Browsing by Author "David, Dezso"
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- Chromosome structural variants: Epidemiology, identification and contribution to human diseasesPublication . Dong, Zirui; David, Dezso; Gonzaga-Jauregui, Claudia; Morton, Cynthia C.; Zepeda-Mendoza, Cinthya J.Human chromosome structural variants (SVs) are balanced/unbalanced genomic abnormalities that include translocation, inversion, insertion, and deletion/duplication (also known as copy-number variants, CNVs) events with a size of >50 bp. Currently, the capability of genome sequencing in the research and clinical fields has increased our capacity to detect cryptic SVs and further delineate the complexity of karyotypically/microarray detectable SVs. This has increased our knowledge of pathogenicity mechanisms by considering dysregulation of gene expression through position effects and complex interactions between gene dosage and mutational burden. However, much of the contribution of SVs to human disease is left to explore, as the incidence of SVs is still underestimated owing to limitations of current sequencing technologies and analytical pipelines, and few studies have comprehensively integrated SV information with single nucleotide variants in congenital diseases. Rigorous investigation of SV pathogenicity is warranted for clinical applications. The Research Topic in this issue is divided into three main sections: three articles demonstrate methodologies in SV identification and pathogenicity annotation; five papers discuss the spectrum of SVs in individuals with different indications; and two reports characterize sequence complexity of SVs [...].
- Identification of OAF and PVRL1 as candidate genes for an ocular anomaly characterized by Peters anomaly type 2 and ectopia lentisPublication . David, Dezso; Anand, D.; Araújo, C.; Gloss, B.; Fino, J.; Dinger, M.; Lindahl, P.; Pöyhönen, M.; Hannele, L.; Lavinha, J.Keratolenticular dysgenesis (KLD) and ectopia lentis are congenital eye defects. The aim of this study is the identification of molecular genetic alterations responsible for those ocular anomalies with neurologic impairment in an individual with a de novo balanced chromosome translocation t(11;18)(q23.3;q11.2)dn. Disruption of OAF, the human orthologue of the Drosophila oaf, by the 11q23.3 breakpoint results in reduced expression of this transcriptional regulator. Furthermore, four most likely nonfunctional chimeric transcripts comprising up to OAF exon 3, derived from the der(11) allele, have also been identified. This locus has been implicated by publicly available genome-wide association data in corneal disease and corneal topography. The expression of the poliovírus receptor-related 1(PVRL1) or nectin cell adhesion molecule 1 (NECTIN1), a paralogue of nectin cell adhesion molecule 3 (PVRL3) associated with congenital ocular defects, situated 500 kb upstream from 11q23.3 breakpoint, is increased. The 18q11.2 breakpoint is localized between cutaneous T-cell lymphoma-associated antigen 1(CTAGE1) and retinoblastoma binding protein 8 (RBBP8) genes. Genomic imbalance that could contribute to the observed phenotype was excluded. Analysis of gene expression datasets throughout normal murine ocular lens embryogenesis suggests that OAF expression is significantly enriched in the lens from early stages of development through adulthood, whereas PVRL1 is lens-enriched until E12.5 and then down-regulated. This contrasts with the observation that the proposita's lymphoblastoid cell lines exhibit low OAF and high PVRL1 expression as compared to control, which offers further support that the alterations described above are most likely responsible for the clinical phenotype. Finally, gene interaction topology data for PVRL1 also agree with our proposal that disruption of OAF by the translocation breakpoint and misregulation of PVRL1 due to a position effect contribute to the observed ocular and neurological phenotype.
- 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.
- Projeto Doenças Genómicas e Rearranjos Cromossómicos: dificuldades diagnósticas e o impacto para a famíliaPublication . David, DezsoStructural chromosomal rearrangements (SCRs) have long been recognized as a major source of human developmental anomalies, including, among others, congenital anomalies, and neurodevelopmental, intellectual and cognitive disabilities. Indeed, causal relationship between congenital anomalies and related SCRs are expected to occur in up to 40% of the affected subjects. Approaches used for detection of such SCRs evolved significantly from classical and molecular cytogenetic technologies, such as FISH and microarrays, to whole genome sequencing (WGS) with high physical and low sequence coverage, also known as large-insert WGS.
- Ring chromosome 6 in a child with anterior segment dysgenesis and review of its overlap with other FOXC1 deletion phenotypesPublication . Corona-Rivera, Jorge Román; Corona-Rivera, Alfredo; Zepeda-Romero, Luz Consuelo; Rios-Flores, Izabel Maryalexandra; Rivera-Vargas, Jehú; Orozco-Vela, Mireya; Santana-Bejarano, Uriel Francisco; Torres-Anguiano, Elizabeth; Pinto-Cardoso, Manuela; David, Dezso; Bobadilla-Morales, LucinaHere, we report a patient with ring chromosome 6 [r(6)], associated with anterior segment dysgenesis (ASD) and other anomalies. The phenotype was due to a 1880 kb microdeletion at 6p25.3 identified by whole-genome array analysis, and was mainly attributable to a FOXC1 haploinsufficiency. Currently 37 patients with r(6) have been reported. We found that facial dysmorphism, ASD, heart anomalies, brain anomalies, and hearing loss are constant features only in severe cases of r(6), mainly related to hemizygosity of FOXC1. Thus, overlaps with other FOXC1 related phenotypes, such as the 6p25 deletion syndrome, Axenfeld-Rieger syndrome type 3, and ASD type 3. Contrarily, those patients whose r(6) does not disrupt FOXC1, have mild or moderate phenotypes and do not exhibit ASD.
- Spectrum of structural genomic abnormalities in subjects carrying disease-associated chromosome rearrangements and their pathogenic implicationsPublication . David, DezsoStructural chromosomal rearrangements (SCRs) have long been recognized as a major source of human developmental anomalies, including, among others, congenital anomalies, and neurodevelopmental, intellectual and cognitive disabilities. Indeed, causal relationship between congenital anomalies and related SCRs are expected to occur in up to 40% of the affected subjects. Approaches used for detection of such SCRs evolved significantly from classical and molecular cytogenetic technologies, such as FISH and microarrays, to whole genome sequencing (WGS) with high physical and low sequence coverage, also known as large-insert WGS. The spectrum of SCRs, at DNA sequence-level resolution, in subjects carrying disease-associated SCRs, and the emerging pathogenic mechanisms will be presented. Like classical haploinsufficiency due to point mutations, disruption of the coding regions or genomic elements controlling quantitative expression of a dosage-sensitive gene will lead to a haploinsufficient phenotype. Position effect is a complex pathogenic mechanism of these SCR-associated disorders, resulting from disruption of native gene-specific and adoption of alien long-range cis-acting control elements. Haploinsufficiency or position effect on the same gene may lead to dissimilar clinical phenotypes. Certain balanced translocations can yield clinical phenotypes that are similar to microdeletion syndromes caused by hemizygosity of a major causal gene locus or of a variable number of contiguous genes. In such cases, haploinsufficiency of the causal gene with or without position effect on the contiguous genes can be considered as possible pathogenic mechanisms. Occasionally, gene fusions occur through SCRs that may lead to fusion transcripts. Although formation of such transcripts is a fundamental pathogenic mechanism behind different forms of cancer, apparently this is insignificant in SCR-associated disorders, mainly because many of such transcripts are non-functional and therefore non-pathogenic. There is no direct correlation between complexity of chromosomal rearrangements and severity of clinical phenotypes. Such genomic approach, that allows personalised medical genetics care, have necessarily to be accompanied by deep phenotyping. The emerging picture from these SCRs data highlights the extent to which the human genome can be affected by these rearrangements, its tremendous plasticity, and the intricacy of pathogenic mechanisms leading to SCRs-associated disorders.
- 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.