RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data

Tomasz Stokowy; Mateusz Garbulowski; Torunn Fiskerstrand; Rita Holdhus; Kornel Labun; Pawel Sztromwasser; Christian Gilissen; Alexander Hoischen; Gunnar Houge; Kjell Petersen; Inge Jonassen; Vidar M Steen

doi:10.1093/bioinformatics/btw359

RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data

Bioinformatics. 2016 Oct 1;32(19):3018-20. doi: 10.1093/bioinformatics/btw359. Epub 2016 Jun 10.

Authors

Affiliations

¹ Department of Clinical Science, University of Bergen, Bergen 5020, Norway Department of Informatics, Computational Biology Unit, University of Bergen, Bergen 5020, Norway.
² Department of Informatics, Silesian University of Technology, Gliwice 44-100, Poland.
³ Department of Clinical Science, University of Bergen, Bergen 5020, Norway Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen 5021, Norway.
⁴ Department of Clinical Science, University of Bergen, Bergen 5020, Norway.
⁵ Department of Informatics, Computational Biology Unit, University of Bergen, Bergen 5020, Norway.
⁶ Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525, The Netherlands.
⁷ Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen 5021, Norway.

PMID: 27288501
DOI: 10.1093/bioinformatics/btw359

Abstract

Motivation: The search for causative genetic variants in rare diseases of presumed monogenic inheritance has been boosted by the implementation of whole exome (WES) and whole genome (WGS) sequencing. In many cases, WGS seems to be superior to WES, but the analysis and visualization of the vast amounts of data is demanding.

Results: To aid this challenge, we have developed a new tool-RareVariantVis-for analysis of genome sequence data (including non-coding regions) for both germ line and somatic variants. It visualizes variants along their respective chromosomes, providing information about exact chromosomal position, zygosity and frequency, with point-and-click information regarding dbSNP IDs, gene association and variant inheritance. Rare variants as well as de novo variants can be flagged in different colors. We show the performance of the RareVariantVis tool in the Genome in a Bottle WGS data set.

Availability and implementation: https://www.bioconductor.org/packages/3.3/bioc/html/RareVariantVis.html

Contact: tomasz.stokowy@k2.uib.no

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Exome*
Genetic Variation
Genome, Human*
Humans
Rare Diseases / genetics*
Sequence Analysis, DNA / methods*