ONCOCNV statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

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ONCOCNV specifications

Information


Unique identifier OMICS_07427
Name ONCOCNV
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 5.7
Stability Stable
Maintained Yes

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Publication for ONCOCNV

ONCOCNV in publications

 (4)
PMCID: 5863855
PMID: 29566657
DOI: 10.1186/s12885-018-4229-5

[…] number of pcr amplicons, sequence variation, or pcr enrichment efficiency. for cnv detection in our pcr-enriched amplicon sequencing data of the 20 genes, we used two algorithms, quandico [] and oncocnv [], specifically developed for cnv analysis of amplicon sequencing data. the cnvs detected with these algorithms were then verified experimentally using the multiplex ligation-dependent probe […]

PMCID: 5491498
PMID: 28685159
DOI: 10.1038/s41523-017-0026-6

[…] settings were kept at default values and all computations were done using r/bioconductor., the read counts from aligned and sorted bam files of the ion torrent sequencing were processed using oncocnv with default parameter settings to correct for library size, gc content and amplicon length. the pool of normal samples was used as baseline control to capture the technology specific bias […]

PMCID: 5564634
PMID: 28636991
DOI: 10.18632/oncotarget.18325

[…] somatic mutations. the limit of detection (lod) and the limit of quantification (loq) were at 1% of maf, as set by the manufacturer. copy number variation (cnv) analysis was performed using the oncocnv package []., blood samples were obtained postoperatively and before the first-line treatment. plasma was extracted from edta-anticoagulated blood samples by centrifuging once at 2000 g (10 […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] involved in the preparation of amplicon libraries result in high depth of coverage at the expense of coverage homogeneity., the first method designed for the investigation of cnv from ams data is oncocnv. duplicate sequences are not removed, while rc is performed assigning “each read to only one amplicon region, the one with which the read alignment has the maximum overlap” (boeva et al., )., […]


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ONCOCNV institution(s)
Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, Paris, Mines ParisTech, Fontainebleau, Inserm, U830, Genetics and Biology of Cancers, Paris, France; Institut de Pathologie et de Génétique, Gosselies, Belgium; Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris, France; OncoDNA, Gosselies, Belgium

ONCOCNV review

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Antoine Rousselin

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Desktop
I have been using this tool since 2011 for the detection of CNV in genes predisposed to breast and ovarian cancer.
This software is very precise (specificity, sensitivity). I'm now using it in diagnostics, on small and large panels of genes.

Missing an annotation of variants