Browsing by Author "Fino, Joana"
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- Citogenética de Próxima Geração: Implementação e primeiros resultados em PortugalPublication . David, Dezső; Oliva-Teles, Natália; Freixo, João; Fonseca e Silva, ML; Fortuna, Ana; Tkachenko, Natália; Carvalho, Inês; Marques, Mariana; Cardoso, Manuela; Fino, Joana; Marques, Bárbara; Alves, Ana Cristina; Dória, Sófia; Pinto de Moura, Carla; Marques Carreira, Isabel; Correia, Hildeberto; Gonçalves, Rui Miguel; Lavinha, João; Kay, Teresa; Talkowski, Michael; Morton, CynthiaIntrodução: As alterações cromossómicas estruturais provocam doenças de severidade variável que acarretam sofrimento individual e familiar signifi cativo. Para compreensão da sua etiologia e estabelecimento de um possível prognóstico, uma adequada correlação fenótipo-genótipo é fundamental. O presente estudo faz parte do projeto intitulado àCitogenética de Próxima Geração Irrompe nos Cuidados de Saúde e Contribui para Anotação do Genoma Humanoà, que visa a introdu- ção da sequenciação de próxima geração (NGS) na citogené- tica clínica, tirando partido dessa inovação única na deteção de variantes estruturais, com uma resolução de um nucleótido para a criação de uma citogenética de alto rendimento, catalisadora de notáveis avanços no diagnóstico clínico e resulta da colaboração entre seis Instituições nacionais e a Harvard Medical School. Estima-se que exista um número considerável de indivíduos portadores de diversas patologias, incluindo algumas de início tardio associadas a rearranjos genómicos por identifi car. Assim, é fundamental a identifi cação e a referência destes indivíduos com possíveis rearranjos cromossómicos associados a doenças.
- Comprehensive clinically oriented workflow for nucleotide level resolution and interpretation in prenatal diagnosis of de novo apparently balanced chromosomal translocations in their genomic landscapePublication . David, Dezső; Freixo, João P.; Fino, Joana; Carvalho, Inês; Marques, Mariana; Cardoso, Manuela; Piña-Aguilar, Raul E.; Morton, Cynthia C.We present a comprehensive clinically oriented workflow for large-insert genome sequencing (liGS)-based nucleotide level resolution and interpretation of de novo (dn) apparently balanced chromosomal abnormalities (BCA) in prenatal diagnosis (PND). Retrospective or concomitant with conventional PND and liGS, molecular and newly developed clinically inspired bioinformatic tools (TAD-GConTool and CNV-ConTool) are applied to analyze and assess the functional and phenotypic outcome of dn structural variants (dnSVs). Retrospective analysis of four phenotype-associated dnSVs identified during conventional PND precisely reveal the genomic elements disrupted by the translocation breakpoints. Identification of autosomal dominant disease due to the disruption of ANKS1B and WDR26 by t(12;17)(q23.1;q21.33)dn and t(1;3)(q24.11;p25.3)dn breakpoints, respectively, substantiated the proposed workflow. We then applied this workflow to two ongoing prenatal cases with apparently balanced dnBCAs: 46,XX,t(16;17)(q24;q21.3)dn referred for increased risk on combined first trimester screening and 46,XY,t(2;19)(p13;q13.1)dn referred due to a previous trisomy 21 pregnancy. Translocation breakpoints in the t(16;17) involve ANKRD11 and WNT3 and disruption of ANKRD11 resulted in KBG syndrome confirmed in postnatal follow-up. Breakpoints in the t(2;19) are within ATP6V1B1 and the 3' UTR of CEP89, and are not interpreted to cause disease. Genotype-phenotype correlation confirms the causative role of WDR26 in the Skraban-Deardorff and 1q41q42 microdeletion phenocopy syndromes, and that disruption of ANKS1B causes ANKS1B haploinsufficiency syndrome. In sum, we show that an liGS-based approach can be realized in PND care providing additional information concerning clinical outcomes of dnBCAs in patients with such rearrangements.
- Doenças genómicas no Departamento de Genética Humana do INSA: da resolução de mapa físico à medicina genómica personalizadaPublication . David, Dezső; Marques, Bárbara; Fino, Joana; Gal, Andreas
- Early results of next-gen cytogenetics implementation in PortugalPublication . David, Dezső; Freixo, João; Marques, Bárbara; Carvalho, Inês; Tkachenko, Natália; Oliva-Teles, Natália; Marques, Mariana; Cardoso, Manuela; Fino, Joana; Alves, Cristina; Fortuna, Ana; Sófia, Dória; Pinto de Moura, Carla; Correia, Hildeberto; Marques Carreira, Isabel; Sá, Joaquim; Gonçalves, Rui Miguel; Lavinha, João; Kay, Teresa; Talkowski, Michael; Morton, CynthiaBackground: Most approaches are insensitive to the full mutational spectrum of chromosome rearrangements associated with human developmental abnormalities. Therefore, our aim is to introduce next-generation sequencing (NGS) into clinical cytogenetics, creating a sequence-based NextGen Cytogenetics to catalyze a dramatic advancement in clinical diagnostics. Methods: Twenty families with chromosome rearrangement-associated diseases, including two prenatal (PN) cases, have been enrolled. Fourteen of these were also analyzed by NGS using large-insert paired-end libraries. Results: The majority of these cases were confirmed to be balanced reciprocal rearrangements, whereas 4 were complex chromosomal rearrangements including 1 of chromothripsis. Thus far, over 50 breakpoints were identified disrupting protein coding genes, lncRNAs, or intergenic regions, thus revealing candidate genes or genomic loci. These cases are further assessed for pathogenicity from positional effects on genes located within topological domains (TADs) containing the breakpoints using DECIPHER predictions of haploinsufficiency. In one PN case, the 16q24 breakpoint disrupts ANKRD11, etiologic in the autosomal dominant KBG syndrome (OMIM #148050), predicting an abnormal phenotype. The chromothripsis case, submitted as 46,XY,t(7;14)(q22;q32.1),inv(15)(q21.2q26.1), proved by NGS to carry two further deletions, at 3p12 (5.3 Mb) and 15q14 (488 kb), as well as an insertion of 644.4 kb from 15q14 into 3p14. The inv(15) is in fact a complex rearrangement of 15q with eight breakpoints. Conclusions: We demonstrate that NGS-based chromosomal rearrangement characterization leads to major improvements in identification of chromosomal aberrations and in prediction of clinical outcomes of postnatally and prenatally detected genomic rearrangements, and to contributions to human genome annotation.
- Identification of two new candidate genes OAF and PVRL1 for Peters anomaly and ectopia lentisPublication . David, Dezső; Anand, Deepti; Araújo, Carlos; Gloss, Brian; Fino, Joana; Marques, Bárbara; Dinger, Marcel; Lindahl, Päivi; Pöyhönen, Minna; Laivuori, Hannele
- A Novel Frameshift CHD4 Variant Leading to Sifrim-Hitz-Weiss Syndrome in a Proband with a Subclinical Familial t(17;19) and a Large dup(2)(q14.3q21.1)Publication . Da Silva, Jorge Diogo; Oliva-Teles, Natália; Tkachenko, Nataliya; Fino, Joana; Marques, Mariana; Fortuna, Ana Maria; David, DezsoThe genetic complexity of neurodevelopmental disorders (NDD), combined with a heterogeneous clinical presentation, makes accurate assessment of their molecular bases and pathogenic mechanisms challenging. Our purpose is to reveal the pathogenic variant underlying a complex NDD through identification of the "full" spectrum of structural genomic and genetic variants. Therefore, clinical phenotyping and identification of variants by genome and exome sequencing, together with comprehensive assessment of these and affected candidate genes, were carried out. A maternally-inherited familial translocation [t(17;19)(p13.1;p13.3)mat] disrupting the GSG1 like 2 gene (GSG1L2), a 3.2 Mb dup(2)(q14.3q21.1) encompassing the autosomal dominant OMIM phenotype-associated PROC and HS6ST1 gene, and a novel frameshift c.4442del, p.(Gly1481Valfs*21) variant within exon 30 of the Chromodomain helicase DNA binding protein 4 (CHD4) have been identified. Considering the pathogenic potential of each variant and the proband's phenotype, we conclude that this case basically fits the Sifrim-Hitz-Weiss syndrome or CHD4-associated neurodevelopmental phenotype. Finally, our data highlight the need for identification of the "full" spectrum of structural genomic and genetic variants and of reverse comparative phenotyping, including unrelated patients with variants in same genes, for improved genomic healthcare of patients with NDD.
- Structure_threader: an improved method for automation and parallelization of programs structure, fastStructure and MavericK on multicore CPU systemsPublication . Pina-Martins, Francisco; Silva, Diogo N.; Fino, Joana; Paulo, Octávio S.Structure_threader is a program to parallelize multiple runs of genetic clustering software that does not make use of multithreading technology (structure, fastStructure and MavericK) on multicore computers. Our approach was benchmarked across multiple systems and displayed great speed improvements relative to the single-threaded implementation, scaling very close to linearly with the number of physical cores used. Structure_threader was compared to previous software written for the same task-ParallelStructure and StrAuto and was proven to be the faster (up to 25% faster) wrapper under all tested scenarios. Furthermore, Structure_threader can perform several automatic and convenient operations, assisting the user in assessing the most biologically likely value of 'K' via implementations such as the "Evanno," or "Thermodynamic Integration" tests and automatically draw the "meanQ" plots (static or interactive) for each value of K (or even combined plots). Structure_threader is written in python 3 and licensed under the GPLv3. It can be downloaded free of charge at https://github.com/StuntsPT/Structure_threader.
- SVInterpreter: A Comprehensive Topologically Associated Domain-Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural VariantsPublication . Fino, Joana; Marques, Barbara; Dong, Zirui; David, DezsoWith the advent of genomic sequencing, a number of balanced and unbalanced structural variants (SVs) can be detected per individual. Mainly due to incompleteness and the scattered nature of the available annotation data of the human genome, manual interpretation of the SV’s clinical significance is laborious and cumbersome. Since bioinformatic tools developed for this task are limited, a comprehensive tool to assist clinical outcome prediction of SVs is warranted. Herein, we present SVInterpreter, a free Web application, which analyzes both balanced and unbalanced SVs using topologically associated domains (TADs) as genome units. Among others, gene-associated data (as function and dosage sensitivity), phenotype similarity scores, and copy number variants (CNVs) scoring metrics are retrieved for an informed SV interpretation. For evaluation, we retrospectively applied SVInterpreter to 97 balanced (translocations and inversions) and 125 unbalanced (deletions, duplications, and insertions) previously published SVs, and 145 SVs identified from 20 clinical samples. Our results showed the ability of SVInterpreter to support the evaluation of SVs by (1) confirming more than half of the predictions of the original studies, (2) decreasing 40% of the variants of uncertain significance, and (3) indicating several potential position effect events. To our knowledge, SVInterpreter is the most comprehensive TAD-based tool to identify the possible disease-causing candidate genes and to assist prediction of the clinical outcome of SVs. SVInterpreter is available at http://dgrctools-insa.min-saude.pt/cgi-bin/SVInterpreter.py.
- SVInterpreter: a web-based tool for structural variants inspection and identification of possible disease-causing candidate genesPublication . Fino, Joana; Marques, Barbara; Dong, Zirui; David, DezsoIntroduction: With the advent of genomic sequencing, the identification of structural variants (SVs) is no longer a challenge, being possible to detect an average of 5 K SVs by individual. Contrarily, the annotation of the genome is incomplete, and the data is scattered along different databases, making SV manual evaluation complicated and time-consuming. Also, the available tools are limited on their scope. Thus, to address the need of a comprehensive application to assist evaluation of clinical outcome of SVs, we developed Structural Variant Interpreter (SVInterpreter). Methods: SVInterpreter is a free Python-CGI developed Web application able to analyze SVs using Topologically Associated Domains as genome units, within which genome browsers data, medically actionable genes, virtual gene panels and HPO similarity results, among other information, is retrieved. Results: We started by re-analysing 220 published SVs, of which about 50% were previously classified as VUS. SVInterpreter corroborated the previous classification in about 84% of the SVs. In about 5% of the SVs, SVInterpreter gave indication of possible position effect, through phenotype similarity, disrupted chromatin loops or genome wide association studies. Then, we show the applicability of SVInterpreter on the clinical setting, by inspecting 15 cases analysed by chromosomal microarray or genome sequencing. Conclusions: To our knowledge, SVInterpreter is the most comprehensive TAD based tool to assist prediction of clinical outcome of SVs. Based on gathered information, identification of possible disease-causing candidate genes and SVs is easily achievable. SVInterpreter is available at http://dgrctools-insa.min-saude.pt/cgi-bin/SVInterpreter.py
- TAD-GConTool and CNV-ConTool to assist prediction of phenotypic outcome of chromosomal rearrangementsPublication . Fino, Joana; David, DezsoWith the advance of genome sequencing technologies, it is currently possible to identify a large number of chromosomal or genomic structural variants in a single individual. Therefore, the validation and manual assessment of structural variants clinical significance becomes unpractical and time consuming when performed with previous methodologies. In order to assist the validation process, we developed two clinically inspired bioinformatics tools - TADGConTool and CNV-ConTool. They were developed in python with a Common Gateway Interface that allows easy and user-friendly access through any standards compliant web browser (available at: http://dgrctools.insa.min- saude.pt/). TAD-GConTool collects genomic information of breakpoint regions, using topological associated domains (TADs) as reference. It then accesses public databases to retrieve elements found inside TADs, and the associated clinical phenotypes, highlighting those causing dominant disorders. CNV-ConTool searches for overlaps between patient-specific breakpoints and CNVs, and those reported in several public databases. These tools were already successfully applied to about 40 cases studied under the project “Next-gen cytogenetics enters clinical care and annotates the human genome” (HMSPICT/0016/2013) and are now being made available to the broader scientific community. These tools allowed a faster and more informed evaluation of the genomic structural variants, helping select potential pathogenic variants, either by identifying phenotype- associated genes, or by overlapping deletions and duplications with already described benign or pathogenic CNVs. As genome sequencing is becoming more and more a routine method for identification of chromosomal and genomic structural variants, such clinically oriented bioinformatics tools are crucial and represent the first level of analysis toward personalized genomic medicine. This research was supported by national funds through FCT - Fundação para a Ciência e a Tecnologia, Research Grant HMSP-ICT/0016/2013.