Search results for "sequencing"
showing 10 items of 1087 documents
Data from: GIbPSs: a toolkit for fast and accurate analyses of genotyping-by-sequencing data without a reference genome
2016
Genotyping-by-sequencing (GBS) and related methods are increasingly used for studies of non-model organisms from population genetic to phylogenetic scales. We present GIbPSs, a new genotyping toolkit for the analysis of data from various protocols such as RAD, double-digest RAD, GBS, and two-enzyme GBS without a reference genome. GIbPSs can handle paired-end GBS data and is able to assign reads from both strands of a restriction fragment to the same locus. GIbPSs is most suitable for population genetic and phylogeographic analyses. It avoids genotyping errors due to indel variation by identifying and discarding affected loci. GIbPSs creates a genotype database that offers rich functionality…
Data from: The population genomics of archaeological transition in west Iberia: investigation of ancient substructure using imputation and haplotype-…
2018
We analyse new genomic data (0.05–2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200–3500 BC) to the Middle Bronze Age (1740–1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, t…
Filamin C variants are associated with a distinctive clinical and immunohistochemical arrhythmogenic cardiomyopathy phenotype.
2020
Background: Pathogenic variants in the filamin C (FLNC) gene are associated with inherited cardiomyopathies including dilated cardiomyopathy with an arrhythmogenic phenotype. We evaluated FLNC variants in arrhythmogenic cardiomyopathy (ACM) and investigated the disease mechanism at a molecular level. Methods: 120 gene-elusive ACM patients who fulfilled diagnostic criteria for arrhythmogenic right ventricular cardiomyopathy (ARVC) were screened by whole exome sequencing. Fixed cardiac tissue from FLNC variant carriers who had died suddenly was investigated by histology and immunohistochemistry. Results: Novel or rare FLNC variants, four null and five variants of unknown significance, were id…
Intraoperative DNA methylation classification of brain tumors impacts neurosurgical strategy
2021
Abstract Background Brain tumor surgery must balance the benefit of maximal resection against the risk of inflicting severe damage. The impact of increased resection is diagnosis-specific. However, the precise diagnosis is typically uncertain at surgery due to limitations of imaging and intraoperative histomorphological methods. Novel and accurate strategies for brain tumor classification are necessary to support personalized intraoperative neurosurgical treatment decisions. Here, we describe a fast and cost-efficient workflow for intraoperative classification of brain tumors based on DNA methylation profiles generated by low coverage nanopore sequencing and machine learning algorithms. Met…
LARP7 variants and further delineation of the Alazami syndrome phenotypic spectrum among primordial dwarfisms: 2 sisters.
2019
Abstract Alazami syndrome (AS) (MIM# 615071 ) is an autosomal recessive microcephalic primordial dwarfism (PD) with recognizable facial features and severe intellectual disability due to depletion or loss of function variants in LARP7. To date, 15 patients with AS have been reported. Here we describe two consanguineous Algerian sisters with Alazami PD due to LARP7 homozygous pathogenic variants detected by whole exome sequencing. By comparing these two additional cases with those previously reported, we strengthen the key features of AS: severe growth restriction, severe intellectual disability and some distinguishing facial features such as broad nose, malar hypoplasia, wide mouth, full li…
Rare dyslipidaemias, from phenotype to genotype to management: a European Atherosclerosis Society task force consensus statement
2020
Genome sequencing and gene-based therapies appear poised to advance the management of rare lipoprotein disorders and associated dyslipidaemias. However, in practice, underdiagnosis and undertreatment of these disorders are common, in large part due to interindividual variability in the genetic causes and phenotypic presentation of these conditions. To address these challenges, the European Atherosclerosis Society formed a task force to provide practical clinical guidance focusing on patients with extreme concentrations (either low or high) of plasma low-density lipoprotein cholesterol, triglycerides, or high-density lipoprotein cholesterol. The task force also recognises the scarcity of qua…
Dinámica de la microbiota en niños, adolescentes y adultos
2022
La microbiota intestinal se implanta a lo largo del desarrollo del individuo y su composición y funciones difieren según la edad. Conocer los cambios que se producen en la microbiota intestinal a lo largo de la vida puede ayudar al diagnóstico, tratamiento y prevención de enfermedades relacionadas con alteraciones metabólicas e inmunitarias. Con este trabajo pretendemos contribuir a la comprensión del proceso de desarrollo de la microbiota intestinal, centrándonos en dos períodos que han recibido poca atención: los primeros años y la adolescencia. Hemos determinado la composición y la función de la microbiota a través de enfoques metagenómicos de genoma completo y basados en ARN ribosómic…
Vibrio vulnificus: from water to host
2017
Vibrio vulnificus is an aquatic pathogen autochthonous from temperate, tropical and subtropical ecosystems where it lives either as a sessile cell, forming biofilms or as a free-swimming cell. From these locations, the pathogen can occasionally infect humans and fish causing a disease named vibriosis. The most severe form of human and fish vibriosis is associated with the pathogen’s ability to spread from the infection site to the bloodstream and multiply, process known as invasion. Before invasion, the pathogen has to colonize the mucosal host surface, process that involves not only bacterial attachment/adhesion but also resistance to mucosal immunity, commensal microbiota (competitors) an…
Amplicon-based high-throughput pooled sequencing identifies mutations in CYP7B1 and SPG7 in sporadic spastic paraplegia patients
2011
Hereditary spastic paraplegia (HSP) is a neurodegenerative disorder defined clinically by progressive lower limb spasticity and weakness. HSP is a genetically highly heterogeneous condition with at least 46 gene loci identified so far, involving X-linked, autosomal recessive (AR) and autosomal dominant inheritance. For correct diagnosis, molecular testing is essential because clinical parameters by themselves are not reliable to differentiate HSP forms. The purpose of this study was to establish amplicon-based high-throughput genotyping for AR-HSP. A sample of 187 index cases with apparently sporadic or recessive spastic paraplegia were analyzed by applying an array-based amplification stra…
Applied genomics for tuberculosis diagnosis and surveillance
2020
La tuberculosis es una de las principales causas de muerte a nivel mundal. A lo largo de los ultimos años, la secuenciación de genoma comleto de Myobacterium tuberculosis, el agente infeccioso, se ha convertido en una herramienta extraordinaria en el estudio, diagnóstico y vigilancia epidemiológica de la enfermedad. Analizar el genoma completo de la bacteria permite la predicción precisa de resistencias a antibióticos, estudiar brotes con una resolución sin preecdentes, a la vez que permite estudiar la evolución y la diversidad genética del patógeno. Sin embargo el uso de la secuenciación genómica se ha visto dificultado por la dependencia de un proceso largo y costoso de cultivo microbiano…