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- Detection and Identification of Haemoglobin Variants: Experience with a Point of Care Test - GazellePublication . Fernandes, Lilia; Seuanes, Filomena; Vieira, Cristina; Martins, Silvia; Samuel, Luzia; Chico, Marta; Costa, Alcina; Miranda, ArmandinaThe aim of this study was to evaluate the performance of a point-of-care test (POCT) – Gazelle, a cellulose acetate electrophoresis rapid test in the detection and identification of Hb variants, in comparison with the diagnostic methods used in the laboratory, with a view to future implementation of this equipment in African countries.
- Alle Frequency Distribution Of Clinicaly Relevant Pharmacogenetic Variants In Genes With CPIC Guidelines Across European Populations: A Scoping ReviewPublication . Simões, Raquel; Cardoso, Maria Luis; Martiniano, Hugo F. M. C.; Vicente, Astrid MouraIntroduction: Pharmacogenetics (PGx) is the study of how genetic variants affect drug response. PGx variants can affect either pharmacokinetics – the processes of drug absorption, distribution, metabolism, and elimination – or pharmacodynamics – the biochemical and physiological effects of drugs and their mechanisms of action. Pharmacokinetics gene variants often define haplotypes, which are described using the star (*) allele nomenclature for genes such as those in the Cytochrome P450 (CYP450) family. This results in phenotypes of normal, rapid, ultrarapid, or poor metabolisers, leading to various drug responses (1). In recognition of the importance of understanding the clinical impact of PGx variants, the Clinical Pharmacogenetics Implementation Consortium (CPIC) has developed guidelines that translate PGx test results into clinical recommendations for drug selection and dosing (2). Reports in the literature on ancestry‑related differences in drug response highlight the need for a broader investigation of PGx variants, namely in CYP450 genes, across diverse groups(3).
- From Uncertainty To Diagnosis: Functional Reclassification Of LDLR Variants In Familial HypercholesterolemiaPublication . Chora, Joana Rita; Islam, Mohammad Majharul; Alves, Ana Catarina; Pfisterer, Simon; Bourbon, MafaldaObjectives: Familial hypercholesterolaemia (FH) is a common disorder of lipid metabolism marked by an increased risk of premature atherosclerotic cardiovascular disease. While genetic testing confirms diagnosis, many LDLR variants are classified as variants of uncertain significance (VUS) due to lack of evidence, limiting clinical actionability. Functional assays can support reclassification, but conventional approaches are time-consuming. This study aims to use a high-throughput functional pipeline to evaluate LDLR VUS and improve diagnostic precision in FH. Methods: We analysed 133 LDLR VUS lacking functional evidence using an automated analysis platform based on multiplexed high-content imaging to quantify LDL uptake. Variants were classified based on uptake relative to wild-type: <70% for PS3_Supporting (pathogenic) and >90% for BS3_Supporting (benign), according to LDLR-specific ACMG/AMP guidelines. A subset of 46 “hot VUS” required only one supporting criterion to reach a likely benign or likely pathogenic classification. Results: Of the 133 variants, 53 showed <70% uptake and were assigned PS3_Supporting, while 41 showed >90% uptake and received BS3_Supporting. The remaining 39 variants exhibited intermediate activity (70–90%). Among the 46 hot VUS, 12 were reclassified as likely benign and 11 as likely pathogenic. An additional 43 variants are now one supporting criterion away from potential reclassification. Conclusions: High-throughput functional testing provides robust and rapid evidence for LDLR variant interpretation. By adding evidence about LDLR activity these assays contribute to resolve diagnostic uncertainty and enables earlier and more accurate diagnosis, optimizes cascade screening, and enables better risk stratification to inform treatment options. These findings support a shift toward personalised genomic medicine in lipid disorders, with direct implications for patient care and cardiovascular risk reduction.
- MODY em Contexto Clínico: Impacto do Diagnóstico Genético na Tomada de Decisão TerapêuticaPublication . Vaz, Margarida; Gaspar, Gisela; Dario, Paulo; Bourbon, MafaldaA diabetes monogénica representa 1–5% dos casos de diabetes, destacando-se o subtipo MODY, causado por variantes em 14 genes, dos quais GCK, HNF1A, HNF1B e HNF4A são os mais comuns. Este estudo teve como objetivo identificar casos de diabetes tipo MODY, apoiar a decisão clínica e detetar familiares em risco. Foram analisados 79 casos índex de várias regiões de Portugal e 45 familiares, através de sequenciação por PCR dos quatro genes principais e pesquisa de grandes rearranjos por MLPA. Variantes patogénicas ou provavelmente patogénicas foram encontradas em 48% dos casos índex, e 29 familiares receberam também o diagnóstico de MODY, sendo o gene GCK o mais frequentemente afetado. Até agora, 67 indivíduos foram identificados com variantes causadoras de MODY. A ausência de variantes em metade dos casos índex pode dever-se à não análise de todos os genes associados ou a etiologia poligénica. O diagnóstico molecular revelou-se essencial para orientar a terapêutica personalizada nestes doentes.
- Allele frequency distribution of clinically relevant pharmacogenetic variants across European populations: A Scoping ReviewPublication . Simões, Raquel D.; Cardoso, Maria L.; Martiniano, Hugo F. M. C.; Vicente, Astrid M.Review of the literature on the distribution of pharmacogenetic variants in European populations.. Pharmacogenetics (PGx) is the study of how genetic variants affect drug metabolism, transport and target interactions, impacting efficacy and risk of adverse reactions. PGx variants can affect either pharmacokinetics – the processes of drug absorption, distribution, metabolism and elimination of drugs -or pharmacodynamics - the biochemical and physiological effects of drugs and their mechanisms of action. Pharmacokinetics gene variants often define haplotypes, which are described using the star (*) allele nomenclature for genes such as those in the Cytochrome P450 (CYP450) family. This results in phenotypes of normal, rapid, ultrarapid or poor metabolisers, leading to various drug responses 1. In recognition of the importance of understanding the clinical impact of PGx variants, the Clinical Pharmacogenetics Implementation Consortium (CPIC) has developed guidelines that translate PGx test results into clinical recommendations for drug dosing 2. Reports in the literature of ancestrality differences in drug response highlight the need for a broader investigation of PGx variants, namely in CYP450 genes, across diverse groups.
- Biomarker of Chronic Alcohol Abuse – Carbohydrate-deficient Transferrin (CDT): Methodology VerificationPublication . Gomes, Filomena; Costa, Alcina; Fernandes, Lília; Silva, Ana Maria V. da; Vasconcelos, Miguel; Miranda, ArmandinaIntroduction: Transferrin is a glycoprotein synthesized in hepatocytes that can appear with different isomorphic forms in the plasma, acquiring different levels of sialization (1,2). In a healthy person, penta, tetra and trisial isoforms are detectible in plasma. However, in an alcohol abuse and/or dependence, asialo, monosialo and disialotransferrin isoforms are also present called carbohydrate-deficient transferrin (CDT) (3) . This is considered a specific biomarker of alcohol abusive and/or dependence, being useful in the diagnosis and monitoring of this pathology (4) . Aim: Verify compliance with the requirements of the manufacturer of the capillary electrophoresis method in laboratory practice and its suitability in determining the CDT. Materials and methods: The MiniCap System (Sebia) was used with calibrators traceable to the IFCC international reference procedure and normal and pathological internal control samples. Repeatability and intermediate precision tests were performed on control samples. From participation in External Quality Assessment (EQA) program (5 rounds - 2 samples each), Bias%, Deviation Index (DI) and Total Laboratory Error (TELab) were obtained. The Measurement Uncertainty was calculated by the Top Down Method (combined and expanded with a factor of 1.96), using the internal (CV%) and external (Bias%) quality control results. Results: In the repeatability tests, normal control samples (n=22, mean = 1.4%) were obtained, CV = 5.7%; for the pathological sample (n=24, mean = 5.4%), CV = 2.2%. In intermediate precision tests for the normal control sample, (n= 12, mean = 1.4%), CV = 6.7%; for the pathological sample (n=12, mean = 5.3%), CV = 4.9%. In samples from EQA program, mean Bias = -1.0% and TELab = 11.5. In the evaluation of the method by DI, 1 satisfactory, 7 good and 2 excellent results were obtained. The obtained Expanded Uncertainty (1.3% ± 0.3) is consistent with that indicated by the manufacturer. Conclusion: The TELab obtained meets Westgard`s desirable specifications (5) , being considered an appropriate methodology for use in laboratory practise for diagnosis. However, it is considered important to monitor the method with Internal Control samples, and participate in EQA programs, as well as periodic evaluation of Quality Indicators.
- Avaliação de diferenças bioquímicas entre indivíduos diabéticos com e sem variantes patogénicas causadores de MODY. (PO 47)Publication . Vaz, Margarida; Gaspar, Gisela; Agapito, Ana; Neves, Ana Carolina; Bogalho, Ana Paula; Almeida, Bruno; Pereira, Carla; Fonseca, Fernando; Lobarinhas, Goreti; Luiz, Henrique Vara; Duarte, João Sequeira; Sampaio, Maria de Lurdes; Dario, Paulo; Bourbon, MafaldaA diabetes tipo MODY (Maturity-onset diabetes of the young) é um tipo de diabetes causada por mutações em um único gene. Existe 14 genes associados a essa doença, no entanto, a maioria dos casos de MODY é causada por alterações nos genes GCK, HNF1A, HNF1B e HNF4A. Cada subtipo desta patologia apresenta características fenotípicas, metabólicas e complicações para a saúde distintas o que exige uma adequação terapêutica diferente. Contudo a grane maioria dos casos de MODY é erroneamente diagnosticada como diabetes tipo 1 ou tipo 2, o que prejudica o diagnóstico do doente. O objetivo deste trabalho consiste na caracterização bioquímica dos participantes do Estudo Molecular de diabetes tipo MODY com base nos valores de glicémia e hemoglobina A1c inicial, indicados nos inquéritos do estudo, pelos médicos que os referenciaram, para perceber se estes valores são ou não um bom indicador de diabetes tipo MODY. Para tal foram analisados os valores de 76 participantes do estudo, com e sem mutação. Para análise estatística dos valores utilizou-se o Rstudio. Com os testes de Shapiro e Wilcox para avaliou-se e distribuição das amostras, bem como as diferenças entre os dois grupos. Os resultados desta análises não revelaram diferença estatística significativa (valor p=0.5) entre os valores de glicémia inicial dos participantes do estudo com mutação e sem mutação, nem com os valores de hemoglobina A1c (valor p= 0.19). Os resultados apresentados sustentam o argumento de que não é possível identificar corretamente pacientes com diabetes tipo MODY apenas com base nos resultados bioquímicos da glicémia e da hemoglobina A1c e que o diagnóstico genético é essencial para que o conceito de medicina personalizada seja uma realidade acessível aos pacientes diabéticos em Portugal.
- Ancestry of the major long-range regulatory site of the α-globin genes in the Portuguese population with the common 3.7kb α-thalassemia deletionPublication . Pena, Rita; Lopes, Pedro; Gaspar, Gisela; Miranda, Armandina; Faustino, PaulaThe α-major regulatory element (known as HS-40) has a crucial role in the long-range regulation of the α-globin gene expression. This element is genetically polymorphic and six haplotypes (A to F) have been identified in different populations, with haplotype D almost exclusively found in African populations. This study aimed to identify the HS-40 haplotype associated with the common 3.7kb α-thalassemia deletion (-α3.7del) in the Portuguese population, and investigate its ancestry. We searched for the -α3.7del in 111 selected Portuguese individuals by Gap-PCR. In addition, a DNA fragment containing the HS-40 was amplified by PCR and Sanger sequenced. Statistical analysis was performed using R software. Fifty individuals have the wild-type α-globin genotype (group I), 34 are heterozygous for the -α3.7del (group II) and 27 are homozygous (group III). Regarding the HS-40, four haplotypes were found (A to D). The distribution of HS-40 haplotypes and genotypes are significantly different between groups with and without the -α3.7del (p<0.001), being haplotype D and genotype AD the most prevalent in group III. Furthermore, multiple correspondence analysis revealed that individuals without the -α3.7del are grouped with other European populations, while samples with the -α3.7del are split from these and found more related to the African population. This study revealed for the first time an association of a specific HS-40 haplotype with the -α3.7del in the Portuguese population, and its likely African ancestry. These results may have a clinical importance as in vitro analysis of haplotype D showed a descrease in its enhancer activity on α-globin genes.
- Next Generation Sequencing – a key tool for diagnosis of Familial DyslipidemiasPublication . Miranda, B.; Alves, A.C.; Bourbon, M.Dyslipidemia, a clinical condition defined by abnormal lipid concentrations in blood, can have a genetic etiology. Familial dyslipidemias are a group of genetic diseases, the majority being rare, associated with several serious conditions. Raised triglyceride levels are associated with pancreatic/hepatic complications. Elevated cholesterol levels promote atherosclerosis and increase patients' cardiovascular risk, and low levels of this particle are associated with neurological manifestations and poor weight progression. Nowadays, with the advance in genome sequencing technologies, the investigation and diagnosis of these disorders is expanding
- Deletional alpha-thalassemia and hematological phenotype: predictive parameters of different deletionsPublication . Gaspar, Gisela; Ramalho, Rita de Mira; Seuanes, Filomena; Feliciano, Carla; Duarte, Guida; Copeto, Sandra; Costa, Alcina; Santos, João Xavier; Miranda, ArmandinaIntroduction: Thalassemias are characterized by a quantitative imbalance of the globin chains due to the reduction or suppression of the synthesis of one of the globin chains.The hematological tests usually used as indicative for the investigation of α-thalassemia are the blood count with MCV (Mean Cell Volume) < 80 fL and/or MCH (Mean Cell Hemoglobin) < 27 pg and normal Hb A2 (< 3.5%). Aim: This study aimed to correlate the different deletional α-thalassemia genetic alterations with the corresponding hematological phenotype, based on casuistry from 2015 to 2019. Methodology: Was evaluated retrospectively 496 cases suspected of deletional α-thalassemia from 2015 to 2019 and correlated them with the hematological data available. We searched for α-thalassemia deletions by Gap-PCR and Multiplex Gap-PCR. Haematological evaluation was carried out by the erythrogram, Hb isoelectric focusing and quantification of Hb A2 and Hb F (Ion exchange high performance liquid chromatography). The statistical analysis of the results was carried out through calculating the mean, standard deviation, median, and t-Student test, with a significance level of 0.05. Results and discussion: Most patients (n=190) had a normal genotype (αα/αα), followed by heterozygosity (-α3.7/αα) (n=148) and homozygosity (-α3.7/α3.7) (n=141) for the 3.7kb deletion. We also detected 5 cases of heterozygosity for the 4.2Kb deletion (-α4.2/αα), 4 of double heterozygosity (α3.7/α4.2), 7 heterozygosity α0 (--SEA /αα) and 1 of HbH (--SEA/-α3.7). The results showed that the MCV and the MCH are excellent hematological indices for screening and selection of patients for molecular testing (their value being the lower the greater the number of deleted genes). Our results are in line with those described in the literature and reinforce that the cut-off value of 25 pg (MCH) is sensitive enough to infer the presence of α0 -thalassemia deletion. The detection of the α0 deletion is very important in preventing the occurrence of Hb Bart's in the offspring of a carrier couple. The diagnosis of deletional α-thalassemia is realised by genetic testing, however hematological indices are relevant predictive markers of the number of deleted alpha genes and the phenotype /genotype correlation.