Affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Hernandez-Ferrer, Carles; Quintela Garcia, Ines; Danielski, Katharina; Carracedo, Ángel; Pérez-Jurado, Luis; González, Juan
• Is Part Of: BMC bioinformatics. Volume 16:Issue 1(2015)
• Page Start: 1
• Page End: 11
• Publication Date: 2015-12
• Subjects: Affymetrix -- CytoScan -- CytoScan HD -- CytoScan 750k -- CNV -- Inversion -- Mosaicism -- Structural variants; Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-015-0608-y
• Languages: English
• ISSNs: 1471-2105

Abstract

Abstract Background The well-known Genome-Wide Association Studies (GWAS) had led to many scientific discoveries using SNP data. Even so, they were not able to explain the full heritability of complex diseases. Now, other structural variants like copy number variants or DNA inversions, either germ-line or in mosaicism events, are being studies. We present the R packageaffy2sv to pre-process Affymetrix CytoScan HD/750k array (also for Genome-Wide SNP 5.0/6.0 and Axiom) in structural variant studies. Results We illustrate the capabilities ofaffy2sv using two different complete pipelines on real data. The first one performing a GWAS and a mosaic alterations detection study, and the other detecting CNVs and performing an inversion calling. Conclusion Both examples presented in the article show up howaffy2sv can be used as part of more complex pipelines aimed to analyze Affymetrix SNP arrays data in genetic association studies, where different types of structural variants are considered.