Document Details

Document Type : Article In Journal 
Document Title :
affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling
affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling
 
Document Language : English 
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. 
ISSN : 1471-2105 
Journal Name : BMC bioinformatics 
Volume : 16 
Issue Number : 1 
Publishing Year : 1436 AH
2015 AD 
Article Type : Article 
Added Date : Wednesday, April 20, 2016 

Researchers

Researcher Name (Arabic)Researcher Name (English)Researcher TypeDr GradeEmail
Carles Hernandez-FerrerHernandez-Ferrer, Carles Investigator  
Ines Quintela GarciaGarcia, Ines QuintelaResearcher  
Katharina DanielskiDanielski, Katharina Researcher  
Ángel CarracedoCarracedo, Ángel Researcher  
Luis A. Pérez-JuradoPérez-Jurado, Luis A.Researcher  
Juan R. GonzálezGonzález, Juan R.Researcher  

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