Search results for " NGS"

A NEXT GENERATION SEQUENCING APPROACH FOR MOLECULAR DIAGNOSIS OF MONOGENIC DYSLIPIDEMIAS

Exome sequencing in a child with neurodevelopmental disorder and epilepsy: Variant analysis of the AHNAK2 gene

2022

Background The AHNAK2 gene encodes a large nucleoprotein expressed in several tissues, including brain, squamous epithelia, smooth muscle, and neuropil. Its role in calcium signaling has been suggested and to date, clear evidence about its involvement in the pathogenesis of clinical disorders is still lacking. Methods Here, we report a female 24-year-old patient diagnosed with a cardio-facio-cutaneous-like phenotype (CFC-like), characterized by epilepsy, psychomotor development delay, atopic dermatitis, congenital heart disease, hypotonia, and facial dysmorphism, who is compound heterozygote for two missense mutations in the AHNAK2 gene detected by exome sequencing. Results This patient had…

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

2020

8 páginas, 3 figuras

NS5A gene analysis by next generation sequencing in HCV nosocomial transmission clusters of HCV genotype 1b infected patients

2019

Background: The aim of the study was to investigate the intra-host variability through next-generation-sequencing (NGS) of the NS5A-gene in nosocomial transmission-clusters observed in two Italian hospitals among hepatitis C virus (HCV)-genotype-1b infected patients. Methods: HCV-sequencing was performed by Sanger-sequencing (NS3 + NS5A + NS5B) and by NGS (NS5A, MiSeq-Illumina) in 15 HCV-1b infected patients [five acute with onco-hematologic-disease and 10 (4/6 acute/chronic) with &beta

Role of Microbiota in development, gene expression and epigenetic modifications in D. melanogaster host model

Eukaryotes and prokaryotes have developed mutually beneficial relationships over millennia of evolutionary adaptation. Recent observations suggest a strong correlation between the presence of Microbiota and host homeostasis, but little is known about the mechanisms they use to shape the physiology and to reprogram gene expression of their host. Using both conventionally reared and germ-free D. melanogaster as a model system, I found a role of bacteria in host protein expression and development, as germ-free flies develop more slowly than their conventional counterpart. Remarkably, using the classic variegated In(1)wm4 inversion, I identified a role of Microbiota as modifier of white Positio…

Novel mutations of the ABCA12, KRT1 and ST14 genes in three unrelated newborns showing congenital ichthyosis.

2022

Abstract Background Congenital ichthyosis (CI) is a heterogeneous group of genetic disorders characterized by generalized dry skin, scaling and hyperkeratosis, often associated to erythroderma. They are rare diseases, with overall incidence of 6.7 in 100,000. Clinical manifestations are due to mutations in genes mostly involved in skin barrier formation. Based on clinical presentation, CI is distinguished in non-syndromic and syndromic forms. To date, mutations of more than 50 genes have been associated to different types of CI. Cases presentation We report on three Italian unrelated newborns showing clinical signs compatible with different forms of CI of variable severity, namely Harlequin…

Characterization of the microbiota from coelomic fluid of the sea urchin Paracentrotus lividus

2016

The study of the microbiota is a subject of considerable and growing interest since it is drawing new important perspectives in the life sciences concerning the functional relationships between metazoans and microbial cells. In fact, it has already shown that the endogenous microbial community affects various physiological activities of multicellular organisms. The coelomic cavity of echinoderms contains a fluid in which coelomocytes are reported to exert immune functions like phagocytosis, opsonization and production of antimicrobial agents against marine bacteria [1, 2]. However, up to day nothing is known about the endogenous bacterial population of coelomic fluid. We focused on this iss…

A pipeline for variants discovery using next-generation DNA sequencing data

2017

Recent advances in next generation sequencing (NGS) technology provide a cost-effective approach to large-scale resequencing of livestock samples in order to study several biological phenomena. NGS produces millions of short DNA sequences that require an unbiased way to make possible comprehensive searches for variation to identify putative causative mutations for economically important traits. The aim of this work was to present a bioinformatics pipeline analysis for variants discovery in ovine genome. A total of 30 individuals belonging to Valle del Belice dairy ewes was used for whole genome sequencing of pooled libraries prepared using Illumina Nextera Kit. Paired-end sequencing was car…

Next generation diagnostic algorithm in non-small cell lung cancer predictive molecular pathology: The KWAY Italian multicenter cost evaluation study

2022

Abstract Aims The KWAY project aims to investigate the economic sustainability of the up-front NGS technologies adoption in the analysis of clinically relevant molecular alterations in NSCLC patients. Methods The diagnostic workflow and the related sustained costs of five Italian referral centers were assessed in four different evolving scenarios were analyzed. For each scenario, two alternative testing strategies were evaluated: the Maximized Standard strategy and the Maximized NGS strategy. Results For each center, the robustness of obtained results was verified through a deterministic sensitivity analysis, observing the variation of total costs based on a variation of ±20 % of the input …

Real-time detection of BRAF V600E mutation from archival hairy cell leukemia FFPE tissue by nanopore sequencing

2018

The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirable, but their adoption for molecular assays is hurdled by the high degree of fragmentation and by the chemical-induced mutations stemming from the fixation protocols. In order to investigate the suitability of MinION sequencing on formalin-fixed paraffin-embedded samples, the presence and frequency of BRAF c.1799T > A mutation was investigated in two archival tissue specimens of Hairy cell leukemia and Hairy cell leukemia Variant. Despite the poor quality of the starting DNA, BRAF mutation was su…