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- Whole-genome sequencing-based surveillance system for Mycobacterium tuberculosis in PortugalPublication . Pinto, Miguel; Macedo, RitaTo improve TB surveillance and diagnosis, the Portuguese National Reference Laboratory (NRL) began implementing whole-genome sequencing (WGS) for all RR/MDR-TB cases in 2019. Since 2020, this approach has been expanded to indiscriminately include all received isolates. We describe the current WGS-based surveillance system in Portugal, framed in prospective and retrospective data (n = 1171), upgraded for antimicrobial resistance (AMR) prediction and epidemiological analysis. This system relies on three main steps: QC/QA and contamination assessment, with a novel data filtering step; genotyping and AMR prediction; and dynamic SNP-based approach, maximizing variable sites under analysis. While lineage 4 was the most prevalent (84.3 %) followed by lineage 2 (9.1 %), less common EU/EEA sub-lineages (e.g., lineages 3 and 6) showcased cross-border transmissions. Molecular clusters (n = 157) displayed distinct AMR profiles and diverse possible epidemiological contexts. Among the pipeline upgrades, we highlight: i) the novel filtering step that allowed the improvement of 123 out of 128 contaminated samples; ii) tolerating missing data per site more than doubled core variable site resolution; iii) automatic maximization of shared variable sites for in-depth cluster analysis, key for consolidating genetic links in epidemiological investigation. This study highlights the importance of sustained prospective genomic surveillance towards strengthening TB management and diagnosis in Portugal.
- Classification of genetic variants for clinical use – the case of Familial Hypercholesterolemia (Part 2) - How to classify LDLR variantsPublication . Chora, Joana RitaLecture on the Classification of Genetic Variants for Clinical Use – The Case of Familial Hypercholesterolemia (Part 2): How to Classify LDLR Variants, presented within the framework of Genetics and Genomics in Clinical Practice: Advanced Training. This advanced course is aimed at healthcare professionals seeking to understand, interpret, and apply genomic information in clinical practice in a critical, ethical, and effective manner, particularly physicians and professionals with a background in life sciences.
- Classification of genetic variants for clinical use – the case of Familial Hypercholesterolemia (part I)Publication . Bourbon, MafaldaLecture on the Classification of genetic variants for clinical use – the case of Familial Hypercholesterolemia (part I), presented within the framework of Genetics and Genomics in Clinical Practice: Advanced Training. This advanced course is aimed at healthcare professionals seeking to understand, interpret, and apply genomic information in clinical practice in a critical, ethical, and effective manner, particularly physicians and professionals with a background in life sciences.