RT Journal Article
T1 affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling
A1 Hernández Ferrer, Carles
A1 Quintela García, Inés
A1 Danielski, Katharina
A1 Pérez Jurado, Luís Alberto
A1 González, Juan R.
A1 Carracedo Álvarez, Ángel
K1 Affymetrix
K1 CytoScan
K1 CytoScan HD
K1 CytoScan 750k
K1 CNV
K1 Inversion
K1 Mosaicism
K1 Structural variants
AB 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.
PB BMC
SN 1471-2105
YR 2015
FD 2015
LK http://hdl.handle.net/10347/23016
UL http://hdl.handle.net/10347/23016
LA eng
NO Hernandez-Ferrer, C., Quintela Garcia, I., Danielski, K. et al. affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling. BMC Bioinformatics 16, 167 (2015). https://doi.org/10.1186/s12859-015-0608-y
NO This work was partly supported by the Spanish Ministry of Science and Innovation (MTM2011-26515), FIS PI1002512 and a predoctoral fellowship of the Universitat Pompeu Fabra (to CH-F)
DS Minerva
RD 24 abr 2026