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Protocols

ViVar specifications

Information


Unique identifier OMICS_07111
Name ViVar
Alternative name arrayCGHbase
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Filip Pattyn
  • person_outline Piet Robbrecht
  • person_outline Evi Michels
  • person_outline Bjorn Menten
  • person_outline Katleen De Preter

Publications for ViVar

ViVar citations

 (22)
call_split

The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease

2017
Oncotarget
PMCID: 5823580
PMID: 29492199
DOI: 10.18632/oncotarget.23614
call_split See protocol

[…] hnologies). Fluorescence intensities were measured on an Agilent G2505C scanner. Data were extracted using the Feature Extraction v10.1.1.1 software (Agilent Technologies), and further processed with ViVar []. Gains and losses were determined using the circular binary segmentation algorithm []. […]

library_books

Early onset primary antibody deficiency resembling common variable immunodeficiency challenges the diagnosis of Wiedeman Steiner and Roifman syndromes

2017
Sci Rep
PMCID: 5473876
PMID: 28623346
DOI: 10.1038/s41598-017-02434-4

[…] performed on the affected sibling pairs of families A and B using the SurePrint G3 Human CGH Microarray Kit according to manufacturer’s instructions (Agilent Technologies). Results were analyzed with arrayCGHbase. Karyotype analysis was performed on the family A twins using the conventional G-banding technique. To screen the family A twins for submicroscopic subtelomeric rearrangements, multiplex […]

library_books

Mutations in Splicing Factor Genes Are a Major Cause of Autosomal Dominant Retinitis Pigmentosa in Belgian Families

2017
PLoS One
PMCID: 5226823
PMID: 28076437
DOI: 10.1371/journal.pone.0170038

[…] as used for high-resolution copy number variant analysis of 106 known and 60 candidate genes for iRD and 196 retina-expressed non-coding RNAs (ncRNAs) []. The data was processed and analyzed with the ViVar software (http://www.cmgg.be/vivar/). […]

library_books

arrEYE: a customized platform for high resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs

2016
Genet Med
PMCID: 5392597
PMID: 27608171
DOI: 10.1038/gim.2016.119

[…] es were scanned using an Agilent DNA Microarray Scanner and quantified with Agilent Feature Extraction Software (version 10.7.1.1). The data were further processed, analyzed, and visualized using the ViVar platform (October 2015; https://www.cmgg.be/vivar/) using a circular binary segmentation algorithm. Prior to the validation, we considered a region deleted or duplicated when the log2 ratio enco […]

library_books

Performance of a TthPrimPol based whole genome amplification kit for copy number alteration detection using massively parallel sequencing

2016
Sci Rep
PMCID: 4992833
PMID: 27546482
DOI: 10.1038/srep31825

[…] Fastq files of the samples were automatically analyzed using the Vivar software. The Vivar software performs CNA detection using the QDNAseq algorithm. After removal of poorly mapped reads, this algorithm normalizes the number of reads mapped in non-overlapping, fi […]

library_books

DNA methylation profiling of primary neuroblastoma tumors using methyl CpG binding domain sequencing

2016
Sci Data
PMCID: 4736656
PMID: 26836295
DOI: 10.1038/sdata.2016.4

[…] 38 tumors are available through the NCBI Gene Expression Omnibus (GEO) database (GSE21713 and GSE32664; sample IDs in (available online only)). Matching aCGH data of 38 tumors are available through ViVar (https://www.cmgg.be/vivar/; login: review, password: review, project: Kumps et al. 2013; sample IDs in (available online only)). […]

Citations

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ViVar institution(s)
Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium; Department of Medical Genetics, University Medical Center Utrecht, Utrecht, Netherlands; BioBix, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium

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