affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling

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...

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Bibliographic Details
Published in:BMC bioinformatics 2015-05, Vol.16 (1), p.167-167, Article 167
Main Authors: Hernandez-Ferrer, Carles, Quintela Garcia, Ines, Danielski, Katharina, Carracedo, Ángel, Pérez-Jurado, Luis A, González, Juan R
Format: Article
Language:English
Subjects:
Algorithms
Chromosome Inversion - genetics
DNA Copy Number Variations - genetics
Genetic Association Studies
Genoma humà
Genome, Human
Genome-Wide Association Study
Humans
In Situ Hybridization, Fluorescence
Mosaicism
Oligonucleotide Array Sequence Analysis - methods
Oligonucleòtids
Paraffin Embedding
Polymorphism, Single Nucleotide - genetics
Software
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Summary: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 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. We 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. 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.
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-015-0608-y