ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation

Sante, Tom; Vergult, Sarah; Volders, Pieter-Jan; Kloosterman, Wigard P.; Trooskens, Geert; Preter, Katleen De; Dheedene, Annelies; Speleman, Franki; Meyer, Tim De; Menten, Björn

doi:10.1371/journal.pone.0113800

Cited by 52 publications

(32 citation statements)

References 29 publications

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“…With these values, a Z‐score (standard score) for each chromosome in each sample could be calculated. QDNAseq values were imported and processed in Vivar . Aberrant results (for all chromosomes) were manually checked on a comprehensive chromosome profile by Wisecondor and Vivar to exclude large (maternal) segmental aberrations.…”

Section: Methodsmentioning

confidence: 99%

Implementation of non‐invasive prenatal testing by semiconductor sequencing in a genetic laboratory

et al. 2016

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ObjectivesTo implement non‐invasive prenatal testing (NIPT) for fetal aneuploidies with semiconductor sequencing in an academic cytogenomic laboratory and to evaluate the first 15‐month experience on clinical samples.MethodsWe validated a NIPT protocol for cell‐free fetal DNA sequencing from maternal plasma for the detection of trisomy 13, 18 and 21 on a semiconductor sequencing instrument. Fetal DNA fraction calculation for all samples and several quality parameters were implemented in the workflow. One thousand eighty‐one clinical NIPT samples were analysed, following the described protocol.ResultsNon‐invasive prenatal testing was successfully implemented and validated on 201 normal and 74 aneuploid samples. From 1081 clinical samples, 17 samples showed an abnormal result: 14 trisomy 21 samples, one trisomy 18 and one trisomy 16 were detected. Also a maternal copy number variation on chromosome 13 was observed, which could potentially lead to a false positive trisomy 13 result. One sex discordant result was reported, possibly attributable to a vanishing twin. Moreover, our combined fetal fraction calculation enabled a more reliable risk estimate for trisomy 13, 18 and 21.ConclusionsNon‐invasive prenatal testing for trisomy 21, 18 and 13 has a very high specificity and sensitivity. Because of several biological phenomena, diagnostic invasive confirmation of abnormal results remains required. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.

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Section: Methodsmentioning

confidence: 99%

Implementation of non‐invasive prenatal testing by semiconductor sequencing in a genetic laboratory

et al. 2016

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“…We organized the displaying methods into ten major categories (Table 1; Fig. 1), namely, linear genome browser, Fastbreak [30], Gremlin [51], ViVar [52] Two-way view --…”

Section: View Modules For Visualizing Svmentioning

confidence: 99%

Visualization tools for human structural variations identified by whole-genome sequencing

Yokoyama

Kasahara

2019

J Hum Genet

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Visualizing structural variations (SVs) is a critical step for finding associations between SVs and human traits or diseases. Given that there are many sequencing platforms used for SV identification and given that how best to visualize SVs together with other data, such as read alignments and annotations, depends on research goals, there are dozens of SV visualization tools designed for different research goals and sequencing platforms. Here, we provide a comprehensive survey of over 30 SV visualization tools to help users choose which tools to use. This review targets users who wish to visualize a set of SVs identified from the massively parallel sequencing reads of an individual human genome. We first categorize the ways in which SV visualization tools display SVs into ten major categories, which we denote as view modules. View modules allow readers to understand the features of each SV visualization tool quickly. Next, we introduce the features of individual SV visualization tools from several aspects, including whether SV views are integrated with annotations, whether long-read alignment is displayed, whether underlying data structures are graph-based, the type of SVs shown, whether auditing is possible, whether bird's eye view is available, sequencing platforms, and the number of samples. We hope that this review will serve as a guide for readers on the currently available SV visualization tools and lead to the development of new SV visualization tools in the near future.

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“…Segmentation is achieved using the circular binary segmentation algorithm in the DNACopy R package. Visual inspection and creation of the copy number profile plots is performed with 'Vivar' (26). All raw array CGH data files are made publically available through the Gene Expression Omnibus (GEO) website using the accession number GSE85444.…”

Section: Array Cghmentioning

confidence: 99%

Targeted genomic screen reveals focal long non-coding RNA copy number alterations in cancer

Volders

Vandesompele

Lefever

et al. 2017

Preprint

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The landscape of somatic copy-number alterations (SCNAs) affecting long non-coding RNAs (lncRNAs) in human cancer remains largely unexplored. While the majority of lncRNAs remains to be functionally characterized, several have been implicated in cancer development and metastasis. Considering the plethora of lncRNAs genes that is currently reported, it is conceivable that several lncRNAs might function as oncogenes or tumor suppressor genes.We devised a strategy to detect focal lncRNA SCNAs using a custom DNA microarray platform probing 20 418 lncRNA genes. By screening a panel of 80 cancer cell lines, we detected numerous focal aberrations targeting one or multiple lncRNAs without affecting neighboring protein-coding genes. These focal aberrations are highly suggestive for a tumor suppressive or oncogenic role of the targeted lncRNA gene.Although functional validation remains an essential step in the further characterization of the involved candidate cancer lncRNAs, our results provide a direct way of prioritizing candidate lncRNAs involved in cancer pathogenesis.

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ViVar: A Comprehensive Platform for the Analysis and Visualization of Structural Genomic Variation

Cited by 52 publications

References 29 publications

Implementation of non‐invasive prenatal testing by semiconductor sequencing in a genetic laboratory

Implementation of non‐invasive prenatal testing by semiconductor sequencing in a genetic laboratory

Visualization tools for human structural variations identified by whole-genome sequencing

Targeted genomic screen reveals focal long non-coding RNA copy number alterations in cancer

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