Search results for " Sequencing"

PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment

2017

The progress of next-generation sequencing has a major impact on medical and genomic research. This technology can now produce billions of short DNA fragments (reads) in a single run. One of the most demanding computational problems used by almost every sequencing pipeline is short-read alignment; i.e. determining where each fragment originated from in the original genome. Most current solutions are based on a seed-and-extend approach, where promising candidate regions (seeds) are first identified and subsequently extended in order to verify whether a full high-scoring alignment actually exists in the vicinity of each seed. Seed verification is the main bottleneck in many state-of-the-art a…

Human Leukocyte Antigen Typing Using High-Throughput DNA and RNA Sequencing and Application for Cell Line Identification

2019

A multi-omic liquid biopsy-based signature as a valuable tool to assess minimal residual disease in localised colorectal cancer

2019

El cáncer colorrectal (CCR) es un importante problema de salud pública. Más de 1.2 millones de pacientes se diagnostican de CCR cada año, y más de 600.000 mueren a causa de la enfermedad. El pronóstico de los pacientes con CCR ha mejorado durante las últimas décadas, con una supervivencia a los 5 años que ha alcanzado casi el 65% en países desarrollados. El estadio al diagnóstico es actualmente el factor pronóstico más importante. Aunque la clasificación clásica de estadiaje proporciona información pronóstica y guía las decisiones terapéuticas, no disponemos hoy en día de marcadores predictivos de la respuesta y del resultado clínico de la terapia individual del paciente. Esto es relevante …

Taxonomical and Functional Assessment of the Endometrial Microbiota in A Context of Recurrent Reproductive Failure: A Case Report

2019

Investigation of the microbial community in the female reproductive tract has revealed that the replacement of a community dominated by Lactobacillus with pathogenic bacteria may be associated with implantation failure or early spontaneous abortion in patients undergoing assisted reproductive technology (ART) treatment. Herein we describe taxonomically and functionally the endometrial microbiome of an infertile patient with repeated reproductive failures (involving an ectopic pregnancy and two clinical miscarriages). The microbiological follow-up is presented over 18-month in which the microbiota was evaluated in six endometrial fluid samples. The microbial profile of 16S rRNA gene sequenci…

Serological and molecular characteristics of Vibrio vulnificus biotype 3: evidence for high clonality.

2007

Vibrio vulnificus biotype 3 has been implicated as the causative pathogen of an ongoing disease outbreak that erupted in Israel in 1996. Recent work based on multi-locus sequence typing (MLST) showed that V. vulnificus biotype 3 is genetically homogeneous. The aim of this study was to investigate the existence of subpopulations within this homogeneous biotype by characterizing the surface antigens and analysing the sequence diversity of selected outer-membrane protein (OMP)-encoding genes. Rabbit antisera were prepared against biotype 1, 2 and 3 strains. The results of the slide-agglutination test, dot-blot assay (using fresh and boiled cells), and immunoblotting of lipopolysaccharides (LPS…

ANKRD26-RET - A novel gene fusion involving RET in papillary thyroid carcinoma

2018

Abstract Background Rearrangements of RET are drivers of oncogenesis, traceable in different cancer types as papillary thyroid carcinoma (PTC), non-small cell lung cancer, colorectal or breast cancer. Anchored multiplex PCR based next-generation sequencing (NGS) can detect RET rearrangements involving previously unknown partner genes. Methods A sample of PTC underwent NGS, following detection of RET rearrangement by fluorescence in situ hybridization. Expression analysis of ANKRD26 and RET was performed for the tumor harboring ANKRD26-RET, for corresponding normal thyroid tissue and PTC tumors with representative genetic alterations (BRAFV600E, CCDC6-RET), complemented by a comparative sear…

Selective enrichment of heterotrophic nitrifiers

2019

Removal of nitrogen from wastewaters (WW) represents a global problem. The low nitrification rate during WW treatment is often caused by ecotoxicity. This problem is attributed mostly to the industrial WW. Our study was focused on the testing of industrial WW and activated sludge (AS) with the aim to reveal the abundance of nitrifiers and increase their biomass, thus, providing the additional step, i.e., bioaugmentation, within the technological process of WW treatment. Plating of AS on the selective solidified media designated for the 1st and 2nd nitrification stages, resulted in the shift in bacterial community structure with dominated Alcaligenaceae and Alcanivorax for the 1st stage, and…

Dynamique de la communauté microbienne de sols tropicaux suite à une application répétée de fertilisants organiques et minéraux

2019

Organic waste products (OWP) with NPK mineral fertilization are known to have an impact on soil microbial communities. However, dynamic of these communities following a repeated OWP and NPK application has not been well described. In the present study, this dynamic was observed on soil sampled at the La Mare (La Réunion) field experiment, which was set up in 2013. This experiment includes control plot (without organic input, but mineral fertilization) and several plots receiving different types of OWP coupled with NPK fertilization. Physico-chemical parameters were measured on soils and OWPs (2013 to 2017). Soil microbial biomass (from 2013 to 2018) and the structure of microbial community …

Consistency of Targeted Metatranscriptomics and Morphological Characterization of Phytoplankton Communities

2020

The composition of phytoplankton community is the basis for environmental monitoring and assessment of the ecological status of aquatic ecosystems. Community composition studies of phytoplankton have been based on time-consuming and expertise-demanding light microscopy analyses. Molecular methods have the potential to replace microscopy, but the high copy number variation of ribosomal genes and the lack of universal primers for simultaneous amplification of prokaryotic and eukaryotic genes complicate data interpretation. In this study, we used our previously developed directional primer-independent high-throughput sequencing (HTS) approach to analyze 16S and 18S rRNA community structures. C…

Capacity building in clinical and molecular characterization of rare neurodegenerative diseases through the development of a local register and impro…

2020

Neurodegenerative diseases (NDs) are very polymorphic and affect people of all ages. They concern both rare diseases and more common diseases. Improving knowledge of NDs in the French Caribbean region requires special attention because of the unique environmental and genetic background of its populations. In Martinique, there is a huge need for scientific research on rare NDs. While epidemiological and clinical research has increased over the past decade in the French West Indies, there is still little or no data on the genetics of NDs in these regions. The advent of Next Generation Sequencing (NGS) on a global scale has the potential to make a difference in this field, provided that techno…