INRAE Bovine long-read WGS
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB68295 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR12770738.fastq.gz | Fastqsanger.gz | |||
| ERR12770739.fastq.gz | Fastqsanger.gz | |||
| ERR12770740.fastq.gz | Fastqsanger.gz | |||
| ERR12770741.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 14 |
Similar Datasets
Project description:Technological advances in Next-Generation Sequencing dramatically increased clinical efficiency of genetic testing, allowing detection of a wide variety of variants, from single nucleotide events to large structural aberrations. Whole Genome Sequencing (WGS) has allowed exploration of areas of the genome that might not have been targeted by other approaches, such as intergenic regions. A single technique detecting all genetic variants at once is intended to expedite the diagnostic process while making it more comprehensive and efficient. Nevertheless, there are still several shortcomings that cannot be effectively addressed by short read sequencing, such as determination of the precise size of short tandem repeat (STR) expansions, phasing of potentially compound recessive variants, resolution of some structural variants and exact determination of their boundaries, etc. Therefore, in some cases variants can only be tentatively detected by short reads sequencing and require orthogonal confirmation, particularly for clinical reporting purposes. Moreover, certain regulatory authorities, for example, New York state CLIA, require orthogonal confirmation of every reportable variant. Such orthogonal confirmations often involve numerous different techniques, not necessarily available in the same laboratory and not always performed in an expedited manner, thus negating the advantages of "one-technique-for-all" approach, and making the process lengthy, prone to logistical and analytical faults, and financially inefficient. Fortunately, those weak spots of short read sequencing can be compensated by long read technology that have comparable or better detection of some types of variants while lacking the mentioned above limitations of short read sequencing. At Variantyx we have developed an integrated clinical genetic testing approach, augmenting short read WGS-based variant detection with Oxford Nanopore Technologies (ONT) long read sequencing, providing simultaneous orthogonal confirmation of all types of variants with the additional benefit of improved identification of exact size and position of the detected aberrations. The validation study of this augmented test has demonstrated that Oxford Nanopore Technologies sequencing can efficiently verify multiple types of reportable variants, thus ensuring highly reliable detection and a quick turnaround time for WGS-based clinical genetic testing.
| S-EPMC10160624 | biostudies-literature
Project description:Characterization of genomic landscape of the 5T murine models for multiple myeloma, by whole-genome sequencing
2018-10-09 | E-MTAB-5302 | biostudies-arrayexpress
Project description:This repository contains whole genome long read sequencing data generated using Oxford Nanopore Technologies from a mouse of the Four Core Genotypes cross. By crossing mice with both a deletion of the sex-determining factor Sry on the Y-chromosome and a transgenic insertion of Sry on Chromosome 3, four combinations of gonadal (testis or ovaries) and chromosomal (XX or XY) are generated, namely XYSry-Chr3Sry+ (gonadal and chromosomal males), XYSry- (gonadal females, chromosomal males), XX (gonadal and chromosomal females), XXChr3Sry+ (gonadal males, chromosomal females). The transgenes were on a C57BL6 genetic background which is crossed with a CAST/EiJ female to allow for the distinction of the parental haplotypes. DNA sequencing was done on a liver sample of the XYSry+ genotype.
2024-10-14 | E-MTAB-14291 | biostudies-arrayexpress
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Whole-genome sequencing on PacBio of laboratory mouse strains. See http://www.sanger.ac.uk/resources/mouse/genomes/ for more details. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2014-10-15 | E-ERAD-328 | biostudies-arrayexpress
Project description:We applied Single Molecule Real-Time long-read whole-genome sequencing in Dux knockout mouse and confirmed the success of our Dux knockout mouse model.
2019-07-31 | GSE134830 | GEO
Project description:NABEC Long-Read Whole-Genome Sequencing
| PRJNA925283 | ENA
Project description:High fertility and low fertility bulls were screened from the a 6000 bull database and then identify the sperm-derived DMR and DMC that assoiated with bull ferrtility via whole genome methtlation sequencing
2024-06-04 | GSE211794 | GEO
Project description:Background and Objectives:Serratia marcescens is an emerging nosocomial pathogen, and the carbapenemase blaNDM has been reported in several surveys in Romania. We aimed to investigate the molecular epidemiology of S. marcescens in two Romanian hospitals over 2010-15, including a neonatal NDM-1 S. marcescens outbreak. Methods:Isolates were sequenced using Illumina technology together with carbapenem-non-susceptible NDM-1-positive and NDM-1-negative Klebsiella pneumoniae and Enterobacter cloacae to provide genomic context. A subset was sequenced with MinION to fully resolve NDM-1 plasmid structures. Resistance genes, plasmid replicons and ISs were identified in silico for all isolates; an annotated phylogeny was reconstructed for S. marcescens. Fully resolved study NDM-1 plasmid sequences were compared with the most closely related publicly available NDM-1 plasmid reference. Results:44/45 isolates were successfully sequenced (S. marcescens, n = 33; K. pneumoniae, n = 7; E. cloacae, n = 4); 10 with MinION. The S. marcescens phylogeny demonstrated several discrete clusters of NDM-1-positive and -negative isolates. All NDM-1-positive isolates across species harboured a pKOX_NDM1-like plasmid; more detailed comparisons of the plasmid structures demonstrated a number of differences, but highlighted the largely conserved plasmid backbones across species and hospital sites. Conclusions:The molecular epidemiology is most consistent with the importation of a pKOX_NDM1-like plasmid into Romania and its dissemination amongst K. pneumoniae/E. cloacae and subsequently S. marcescens across hospitals. The data suggested multiple acquisitions of this plasmid by S. marcescens in the two hospitals studied; transmission events within centres, including a large outbreak on the Targu Mures neonatal unit; and sharing of the pKOX_NDM1-like plasmid between species within outbreaks.
| S-EPMC5890751 | biostudies-literature