2012.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/09/2012] [Accepted: 05/21/2012] [Indexed: 01/28/2023]
Abstract
National/ethnic mutation databases aim to document the genetic heterogeneity in various populations and ethnic groups worldwide. We have previously reported the development and upgrade of FINDbase (www.findbase.org), a database recording causative mutations and pharmacogenomic marker allele frequencies in various populations around the globe. Although this database has recently been upgraded, we continuously try to enhance its functionality by providing more advanced visualization tools that would further assist effective data querying and comparisons. We are currently experimenting in various visualization techniques on the existing FINDbase causative mutation data collection aiming to provide a dynamic research tool for the worldwide scientific community. We have developed an interactive web-based application for population-based mutation data retrieval. It supports sophisticated data exploration allowing users to apply advanced filtering criteria upon a set of multiple views of the underlying data collection and enables browsing the relationships between individual datasets in a novel and meaningful way.
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Affiliation(s)
- Emmanouil Viennas
- Department of Computer Engineering and Informatics, University of Patras, Patras, Greece
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Gialluisi A, Pippucci T, Anikster Y, Ozbek U, Medlej-Hashim M, Mégarbané A, Romeo G. Estimating the allele frequency of autosomal recessive disorders through mutational records and consanguinity: the Homozygosity Index (HI). Ann Hum Genet 2011; 76:159-67. [PMID: 22188137 DOI: 10.1111/j.1469-1809.2011.00693.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In principle mutational records make it possible to estimate frequencies of disease alleles (q) for autosomal recessive disorders using a novel approach based on the calculation of the Homozygosity Index (HI), i.e., the proportion of homozygous patients, which is complementary to the proportion of compound heterozygous patients P(CH). In other words, the rarer the disorder, the higher will be the HI and the lower will be the P(CH). To test this hypothesis we used mutational records of individuals affected with Familial Mediterranean Fever (FMF) and Phenylketonuria (PKU), born to either consanguineous or apparently unrelated parents from six population samples of the Mediterranean region. Despite the unavailability of precise values of the inbreeding coefficient for the general population, which are needed in the case of apparently unrelated parents, our estimates of q are very similar to those of previous descriptive epidemiological studies. Finally, we inferred from simulation studies that the minimum sample size needed to use this approach is 25 patients either with unrelated or first cousin parents. These results show that the HI can be used to produce a ranking order of allele frequencies of autosomal recessive disorders, especially in populations with high rates of consanguineous marriages.
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Affiliation(s)
- Alessandro Gialluisi
- Unità Operativa di Genetica Medica, Dipartimento di Scienze Ginecologiche, Ostetriche e Pediatriche, Policlinico Sant'Orsola Malpighi, Università di Bologna, Bologna, Italy
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Patrinos GP, Al Aama J, Al Aqeel A, Al-Mulla F, Borg J, Devereux A, Felice AE, Macrae F, Marafie MJ, Petersen MB, Qi M, Ramesar RS, Zlotogora J, Cotton RGH. Recommendations for genetic variation data capture in developing countries to ensure a comprehensive worldwide data collection. Hum Mutat 2011; 32:2-9. [PMID: 21089065 PMCID: PMC3058135 DOI: 10.1002/humu.21397] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Developing countries have significantly contributed to the elucidation of the genetic basis of both common and rare disorders, providing an invaluable resource of cases due to large family sizes, consanguinity, and potential founder effects. Moreover, the recognized depth of genomic variation in indigenous African populations, reflecting the ancient origins of humanity on the African continent, and the effect of selection pressures on the genome, will be valuable in understanding the range of both pathological and nonpathological variations. The involvement of these populations in accurately documenting the extant genetic heterogeneity is more than essential. Developing nations are regarded as key contributors to the Human Variome Project (HVP; http://www.humanvariomeproject.org), a major effort to systematically collect mutations that contribute to or cause human disease and create a cyber infrastructure to tie databases together. However, biomedical research has not been the primary focus in these countries even though such activities are likely to produce economic and health benefits for all. Here, we propose several recommendations and guidelines to facilitate participation of developing countries in genetic variation data documentation, ensuring an accurate and comprehensive worldwide data collection. We also summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects. Hum Mutat 31:1–8, 2010. © 2010 Wiley-Liss, Inc.
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Mitropoulou C, Webb AJ, Mitropoulos K, Brookes AJ, Patrinos GP. Locus-specific database domain and data content analysis: evolution and content maturation toward clinical use. Hum Mutat 2011; 31:1109-16. [PMID: 20672379 DOI: 10.1002/humu.21332] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genetic variation databases have become indispensable in many areas of health care. In addition, more and more experts are depositing published and unpublished disease-causing variants of particular genes into locus-specific databases (LSDBs). Some of these databases contain such extensive information that they have become known as knowledge bases. Here, we analyzed 1,188 LSDBs and their content for the presence or absence of 44 content criteria related to database features (general presentation, locus-specific information, database structure) and data content (data collection, summary table of variants, database querying). Our analyses revealed that several elements have helped to advance the field and reduce data heterogeneity, such as the development of specialized database management systems and the creation of data querying tools. We also identified a number of deficiencies, namely, the lack of detailed disease and phenotypic descriptions for each genetic variant and links to relevant patient organizations, which, if addressed, would allow LSDBs to better serve the clinical genetics community. We propose a structure, based on LSDBs and closely related repositories (namely, clinical genetics databases), which would contribute to a federated genetic variation browser and also allow the maintenance of variation data.
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Affiliation(s)
- Christina Mitropoulou
- Erasmus MC, Faculty of Medicine and Health Sciences, MGC-Department of Cell Biology and Genetics, Rotterdam, The Netherlands
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Georgitsi M, Viennas E, Antoniou DI, Gkantouna V, van Baal S, Petricoin EF, Poulas K, Tzimas G, Patrinos GP. FINDbase: a worldwide database for genetic variation allele frequencies updated. Nucleic Acids Res 2010; 39:D926-32. [PMID: 21113021 PMCID: PMC3013745 DOI: 10.1093/nar/gkq1236] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Frequency of INherited Disorders database (FIND base; http://www.findbase.org) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. In addition to the regular data content updates, we report the following significant advances: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for 144 markers in 14 genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection, built around Microsoft's PivotViewer software (http://www.getpivot.com), based on Microsoft Silverlight technology (http://www.silverlight.net) that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics, a new open-access scientific journal, which would serve as a prime example of a non-profit model for sustainable database funding.
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Affiliation(s)
- Marianthi Georgitsi
- Department of Pharmacy, School of Health Sciences, Faculty of Engineering, University of Patras, Patras, Greece
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