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EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow.

ABSTRACT: EPIGEN-Brazil is one of the largest Latin American initiatives at the interface of human genomics, public health, and computational biology. Here, we present two resources to address two challenges to the global dissemination of precision medicine and the development of the bioinformatics know-how to support it. To address the underrepresentation of non-European individuals in human genome diversity studies, we present the EPIGEN-5M+1KGP imputation panel-the fusion of the public 1000 Genomes Project (1KGP) Phase 3 imputation panel with haplotypes derived from the EPIGEN-5M data set (a product of the genotyping of 4.3 million SNPs in 265 admixed individuals from the EPIGEN-Brazil Initiative). When we imputed a target SNPs data set (6487 admixed individuals genotyped for 2.2 million SNPs from the EPIGEN-Brazil project) with the EPIGEN-5M+1KGP panel, we gained 140,452 more SNPs in total than when using the 1KGP Phase 3 panel alone and 788,873 additional high confidence SNPs (info score ? 0.8). Thus, the major effect of the inclusion of the EPIGEN-5M data set in this new imputation panel is not only to gain more SNPs but also to improve the quality of imputation. To address the lack of transparency and reproducibility of bioinformatics protocols, we present a conceptual Scientific Workflow in the form of a website that models the scientific process (by including publications, flowcharts, masterscripts, documents, and bioinformatics protocols), making it accessible and interactive. Its applicability is shown in the context of the development of our EPIGEN-5M+1KGP imputation panel. The Scientific Workflow also serves as a repository of bioinformatics resources.

SUBMITTER: Magalhaes WCS

PROVIDER: S-EPMC6028131 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow.

Magalhães Wagner C S WCS Araujo Nathalia M NM Leal Thiago P TP Araujo Gilderlanio S GS Viriato Paula J S PJS Kehdy Fernanda S FS Costa Gustavo N GN Barreto Mauricio L ML Horta Bernardo L BL Lima-Costa Maria Fernanda MF Pereira Alexandre C AC Tarazona-Santos Eduardo E Rodrigues Maíra R MR

Genome research 20180614 7

EPIGEN-Brazil is one of the largest Latin American initiatives at the interface of human genomics, public health, and computational biology. Here, we present two resources to address two challenges to the global dissemination of precision medicine and the development of the bioinformatics know-how to support it. To address the underrepresentation of non-European individuals in human genome diversity studies, we present the EPIGEN-5M+1KGP imputation panel-the fusion of the public 1000 Genomes Pro ...[more]

PMID: 29903722

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Project description:BackgroundRadiology is a useful tool for diagnosis and intervention in medical practice, and all the components within the teaching-learning process of this subject during undergraduate studies influence successful knowledge application.ObjectiveThis study aimed to describe the level of knowledge in radiology of students in the last two years of medical school and curricular characteristics of their courses in seven Latin American countries.MethodsA multicenter cross-sectional study was carried out on medical students of 7 Latin American countries (Bolivia, Brazil, Colombia, Ecuador, Mexico, Paraguay, and Peru) in their final two years of medical school, using an online questionnaire validated by experts and adapted for each country that assessed knowledge and curricular characteristics in radiology subject. Scores were assigned according to the number of correct answers for the knowledge test. The T-test, and regression analysis with one-way ANOVA were used to search for relationships between the level of knowledge and other variables.ResultsA total of 1514 medical students participated in this study. All countries had similar participation (n > 200); most participants were women 57.8%. The country with the highest knowledge score was Brazil. Male, sixth year (internship) and from public universities students had higher knowledge score (n < 0.05). Participants, who considered radiology more important, and who reported higher compliance with teaching staff with the proposed syllabus, and programmed classes, obtained better scores (n < 0.05).ConclusionsLatin American medical students included in this study have a regular overall level of knowledge of Radiology, apparently influenced by curricular differences such as class and academic program compliance. Efforts to better understand and improve academic training are indispensable.LimitationsThe study was subject to selection bias determined by non-probability convenience sampling. The questionnaire assessed only theoretical knowledge and the evaluation system was designed by the investigators.

Dataset Information

EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow.

Publications

EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow.

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