Browsing by Issue Date, starting with "2019-05-10"
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- Impact of infant pneumococcal vaccination on pneumococcal pneumonia hospitalizations in older adultsPublication . Kislaya, Irina; Rodrigues, Ana Paula; Sousa-Uva, Mafalda; Gómez, Verónica; Gonçalves, Paulo; Froes, Filipe; Nunes, BaltazarPneumonia is an important cause of morbidity, mortality and expenditure of health resources. Since the introduction of conjugated pneumococcal vaccines (PCV) in infant immunization programs in 2000s, there is consistent evidence of pneumonia reduction in vaccinated children1. Limited data are available on indirect effect of infant immunization on pneumonia burden in unvaccinated population subgroups. This study aims to assess the indirect effect of the introduction of infant 7-valent (PCV7) and 13-valent (PCV13) pneumococcal conjugated vaccines on the pneumonia burden among adults aged 65 or more years in Portugal, comparing trends in Pneumococcal Pneumonia (PP) hospitalization rates before and after the introduction of the PCV7/PCV13.
- The Technology and Innovation Unit of the National Institute of Health: a sequencing and bioinformatics core facility specializing in public health genomicsPublication . Silva, Catarina; Ataíde Sampaio, Daniel; Mendonça, Joana; Carpinteiro, Dina; Duarte, Sílvia; Barreiro, Paula; Isidro, Joana; Machado, Miguel; Vieira, LuísThe National Institute of Health (INSA) is the state laboratory in the health sector. INSA has a long tradition in investigating the molecular etiology of genetic and complex diseases and in the identification of pathogenic organisms responsible for disease outbreaks and environmental imbalances. These activities benefit greatly from the existing centralized sequencing services provided by the Technology and Innovation Unit (UTI). Its mission includes performing sequencing and genotyping assays in the framework of research, diagnosis and epidemiological surveillance, as well as implementing data analysis pipelines for the study of variation in human genes. The equipment portfolio includes two next-generation sequencers and two capillary electrophoresis instruments for Sanger sequencing/fragment analysis, that altogether process an average of 36.000 samples/year. The team performed over 300 next-generation sequencing workflows for small genomes, amplicons, gene panels, clinical exome, 16S rRNA gene and RNA/microRNAs. Standard of operation procedures are conducted by trained technicians under a quality control system that includes external quality assessment and ISO 15189 accreditation. UTI plays a key role in public health genomics, providing state-of-the-art equipment, centralized resources, technical expertise and short response times for public health problems.
- Genomics and transcriptomics approach - diagnosis of a challenging case of Niemann-Pick type C (NP-C)Publication . Encarnação, Marisa; Coutinho, Maria Francisca; Cho, Soo-Min; Cardoso, Maria Teresa; Chaves, Paulo; Gaspar, Paulo; Santos, Juliana Inês; Ribeiro, Isaura; Quelhas, Dulce; Lacerda, Lúcia; Leão-Teles, Elisa; Futerman, Anthony H.; Vilarinho, Laura; Alves, SandraNP-C is a neurodegenerative Inherited Metabolic Disease with a heterogeneous clinical presentation, and due to mutations in either the NPC1 or NPC2 genes.We have studied a patient with clinical diagnosis of NP-C but presenting inconclusive results regarding molecular analysis.To better characterize this patient, we have performed NGS-based technologies (targeted DNA sequencing and single cell-RNA sequencing).For the molecular diagnosis we used a NGS gene panel followed by the analysis of cDNA.Latter, we used massively parallel single cell RNA-seq (MARS-Seq) to address gene profiling changes and characterize the pathomechanisms related to specific disease-causing mutations. Using our targeted NGS panel we identified two novel mutations in NPC1 gene.Next, through cDNA analysis of one of the patient parents we were able to understand the impact of the silent mutation.This mutation leads to exon skipping giving origin to an out-of-frame transcript and eliciting the nonsense-mediated decay pathway.Thus, we were not able to easily detect the mutant transcript which turned the molecular diagnosis more challenging. Apparently the presence of the other mutation (a missense mutation) impairs the NPC protein folding leading to its ER retention.The MARS-Seq analysis of this patient showed that a number of upregulated genes are related to the unfold protein response (UPR) and ER stress, which deserves further studies.
- The European 1M+ Genomes InitiativePublication . Moura Vicente, AstridPersonalised Medicine - concept: Characterisation of individuals’ phenotypes and genotypes (e.g. molecular profiling, medical imaging, lifestyle data) for tailoring the right therapeutic strategy for the right person at the right time, and/or to determine the predisposition to disease and/or to deliver timely and targeted prevention". According to: Horizon2020 and the European Council Conclusions on personalised medicine for patients (2015/C 421/03)
- Detection of structural variants in the human genome using nanopore sequencingPublication . Silva, Catarina; Vieira, LuísNanopore sequencing is a recent technology that allows direct real-time sequencing of DNA/RNA molecules with read lengths as long as the size of the original fragments. The characteristics of nanopore sequencing make it well suited for whole genome sequencing and as a preferential tool to identify structural variants (SV), namely those associated with tumours. In this work, we present a complete workflow to detect SV in tumour samples using nanopore sequencing. We used a tumour sample to prepare DNA libraries using the Rapid Sequencing kit (Oxford Nanopore Technologies-ONT), sequenced those on the MinION device (ONT) and implemented a pipeline for SV detection using multiple bioinformatics tools. The MinION generated a total of 2.34 Gb of sequence. Overall, 87.8% of reads had a quality (Q) value >7 (quality threshold). The longest read obtained had 74369 bases and the mean read length was of 4508 bases. A total of 3470 SV were identified, including deletions, duplications, translocations, insertions and inversions. Nanopore sequencing is a fast and sensitive approach of great potential for human genomics research, namely in the detection of SV in the human genome.