Browsing by Author "Pereira-Caetano, Iris"
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- Aplicação da sequenciação de nova geração ao diagnóstico genético do cancro da mama hereditárioPublication . Theisen, Patrícia I.; Silva, Catarina; Pereira-Caetano, Iris; Rodrigues, Pedro; Isidro, Glória; Vieira, Luís; Gonçalves, JoãoIntrodução: O cancro da mama hereditário (CMH) constitui 5-10% dos casos de cancro da mama, dos quais cerca de 30% se devem a mutações germinais de elevada penetrância nos genes BRCA1 e BRCA2. Embora tenham sido identificadas mutações noutros genes de suscetibilidade para cancro da mama, estas são raras, pelo que a análise sequencial de múltiplos genes se torna ineficaz e dispendiosa pelos métodos convencionais(1,2). A determinação da causa genética subjacente ao CMH permite não só identificar os indivíduos com risco aumentado de cancro da mama, como oferecer uma medicina personalizada, mais eficaz na redução da incidência de cancro da mama assim como da morbilidade e mortalidade associadas(3). A sequenciação de nova geração (NGS) veio possibilitar a pesquisa de mutações em múltiplos genes em simultâneo, permitindo um diagnóstico molecular rápido, eficaz e com custo inferior ao da sequenciação de Sanger. Objetivos: Otimizar o diagnóstico molecular do CMH através da implementação de um protocolo de NGS baseado num painel abrangente de genes de suscetibilidade para cancro da mama. A 1ª fase de concretização deste objetivo consistiu em validar a utilização da NGS na deteção de mutações nos genes BRCA1, BRCA2 e TP53. Material e métodos: Foram analisadas por NGS 12 amostras de doentes com cancro da mama, previamente sequenciadas pelo método de Sanger para os genes BRCA1, BRCA2 e TP53. As bibliotecas de sequências-alvo foram preparadas a partir de DNA genómico pelo método de captura por hibridação, num protocolo que integrou o Trusight Cancer Sequencing Panel e o kit TruSight Rapid Capture (Illumina), e sequenciadas numa plataforma MiSeq com leituras paired-end de 150 bp. A análise bioinformática incluiu os softwares MiSeq Reporter, VariantStudio e Isaac Enrichment (Illumina). Resultados: Foram detetadas por NGS um total de 97 variantes de sequência nos genes BRCA1, BRCA2 e TP53, das quais 35 são variantes únicas (33 single nucleotide variants e 2 deleções), numa concordância de 100% com a sequenciação de Sanger. Conclusões: Estes resultados preliminares comprovam a eficiência da NGS na deteção de variantes em 3 genes de elevada penetrância para cancro da mama e abrem caminho para a oferta de um painel de genes de suscetibilidade para cancro da mama que permitirá um diagnóstico molecular do CMH mais abrangente, rápido e com custos reduzidos relativamente à sequenciação de Sanger. Bibiografia 1. Tung N, Batteli C, Allen B et al. (2015). Frequency of mutations in individuals with breast cancer referred for BRCA1 and BRCA2 testing using next-generation sequencing with a 25-gene panel. Cancer, 121: 25-33. 2. Apostolou P, Fostira F (2013). Hereditary breast cancer: the era of new susceptibility genes. BioMed Res Int, 2013: 747318. 3. Ellsworth R, Decewicz D, Shriver C, Ellsworth D (2010). Breast cancer in the personal genomics era. Curr Genomics, 11: 146-161.
- Assessing the impact of Copy Number Variation on severe spermatogenic impairment with exome dataPublication . Lopes, Alexandra; Nagirnaja, Liina; Filipa, Carvalho; Gonçalves, João; Fernades, Susana; Pereira-Caetano, Iris; Almstrup, Kristian; Rajpert-De Meyts, Ewa; Seixas, Susana; Houston, Brendan; Barros, Alberto; O’Bryan, Moira; Aston, Kenneth; Conrad, Donald; on Behalf of the GEMINI ConsortiumBackground: Azoospermia, the most severe form of male infertility, affects approximately 1% of men worldwide and in the great majority of the cases the etiology of the disease remains unidentified. Given the large number of genes involved in spermatogenesis it is likely that a proportion of cases of idiopathic azoospermia have a genetic basis. We have previously described, using SNP arrays, an excess of low frequency copy number variants (CNVs) in both the autosomes and the sex chromosomes in non-obstructive azoospermia (NOA) suggesting an heterogeneous genetic ethiology for this condition.
- Avaliação da Frequência de Microdelecções AZF e alterações do cariótipo na OligospermiaPublication . Pereira, Isabel; Barros, Joana; Aguiar, Ana; Sousa, Sandra; Nunes, Joaquim; Rodrigues, Cátia; Soares, Ana Paula; Pereira-Caetano, Iris; Gonçalves, João; Calhaz Jorge, CarlosA infertilidade masculina é uma entidade complexa que afecta um número importante de homens, permanecendo a sua etiologia desconhecida em muitas situações. Alterações do cariótipo podem contribuir para diminuir a quantidade e qualidade dos espermatozóides. A elucidação de eventual base genética subjacente pode ajudar a determinar a razão da alteração espermática e abrir novas perspectivas para tratamentos eficazes. A região AZF (azoospermia factor) do cromossoma Y contém genes essenciais para a espermatogénese.
- Common Variation in the PIN1 Locus Increases the Genetic Risk to Suffer from Sertoli Cell-Only SyndromePublication . Cerván-Martín, Miriam; Bossini-Castillo, Lara; Guzmán-Jimenez, Andrea; Rivera-Egea, Rocío; Garrido, Nicolás; Luján, Saturnino; Romeu, Gema; Santos-Ribeiro, Samuel; Castilla, José A.; Gonzalvo, M. Carmen; Clavero, Ana; Vicente, F. Javier; Maldonado, Vicente; González-Muñoz, Sara; Rodríguez-Martín, Inmaculada; Burgos, Miguel; Jiménez, Rafael; Pinto, Maria Graça; Pereira, Isabel; Nunes, Joaquim; Sánchez-Curbelo, Josvany; López-Rodrigo, Olga; Pereira-Caetano, Iris; Marques, Patricia Isabel; Carvalho, Filipa; Barros, Alberto; Bassas, Lluís; Seixas, Susana; Gonçalves, João; Larriba, Sara; Lopes, Alexandra M.; Carmona, F. David; Palomino-Morales, Rogelio J.We aimed to analyze the role of the common genetic variants located in the PIN1 locus, a relevant prolyl isomerase required to control the proliferation of spermatogonial stem cells and the integrity of the blood-testis barrier, in the genetic risk of developing male infertility due to a severe spermatogenic failure (SPGF). Genotyping was performed using TaqMan genotyping assays for three PIN1 taggers (rs2287839, rs2233678 and rs62105751). The study cohort included 715 males diagnosed with SPGF and classified as suffering from non-obstructive azoospermia (NOA, n = 505) or severe oligospermia (SO, n = 210), and 1058 controls from the Iberian Peninsula. The allelic frequency differences between cases and controls were analyzed by the means of logistic regression models. A subtype specific genetic association with the subset of NOA patients classified as suffering from the Sertoli cell-only (SCO) syndrome was observed with the minor alleles showing strong risk effects for this subset (ORaddrs2287839 = 1.85 (1.17-2.93), ORaddrs2233678 = 1.62 (1.11-2.36), ORaddrs62105751 = 1.43 (1.06-1.93)). The causal variants were predicted to affect the binding of key transcription factors and to produce an altered PIN1 gene expression and isoform balance. In conclusion, common non-coding single-nucleotide polymorphisms located in PIN1 increase the genetic risk to develop SCO.
- Congenital adrenal hyperplasia in paediatric age: molecular analysis of the CYP21A2 gene and implications for genetic counsellingPublication . Gomes, Susana; Silva, Júlia; Pereira-Caetano, Iris; Lopes, Lurdes; Limbert, Catarina; Amaral, Daniela; Pina, Rosa; Kay, Teresa; Sampaio, Lurdes; Pereira, Carla; Moldovan, Oana; Berta, Ana; Rebelo, Irene; Gaspar, Isabel; Cidade Rodrigues, José; Lina, Ramos; Ramos, Fabiana; Dinis, Isabel; Cardoso, Rita; Mirante, Alice; Gonçalves, JoãoIntroduction: Congenital adrenal hyperplasia(CAH) is due to 21-hidroxilase deficiency(21-OHD) in about 95% of the cases. 21-OH is encoded by CYP21A2 gene, and most frequent mutations occurring in CYP21A2 are due to gene conversions originated from its pseudogene(CYP21A1P). The clinical severity of CAH is associated with the impairment of 21-OH activity, which is directly related with the molecular defect. CAH is classified as classic salt-wasting(SW) and simple virilising(SV) forms, and nonclassic(NC) form of the disease. SW and SV are usually diagnosed after birth or during the first years of life, respectively, while most cases of NC-CAH are diagnosed during infancy, puberty or until adult age. Here we present the molecular results performed in paediatric patients with CAH.
- Contribution of TEX15 genetic variants to the risk of developing severe non-obstructive oligozoospermiaPublication . Guzmán-Jiménez, Andrea; González-Muñoz, Sara; Cerván-Martín, Miriam; Rivera-Egea, Rocío; Garrido, Nicolás; Luján, Saturnino; Santos-Ribeiro, Samuel; Castilla, José A.; Gonzalvo, M. Carmen; Clavero, Ana; Vicente, F. Javier; Maldonado, Vicente; Villegas-Salmerón, Javier; Burgos, Miguel; Jiménez, Rafael; Pinto, Maria Graça; Pereira, Isabel; Nunes, Joaquim; Sánchez-Curbelo, Josvany; López-Rodrigo, Olga; Pereira-Caetano, Iris; Marques, Patricia Isabel; Carvalho, Filipa; Barros, Alberto; Bassas, Lluís; Seixas, Susana; Gonçalves, João; Lopes, Alexandra M.; Larriba, Sara; Palomino-Morales, Rogelio J.; Carmona, F. David; Bossini-Castillo, LaraBackground: Severe spermatogenic failure (SPGF) represents one of the most relevant causes of male infertility. This pathological condition can lead to extreme abnormalities in the seminal sperm count, such as severe oligozoospermia (SO) or non-obstructive azoospermia (NOA). Most cases of SPGF have an unknown aetiology, and it is known that this idiopathic form of male infertility represents a complex condition. In this study, we aimed to evaluate whether common genetic variation in TEX15, which encodes a key player in spermatogenesis, is involved in the susceptibility to idiopathic SPGF. Materials and Methods: We designed a genetic association study comprising a total of 727 SPGF cases (including 527 NOA and 200 SO) and 1,058 unaffected men from the Iberian Peninsula. Following a tagging strategy, three tag single-nucleotide polymorphisms (SNPs) of TEX15 (rs1362912, rs323342, and rs323346) were selected for genotyping using TaqMan probes. Case-control association tests were then performed by logistic regression models. In silico analyses were also carried out to shed light into the putative functional implications of the studied variants. Results: A significant increase in TEX15-rs1362912 minor allele frequency (MAF) was observed in the group of SO patients (MAF = 0.0842) compared to either the control cohort (MAF = 0.0468, OR = 1.90, p = 7.47E-03) or the NOA group (MAF = 0.0472, OR = 1.83, p = 1.23E-02). The genotype distribution of the SO population was also different from those of both control (p = 1.14E-02) and NOA groups (p = 4.33–02). The analysis of functional annotations of the human genome suggested that the effect of the SO-associated TEX15 variants is likely exerted by alteration of the binding affinity of crucial transcription factors for spermatogenesis. Conclusion: Our results suggest that common variation in TEX15 is involved in the genetic predisposition to SO, thus supporting the notion of idiopathic SPGF as a complex trait.
- CYP21A2 gene duplication with a severe pathogenic variant is a benign allele that does not confirm clinical suspicions of 21-hydroxylase deficiencyPublication . Gomes, Susana; Silva, Júlia; Pereira-Caetano, Iris; Gonçalves, JoãoIntroduction: Congenital Adrenal Hyperplasia (CAH), one the most common autosomal recessive disorders, is regularly managed during genetic counselling (GC). The coding gene (CYP21A2) for 21-hydroxylase (21-OH), is located (in cis) with its pseudogene (CYP21A1P) in the RCCX cluster (6p21.3) and, the most common structure of this cluster comprises a single copy of each one. However, genotypes associated with CYP21A2 duplications can be detected in individuals during familial and/or pre-conceptional studies. In this duplicated alleles, the severe variant c.955C>T p.(Glu319*) is frequently detected, but is usually present in the proximal CYP21A2 copy. This means, that even in the presence of a severe variant, its allele is not pathogenic. Therefore, the aim of this work is to emphasize the importance of a better strategy of molecular analysis and an accurate interpretation of its results, in order to establish a correct genotyping of family members and partners, and provide a more reliable genetic counselling.
- CYP21A2 gene mutations, its nature and frequency in a paediatric Portuguese cohort with congenital adrenal hyperplasiaPublication . Rosmaninho-Salgado, Joana; Caetano, Joana Serra; Gomes, Susana; Pereira-Caetano, Iris; Cardoso, Rita; Dinis, Isabel; Ramos, Lina; Ramos, Fabiana; Carvalho, Ana Luisa; Garabal, Ana; Sá, Joaquim; Maia, Sofia; Sousa, Sérgio; Saraiva, Jorge; Gonçalves, João; Mirante, AliceIntroduction: The most common cause of congenital adrenal hyperplasia (CAH) is 21-hydroxylase deficiency (21-OHD) caused by alterations in CYP21A2 gene. The clinical phenotypes of this autosomal recessive disease are classified as classic (saltwasting and simple virilizing) and non-classic forms of CAH. The severity of the disease is directly related with the impairment of the 21-OH enzymatic activity. Genetic testing can confirm the disease and is crucial for familial studies and genetic counseling. Aim: The aim of this work was to perform the clinical and molecular characterization of the patients observed at the Hospital Pediátrico de Coimbra (Portugal) with the clinical suspecion of CAH. Methods: Retrospective analysis of patient medical records of all cases observed in our hospital with suspicion of CAH and detailed literature comparison. CYP21A2 molecular analysis had been performed in 81 unrelated Portuguese patients (51 female, 30 males) with clinical and endocrine laboratorial findings suggestive of CAH, using mini-sequencing, restriction enzyme digestion, Sanger sequencing or/and multiplex ligation-dependent probe amplification (MLPA). Results: CYP21A2 variants were identified in 74/81 (91%) of the patients. Homozygosity for CYP21A2 was found in 39.2% (29/74) of the patients while 55.4% (41/74) were compound heterozygous and, in 5.4% of the cases (4/74), only one pathogenic variant was identified. The most frequent alterations were p.Val281Leu, g.655A/C>G (splicing variant) and p.Ile172Asn, that account for more than 50% of the alleles of this patient’s cohort. All variants were already described except a novel missense variant identified in a salt-wasting patient, g.1173T>C(p.Trp201Arg). The rare variant p.Gly424Ser which was detected in one patient had been previously associated with a possible founder effect in Brazil and the splicing variant g.391G>A, only described in the Portuguese population. Conclusion: Our study provides a detailed clinical and molecular characterization of a large cohort of CAH Portuguese patients. The overall concordance between the clinical phenotype and the inferred phenotype (based on genotype) was 90%.
- Distinct spectrum of apc germline mutations in familial adenomatous polyposis at the center-south of portugal: identification of a mutational hotspot and suggestion of a founder effectPublication . Filipe, B.; Claro, I.; Lage, P.; Ferreira, S.; Rosa, I.; Rodrigues, P.; Spier, I.; Theisen, Patrícia; Pereira-Caetano, Iris; Isidro, Glória; Gonçalves, João; Aretz, S.; Dias Pereira, A.; Albuquerque, C.Introduction: Familial adenomatous polyposis (FAP) is caused by APC germline mutations. These have been reported in classic and attenuated FAP (AFAP) but only two hotspots were described (codons 1309 and 1061-range:0-15%). We aimed to characterize the APC mutation spectrum in a FAP/AFAP population from the familial polyposis registry of the Portuguese Oncology Institute in Lisbon. Methods: We performed mutation analysis in 95 index patients from our FAP/AFAP cohort (61 FAP; 34 AFAP) using PTT, DGGE, sequencing and MLPA. Haplotype analysis was performed using 3 microsatellite markers flanking APC and 2 intragenic SNPs in 12 families with an intron 9 mutation (6 from our registry, 2 from INSA and 4 from IHG), occasionally detected in the literature, in order to evaluate a possible founder effect. All samples were anonymized. Statistics: Fisher’s exact and Χ2. Results: APC mutations were found in 47/61(77%) FAP and in 12/34(35%) AFAP families. The 1309del and 1061del contributed for 6/59(10%) and 2/59(4%) of the families, respectively. Exon 15 mutations were more frequent in FAP than in AFAP [30/47(64%) vs 1/12(8%),P<0.001]. A high mutation frequency was also found in exon 9 and flanking regions (9/59;15%), contributing for the majority of AFAP with APC mutation (8/12;67%). An intron 9 mutation (c.1312+3A>G) was highly represented (6/59,10%), exclusively in AFAP (6/12;50%). Segregating with this mutation, we detected a common haplotype apparently shared by 6 families. For D5S346, the common allele segregating with this haplotype was more frequent in the index patients (11/20;46%) than in a control population (20/90;22%). Discussion: We identified a specific distribution of APC mutations and a mutational hotspot in our population. The higher frequency of the c.1312+3A>G mutation in Center-South Portugal suggest a non-uniform distribution which may be explained by a founder effect. Further studies using SNPs flanking intron 9 and the analysis of more families/relatives are needed.
- Espectro de alterações moleculares detetadas no gene CYP21A2 associadas a deficiência em 21 hidroxilasePublication . Gomes, Susana; Pereira-Caetano, Iris; Lopes, Maria Lurdes; Limbert, Catarina; Amaral, Daniela; Pina, Rosa; Antunes, Diana; Carvalho, Inês; Kay, Teresa; Sampaio, Lurdes; Pereira, Carla; Moldovan, Oana; Berta, Ana; Rebelo, Irene; Gaspar, Isabel; Cardoso, Helena; Rodrigues, José Cidade; Ramos, Lina; Ramos, Fabiana; Dinis, Isabel; Cardoso, Rita; Mirante, Alice; Gonçalves, JoãoA maioria dos doentes com hiperplasia suprarrenal congénita (HSC) apresenta alterações moleculares no gene CYP21A2, o qual codifica a enzima 21-hidroxilase (21-OH). Os doentes com a forma clássica de deficiência em 21-OH (21-OHD) apresentam a síntese de cortisol diminuída no córtex adrenal e, os casos mais graves, também apresentam deficiência de aldosterona. As mulheres com 21-OHD grave apresentam excesso de andrógenos desde a sua vida fetal conduzindo à virilização dos órgãos genitais externos. Tanto homens como mulheres com 21-OHD completa não sintetizam a aldosterona e, consequentemente, logo após o nascimento, podem desenvolver crises de perda de sal se não forem corretamente diagnosticados e tratados. A 21- OHD não clássica é devida à deficiência parcial em 21-OH, os fenótipos clínicos são menos graves, as mulheres não apresentam virilização dos genitais externos ao nascimento, e geralmente os sinais relativos a excesso de androgénios podem surgir durante a infância ou até mais tarde (durante ou após a puberdade). Neste trabalho descrevem-se as alterações e os genótipos mais frequentes encontrados em doentes portugueses não adultos com 21-OHD. As alterações mais frequentes encontradas na forma clássica da HSC são c.293-13C> G, diferentes deleções/quimeras/conversões génicas do gene CYP21A2 e c.518T> A, enquanto na 21-OHD não-clássica a variante c.844G> T é a mais frequente. Estes resultados contribuem para um diagnóstico correto e uma melhor gestão clínica dos doentes, para o seu aconselhamento genético e para oferecer o diagnóstico pré-natal a casais com risco de ter filhos afetados com a forma clássica de 21-OHD.
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