Search results for "Sequencing"
showing 10 items of 1087 documents
Excess of de novo variants in genes involved in chromatin remodelling in patients with marfanoid habitus and intellectual disability.
2020
PurposeMarfanoid habitus (MH) combined with intellectual disability (ID) (MHID) is a clinically and genetically heterogeneous presentation. The combination of array CGH and targeted sequencing of genes responsible for Marfan or Lujan–Fryns syndrome explain no more than 20% of subjects.MethodsTo further decipher the genetic basis of MHID, we performed exome sequencing on a combination of trio-based (33 subjects) or single probands (31 subjects), of which 61 were sporadic.ResultsWe identified eight genes with de novo variants (DNVs) in at least two unrelated individuals (ARID1B, ATP1A1, DLG4, EHMT1, NFIX, NSD1, NUP205 and ZEB2). Using simulation models, we showed that five genes (DLG4, NFIX, …
Familial Hemiplegic Migraine with an ATP1A4 Mutation: Clinical Spectrum and Carbamazepine Efficacy
2020
An Italian family with familial hemiplegic migraine (FHM) with the absence of mutations in the known genes associated with this disorder, namely ATP1A2, ATP1A3, CACNA1A, and SCN1A, has recently been reported. Soon afterward, whole exome sequencing allowed the identification of the carrier status of a heterozygous ATP1A4 mutation c.1798 C >T, in four affected members of this family. Here we compare the clinical symptoms of the affected family members with those from the other FHM families linked to mutations in the known genes associated with this disorder. A further two-year follow-up, including clinical response to carbamazepine administered to the proband and the maternal grandmother due …
High efficiency and clinical relevance of exome sequencing in the daily practice of neurogenetics
2021
ObjectiveTo assess the efficiency and relevance of clinical exome sequencing (cES) as a first-tier or second-tier test for the diagnosis of progressive neurological disorders in the daily practice of Neurology and Genetic Departments.MethodsSixty-seven probands with various progressive neurological disorders (cerebellar ataxias, neuromuscular disorders, spastic paraplegias, movement disorders and individuals with complex phenotypes labelled ‘other’) were recruited over a 4-year period regardless of their age, gender, familial history and clinical framework. Individuals could have had prior genetic tests as long as it was not cES. cES was performed in a proband-only (60/67) or trio (7/67) st…
CandidaDB: a genome database for Candida albicans pathogenomics.
2004
CandidaDB is accessible at http://genolist.pasteur.fr/CandidaDB.; International audience; CandidaDB is a database dedicated to the genome of the most prevalent systemic fungal pathogen of humans, Candida albicans. CandidaDB is based on an annotation of the Stanford Genome Technology Center C.albicans genome sequence data by the European Galar Fungail Consortium. CandidaDB Release 2.0 (June 2004) contains information pertaining to Assembly 19 of the genome of C.albicans strain SC5314. The current release contains 6244 annotated entries corresponding to 130 tRNA genes and 5917 protein-coding genes. For these, it provides tentative functional assignments along with numerous pre-run analyses th…
Widespread selection for high and low secondary structure in coding sequences across all domains of life
2019
AbstractCodon composition, GC-content and local RNA secondary structures can have a profound effect on gene expression and mutations affecting these parameters, even though they do not alter the protein sequence, are not neutral in terms of selection. Although evidence exists that in some cases selection favors more stable RNA secondary structures, we currently lack a concrete idea of how many genes are affected within a species, and if this is a universal phenomenon in nature.We searched for signs of structural selection in a global manner, analyzing a set of one million coding sequences from 73 species representing all domains of life, as well as viruses, by means of our newly developed s…
Extracting similar sub-graphs across PPI Networks
2009
Singling out conserved modules (corresponding to connected sub-graphs) throughout protein-protein interaction networks of different organisms is a main issue in bioinformatics because of its potential applications in biology. This paper presents a method to discover highly matching sub-graphs in such networks. Sub-graph extraction is carried out by taking into account, on the one side, both protein sequence and network structure similarities and, on the other side, both quantitative and reliability information possibly available about interactions. The method is conceived as a generalization of a known technique, able to discover functional orthologs in interaction networks. Some preliminar…
Toward completion of the Earth’s proteome: an update a decade later
2017
Protein databases are steadily growing driven by the spread of new more efficient sequencing techniques. This growth is dominated by an increase in redundancy (homologous proteins with various degrees of sequence similarity) and by the incapability to process and curate sequence entries as fast as they are created. To understand these trends and aid bioinformatic resources that might be compromised by the increasing size of the protein sequence databases, we have created a less-redundant protein data set. In parallel, we analyzed the evolution of protein sequence databases in terms of size and redundancy. While the SwissProt database has decelerated its growth mostly because of a focus on i…
Assessing the low complexity of protein sequences via the low complexity triangle.
2020
Background Proteins with low complexity regions (LCRs) have atypical sequence and structural features. Their amino acid composition varies from the expected, determined proteome-wise, and they do not follow the rules of structural folding that prevail in globular regions. One way to characterize these regions is by assessing the repeatability of a sequence, that is, calculating the local propensity of a region to be part of a repeat. Results We combine two local measures of low complexity, repeatability (using the RES algorithm) and fraction of the most frequent amino acid, to evaluate different proteomes, datasets of protein regions with specific features, and individual cases of proteins…
A Genomic, Transcriptomic and Proteomic Look at the GE2270 Producer Planobispora rosea, an Uncommon Actinomycete.
2015
We report the genome sequence of Planobispora rosea ATCC 53733, a mycelium-forming soil-dweller belonging to one of the lesser studied genera of Actinobacteria and producing the thiopeptide GE2270. The P. rosea genome presents considerable convergence in gene organization and function with other members in the family Streptosporangiaceae, with a significant number (44%) of shared orthologs. Patterns of gene expression in P. rosea cultures during exponential and stationary phase have been analyzed using whole transcriptome shotgun sequencing and by proteome analysis. Among the differentially abundant proteins, those involved in protein metabolism are particularly represented, including the G…
Sialotranscriptomics of the argasid tick ornithodoros moubata along the trophogonic cycle
2021
32 páginas, 8 tablas, 6 figuras