Dataset Information
Affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling.
Ontology highlight
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 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.Results
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.Conclusion
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.
SUBMITTER: Hernandez-Ferrer C
PROVIDER: S-EPMC4438530 | biostudies-literature | 2015 May
REPOSITORIES: biostudies-literature
Publications
affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling.
BMC bioinformatics 20150520
<h4>Background</h4>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 studi ...[more]
