CoNVaQ: a web tool for copy number variation-based association studies

BMC Genomics
Simon Jonas LarsenJan Baumbach

Abstract

Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to disease phenotypes, the extension of GWAS to CNVs has aided the discovery of structural variants associated with human traits and diseases. We present CoNVaQ, an easy-to-use web-based tool for CNV-based association studies. The web service allows users to upload two sets of CNV segments and search for genomic regions where the occurrence of CNVs is significantly associated with the phenotype. CoNVaQ provides two models: a simple statistical model using Fisher's exact test and a novel query-based model matching regions to user-defined queries. For each region, the method computes a global q-value statistic by repeated permutation of samples among the populations. We demonstrate our platform by using it to analyze a data set of HPV-positive and HPV-negative penile cancer patients. CoNVaQ provides a simple workflow for performing CNV-based association studies. It is made available as a web platform in order to provide a user-friendly workflow fo...Continue Reading

References

Feb 10, 2007·Science·Barbara E StrangerEmmanouil T Dermitzakis
Dec 7, 2007·Nature Genetics·Edward J HolloxJoost Schalkwijk
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Apr 28, 2012·Bioinformatics·Ji-Hong KimYeun-Jun Chung
Jan 8, 2013·Nucleic Acids Research·Joseph T GlessnerHakon Hakonarson
Jan 16, 2013·Chemotherapy Research and Practice·Zahi MitriRuth O'Regan
Nov 28, 2014·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
Dec 17, 2014·Cancer Prevention Research·Ariane F Busso-LopesSilvia R Rogatto
Apr 30, 2015·Briefings in Functional Genomics·Eric R Gamazon, Barbara E Stranger
Dec 22, 2015·Nucleic Acids Research·Andrew YatesPaul Flicek
Dec 3, 2016·Nucleic Acids Research·Minoru KanehisaKanae Morishima
Nov 18, 2017·Nucleic Acids Research·Antonio FabregatPeter D'Eustachio

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Citations

Mar 31, 2019·International Journal of Molecular Sciences·Renée Laufer-AmorimSilvia Regina Rogatto
Mar 13, 2020·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Bohai FengJochen Hess
Jan 1, 2021·Frontiers in Oncology·Yongbo YuHaitao Niu

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Software Mentioned

CoNVaQ
CNVRuler
DisGeNET
DOSE
R
clusterProfiler
ParseCNV

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