Browsing by Issue Date, starting with "2019-11-14"
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- Koolen-de Vries syndrome – National Case Series with clinical and molecular characterizationPublication . Soares, Marta P.; Rodrigues, Márcia; Dupont, Juliette; Medeira, Ana; Freixo, João; Nunes, Sofia; Cordeiro, Isabel; Travessa, André; Soares, Gabriela; Fortuna, Ana; Ramos, Fabiana; Sá, Joaquim; Rocha, Susana; Figueiredo, Cristina; Mendonça, Carla; Tapadinhas, Fernando; Silveira-Santos, Rosário; Custódio, Sónia; Barreta, Ana; Serafim, Sílvia; Correia, Hildeberto; Val, Mariana; Carreira, Isabel M.; Rendeiro, Paula; Sousa, Ana; Sousa, Ana BertaIntroduction: Koolen-de Vries Syndrome (KdVS) is a rare genetic condition, caused by a 17q21.31 microdeletion, or a pathogenic variant in KANSL1 gene. The clinical picture includes developmental delay (DD)/intellectual disability (ID) with expressive language particularly impaired, dysmorphisms, neonatal hypotonia, and friendly behaviour. Aim: To characterize at the molecular and clinical levels all patients in Portugal diagnosed with KdVS.
- Newborn whit a derivative chromosome X and ambiguous genitaliaPublication . Simão, Laurentino; Serafim, Sílvia; Brito, Filomena; Alves, Cristina; Silva, Marisa; Peliano, Ricardo; Ferreira, Cristina; Marques, Bárbara; Pedro, Sónia; Oliveira, Juliana; Branco, Tiago; Correia, HildebertoTranslocations involving the short arms of the X and Y in human chromosomes are uncommon. One of the primary functions of the X and Y chromosomes is gender phenotype determination. Here we report a newborn female with ambiguous genitalia and abnormal X chromosome. Karyotype was performed using the standard methods and Fluorescence in situ hybridization (FISH) directed for the SRY gene was used for confirmation of the clinical and cytogenetic suspicion. Chromosomal microarray analysis (CMA) was performed using CytoScan HD (Affimetrix®) to identified gains/loses on the der(X) chromosome. The analyse revealed one abnormal X chromosome in a female karyotype. Considering the ambiguous genitalia clinical information the abnormal X was considered to be compatible with a translocation X/Y. This was confirmed by the presence of signal for the SRY using FISH. CMA allowed to clarify a loss of 12.34 Mb at Xp22.33p22.2 and a gain of 7.41 Mb at Yp11.31p11.2 (ISCN = arr[GRCh37] Xp22.33p22.2(2703632_15050955)x1,Yp11.31p11.2(2650140_10059230)x1). The X deleted region includes several OMIM morbid genes, including CLCN4. Mutations in CLCN4 are associated with intellectual disability and impaired language development, and heterozygous females can be as severely affected as male. The gain on the Y encompasses nine OMIM genes, including the SRY gene, involved in the sexual male development. This additional information can be of great value for the child development. Translocations of segments of Y chromosome containing SRY are described in sexual reversion and true hermafroditism cases, which could explain the reason for referral for the newborn. Nevertheless, translocations between the X/Y chromosomes in females are expected to have a skewed inativation pattern in favour of the abnormal X and X-inativation studies could prove this likelihood. If a normal developmental of the child is observed over time this will be likely due to the preferable inativation of the abnormal X. Presently the child is about 1-year-old and she presents normal uterus, ovarian, and external genitalia, with absence of male gonads. No other clinical features have been identified.
- Decreasing and stabilising trends of antimicrobial consumption and resistance in Escherichia coli and Klebsiella pneumoniae in segmented regression analysis, European Union/European Economic Area, 2001 to 2018Publication . Peñalva, Germán; Högberg, Liselotte Diaz; Weist, Klaus; Vlahović-Palčevski, Vera; Heuer, Ole; Monnet, Dominique L; ESAC-Net study group; EARS-Net study groupInvestments to reduce the spread of antimicrobial resistance (AMR) in the European Union have been made, including efforts to strengthen prudent antimicrobial use. Using segmented regression, we report decreasing and stabilising trends in data reported to the European Surveillance of Antimicrobial Consumption Network and stabilising trends in data reported to the European Antimicrobial Resistance Surveillance Network. Our results could be an early indication of the effect of prioritising AMR on the public health agenda.
- Presumed TP53 mosaicism: variants detected using a NGS hereditary cancer multigene panelPublication . Rodrigues, Pedro; Theisen, Patrícia; Rodrigues, Márcia; Silva, Catarina; Vieira, Luís; Gonçalves, JoãoAims/Context: NGS multigene panels are routinely used to identify germline pathogenic variants in cancer susceptibility genes. In addition, NGS allows the identification of low-level mosaicism events that may not be detectable by conventional Sanger sequencing. We describe two cases of presumed TP53 mosaic variants detected by NGS on blood-derived DNA, and confirmed by ARMS-PCR and Sanger sequencing. Case 1: female, 87 years old, colon cancer at 83 and metachronous breast cancer at 86, no history of familial cancer. Case 2: female, 75 years old, ovarian cancer at 71, local relapse at 74. Methods: NGS using TruSight® Cancer Sequencing Panel and TruSight® Rapid Capture kit (Illumina) and paired-end sequencing on MiSeq® platform (Illumina). Bioinformatic analysis with MiSeq Reporter, Enrichment, VariantStudio, VEP, Alamut Visual, VarAFT, VarSome and IGV. ARMS-PCR and Sanger sequencing were used to confirm the TP53 variants. Results and Conclusions: Two cases of presumed TP53 mosaic variants were studied. Case 1: the missense alteration TP53: c.764T>G, p.(Ile255Ser) was detected with a variant allele frequency (VAF) of 26% (39/150 reads). This variant is described in ClinVar as a somatic alteration, classified as likely pathogenic. It is not reported in gnomAD and VarSome software classified it as a variant of uncertain significance. Case 2: missense variant TP53: c.524G>A, p.(Arg175His) detected with a VAF of 15% (10/58 reads). This variant is described as pathogenic in HGMD Professional, LOVD and ClinVar, in association with Li-Fraumeni syndrome. These two cases seem to represent TP53 mosaicism, supported by: i) VAF lower than 30%, ii) detection at the sensitivity limit of Sanger sequencing and iii) confirmation by ARMS-PCR. Confirming this hypothesis by studying tumor and other tissue samples and offspring analysis (underway in both cases), is essential for disease diagnosis, assessing recurrence risk and genetic counseling. The hypothesis of acquired aberrant clonal expansion limited to the hematologic compartment, versus a germline variant should be considered in similar cases, and confirmatory methodologies are mandatory.
- Avaliação externa da qualidade e acreditação do diagnóstico molecular da alteração JAK2: p.Val617Phe em neoplasias mieloproliferativasPublication . Silva, Elizabeth; Fonseca, Pedro; Theisen, Patrícia; Isidro, Glória; Vieira, Luís; Gonçalves, JoãoA Qualidade no diagnóstico molecular em genética humana é uma presença constante na rotina da nossa Unidade. A participação em programas de Avaliação Externa da Qualidade (AEQ), nomeadamente no United Kingdom National External Quality Assessment Service for Leucocyte Immunophenotyping (UK-NEQAS LI), é fundamental para manter o laboratório atualizado a nível das recomendações sobre as boas práticas em diagnóstico molecular, permitindo também a comparação do desempenho com outros laboratórios europeus e melhorar os relatórios dos testes genéticos. A nossa Unidade participa desde 2007 no programa de AEQ do UK-NEQAS LI para a deteção da alteração JAK2:p.Val617Phe (V617F), essencial no diagnóstico de neoplasias mieloproliferativas. Neste programa de AEQ, realizado três vezes por ano, são fornecidas amostras de linhas celulares liofilizadas para avaliação da presença/ausência da referida alteração. Os resultados dos ensaios e os detalhes da metodologia utilizada, são submetidos anonimizados à entidade organizadora. Desde o início da nossa participação nesta AEQ até 2018, foram analisadas 57 amostras. Destas, a alteração estava presente em 40 amostras e ausente em 17, sem falsos positivos ou falsos negativos. Os resultados todos validados pela entidade organizadora da AEQ, para além de confirmarem a reprodutibilidade, representatividade e repetibilidade para este teste genético, permitem validar anualmente a metodologia usada garantindo a sua especificidade e sensibilidade. Em conformidade com as recomendações específicas da Organização para a Cooperação e Desenvolvimento Económico (OCDE) para controlo de qualidade no diagnóstico genético molecular, possuímos desde 2018 acreditação para a pesquisa da alteração JAK2: p.Val617Phe (V617F), atribuída pelo Instituto Português de Acreditação (IPAC) no âmbito da norma ISO 15189. A acreditação ao abrigo desta norma é exigente, contribui para melhorar os testes genéticos na sua globalidade, pois compreende não só requisitos técnicos, como também requisitos de gestão. Esta acreditação contribui para melhorar a qualidade laboratorial a vários níveis, confere credibilidade, competência técnica e confiança. A acreditação e a participação na AEQ em causa, contribuem para melhorar o diagnóstico molecular dos doentes, para reduzir tempos de resposta, refletindo-se numa melhor vigilância e tratamento dos doentes.
- Biological effects of cellulose nanofibrils in a lung epithelial cell linePublication . Teixeira, Sara Antunes de Almeida; Louro, Henriqueta; Silva, Maria JoãoCellulose nanofibrils (CNFs) are plant-derived nanomaterials, showing advantageous physicochemical properties, renewable nature and low cost. CNFs have great potential in several industries, including forest, food, pharmaceutical and biomedicine, as drug-delivery systems or for tissue repair and regeneration. The increased production and application of CNFs leads to greater exposure of both workers and consumers, being extremely important to evaluate possible negative outcomes for human health. Due to their similarities with other fibers, such as carbon nanotubes, they may reveal adverse effects, such as carcinogenesis. The objective of this work was to evaluate the biosafety of CNFs produced by different pre-treatments - TEMPO-mediated oxidation and enzymatic hydrolysis - from a bleached industrial Eucalyptus globulus kraft pulp. For this purpose, the internalization, cytotoxicity and genotoxicity of these CNFs was analysed through different parameters: intracellular localization, cell viability and chromosome damage. Human lung epithelial cells (A549) were used, since the most frequent route of exposure is inhalation of CNFs, especially in occupational context. Preliminary results suggested that CNFs may not be internalized. Both CNFs did not show cytotoxicity and genotoxicity effects, regardless of dose and exposure time. However, an increase in cell proliferative capacity was observed when exposed to both types of CNFs. In conclusion, although the studied CNFs have different properties, in vitro safety assessment in A549 cells confirmed that both are biocompatible and showed a stimulating action on cell proliferation that needs to be explored through other parameters or in vivo assays. Understanding the physicochemical properties that possibly influence biological effects will contribute to a safe-by-design approach, enabling a more responsible and sustainable development of CNFs.