Abstract
BackgroundThe 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 package affy2sv to pre-process Affymetrix CytoScan HD/750k array (also for Genome-Wide SNP 5.0/6.0 and Axiom) in structural variant studies.ResultsWe illustrate the capabilities of affy2sv 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.ConclusionBoth examples presented in the article show up how affy2sv 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0608-y) contains supplementary material, which is available to authorized users.
Highlights
The well-known Genome-Wide Association Studies (GWAS) had led to many scientific discoveries using single nucleotide polymorphisms (SNPs) data
The two CytoScan HD populations were pre-process using affy2sv and analyzed using different tools including the quality control performed over the SNPs, can be found in supplementary material (Additional file 1)
The mosaicism study in Dataset A was done by using the R package MAD (Additional file 1)
Summary
Both examples presented in the article show up how affy2sv 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.
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