DPSPDNT - Apresentações orais em encontros internacionais
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- 1+MG Coordination GroupPublication . Kok, Ruben; Vicente, AstridThe “1+ Million Genomes” (1+MG) initiative is a cooperation mechanism involving by now 24 countries and was launched on Digital Day 2018. Countries meet on a regular basis in order to make sure that the aim of the 1+MG Declaration - to have at least 1 million sequenced genomes accessible in the EU by 2022 - is achieved. Genomics has the potential to revolutionise healthcare in many ways. It could lead to the development of more targeted personalised medicines, therapies and interventions. It could also enable better diagnostics, boost prevention and make more efficient use of scarce resources. From cancer, to rare diseases, neuro diseases and prevention, genomics can greatly improve health conditions of EU citizens. Equally important, genomics has the potential to improve the effectiveness, accessibility, sustainability and resilience of health systems in the European Union
- 1+Million Genomes Initiative /Beyond 1 Million Genomes CSA UpdatePublication . Vicente, AstridThe 1+ Million Genomes initiative has the potential to improve disease prevention, allow for more personalised treatments and support groundbreaking research. The '1+ Million Genomes' (1+MG) initiative aims to enable secure access to genomics and the corresponding clinical data across Europe for better research, personalised healthcare and health policy making. Since the Digital Day 2018, 22 EU countries, the UK and Norway signed Member States’ declaration on stepping up efforts towards creating a European data infrastructure for genomic data and implementing common national rules enabling federated data access. The initiative forms part of the EU’s agenda for the Digital Transformation of Health and Care and is aligned with the goals of the European Health Data Space.
- ABCG5 and ABCG8 variants associated to sitosterolemia in ClinVar – state of artPublication . Miranda, Beatriz Raposo; Alves, Ana Catarina; Bourbon, MafaldaSitosterolemia is a rare lipid disorder characterized by the accumulation of plant sterols in the blood, which can lead to several cardiovascular complications. This autosomal recessive disorder is due to pathogenic alterations in ABCG5 and ABCG8 genes. We aimed to assess ClinVar information regarding ABCG5/8 variants possibly causing sitosterolemia. ClinVar was consulted, and all variants submitted as related to “sitosterolemia” were considered (even if some of these were also associated with other phenotypes such as “cardiovascular phenotype”). ClinVar review status of two stars (multiple submissions, no conflicts), one star (single submissions or conflicting interpretations) and no stars (no assertion criteria provided) were considered. The file extracted for ABCG5 analysis contained 295 variants and the file extracted for ABCG8 contained 138 variants. In both files appeared variants mentioning both genes ABCG5/ABCG8 (=11). These were not considered for the descriptive analysis to avoid overcounting. Concerning ABCG5 variants (n=295), 24 are classified as pathogenic/likely pathogenic (3 with review status of two stars, 7 with one, and 6 with no stars); 67 as benign/likely benign (25 with two stars and 42 with one star). Additionally, 160 were classified as variants of uncertain significance (VUS) (61 with two stars, 98 with one, and 1 with no stars), and 44 have conflicting interpretations of pathogenicity (review status of one star). In the ABCG8 variants file (n=138), 16 are classified as pathogenic/likely pathogenic (7 with review status of two stars, 5 with one star, and 4 with no stars); and 26 as benign/likely benign (all with two stars). Additionally, 59 were found classified as VUS (28 with two stars and 31 with one star), and 37 have conflicting interpretations of pathogenicity (review status of one star). Despite there is information in ClinVar about these variants being found in homozygosity/compound heterozygosity in sitosterolemia patients (enabling a genotype-phenotype analysis), the great majority of variants in both genes lack other kind of information as functional characterization and in silico prediction analysis. ClinVar constitutes a fundamental tool for data sharing and to be consulted to know if a specific variant has been reported elsewhere but lacks other important information for variant classification. Although the majority are nonsense variants there are still many missense variants that need other type of information to be classified as pathogenic and this poses an important gap in sitosterolemia diagnosis. It remains crucial to improve the classification and knowledge of ABCG5/8 variants since the correct genetic diagnosis of sitosterolemia is vital for a personalized treatment.
- B1MG General Assembly meeting WP5 - Delivering Personalised Medicine cross borders: Implementation in Healthcare systems and Societal ImpactPublication . Vicente, Astrid; Scollen, Serena; Custers, IlseWP5 - Objectives: • O5.1: To define a B1MG maturity level model framework for profiling the maturity level of European healthcare systems and a path to optimisation of 1+MG data use in healthcare. • O5.2: To establish a roadmap as a guideline tool to support the progress towards implementation of genomic data in healthcare systems throughout Europe. • O5.3: To develop tools to assess the economic viability of the integration of genomics into healthcare in diverse European countries. • O5.4: To improve the understanding about the potential of genomic medicine in healthcare systems and promote knowledge exchange on implementation.
- Beyond 1M Genomes (B1MG)Publication . Vicente, AstridThe “1+ Million Genomes” (1+MG) initiative is a cooperation mechanism involving by now 24 countries and was launched on Digital Day 2018. Countries meet on a regular basis in order to make sure that the aim of the 1+MG Declaration - to have at least 1 million sequenced genomes accessible in the EU by 2022 - is achieved. Genomics has the potential to revolutionise healthcare in many ways. It could lead to the development of more targeted personalised medicines, therapies and interventions. It could also enable better diagnostics, boost prevention and make more efficient use of scarce resources. From cancer, to rare diseases, neuro diseases and prevention, genomics can greatly improve health conditions of EU citizens. Equally important, genomics has the potential to improve the effectiveness, accessibility, sustainability and resilience of health systems in the European Union
- Biomedical Knowledge Graph Embeddings for Personalized MedicinePublication . Vilela, Joana; Asif, Muhammad; Marques, Ana Rita; Xavier Santos, João; Rasga, Célia; Vicente, Astrid; Martiniano, HugoPersonalized medicine promises to revolutionize healthcare in the coming years. However significant challenges remain, namely in regard to integrating the vast amount of biomedical knowledge generated in the last few years. Here we describe an approach that uses Knowledge Graph Embedding (KGE) methods on a biomedical Knowledge Graph as a path to reasoning over the wealth of information stored in publicly accessible databases. We use curated databases such as Ensembl, DisGeNET and Gene Ontology as data sources to build a Knowledge Graph containing relationships between genes, diseases and other biological entities and explore the potential of KGE methods to derive medically relevant insights from this KG. To showcase the method’s usefulness we describe two use cases: a) prediction of gene-disease associations and b) clustering of disease embeddings. We show that the top gene-disease associations predicted by this approach can be confirmed in external databases or have already been identified in the literature. An analysis of clusters of diseases, with a focus on Autism Spectrum Disorder (ASD), affords novel insights into the biology of this paradigmatic complex disorder and the overlap of its genetic background with other diseases
- Clinical Research In Rare Diseases: The Example of HoFHPublication . Medeiros, AnaLecture on an Example of Homozygous Familial Hypercholesterolemia (HoFH), within the framework of Clinical Research in Rare Diseases.
- Comprehensive Genetic Analysis Provides Novel Insights Into The MicroRNA Regulatory Landscape of Autism Spectrum DisorderPublication . Marques, Ana Rita; Martiniano, Hugo; Santos, João Xavier; Vilela, Joana; Asif, Muhammad; Sousa, Lisete; Oliveira, Guiomar; Vicente, Astrid MouraBackground: Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a strong genetic component. Many risk genes are associated with ASD, however most of the genetic determinants are still unknown and a role for gene regulatory mechanisms is likely. MicroRNAs (miRNAs) regulate gene expression, playing key roles in neural development and function, and have been implicated in ASD onset and progression. Methods: To identify miRNA potentially associated with ASD, we conducted a comprehensive analysis of Single Nucleotide Variants (SNVs) and Copy Number Variants (CNVs) from ASD patients (N = 4300 and N = 3570, respectively) and control subjects (N = 67442 and N = 9649, respectively). We further performed functional enrichment analysis to understand the functional impact of these miRNAs variants. Results: Our results identified 28 miRNAs significantly enriched for putative disrupted SNVs and 31 miRNAs exclusively or more frequently targeted by CNVs in ASD cases, when compared to controls (α=0.05). These genes encode 70 mature miRNAs, including some novel and others previously implicated in ASD, that are predicted to target 2745 brain-expressed genes. Functional analysis indicates they are enriched in processes such as cellular signaling, gene regulation, protein metabolism, and chromatin structure, all of which are critical for ASD development. Interestingly, 44 of the identified miRNAs are predicted to regulate 71 genes strongly associated with increased ASD risk. Conclusion: This comprehensive gene-based analysis highlights miRNAs that regulate gene networks and cellular pathways essential for brain function and plasticity, which are often disrupted in ASD patients.
- Controlo da Qualidade em HemoglobinopatiasPublication . Miranda, ArmandinaExperiência do Controlo da qualidade em Hemoglobinopatias, pelo Grupo de Trabalho de Hematologia do Programa Nacional de Avaliação Externa da Qualidade (PNAEQ), INSA. As Hemoglobinopatias são doenças monogénicas hereditárias de transmissão autossómica recessiva resultantes de mutações que afetam os genes responsáveis pela síntese das cadeias de globina da hemoglobina, ou as suas regiões regulatórias.
- Controlo da Qualidade Laboratorial PLP na área clínica: ponto de situação - PortugalPublication . Vilaça, Manuela; Guimarães, Luís Filipe; Botelho, Mónica; Alves, HelenaExperiência do Laboratório de Hematologia/Química Clínica do INSA Porto no Controlo da qualidade interno (CQI) e Avaliação Externa da Qualidade (AEQ).