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BMC Bioinformatics. 2015 May 20;16:167. doi: 10.1186/s12859-015-0608-y.

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

Author information

1
Center for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, 08003, Barcelona, Spain. chernandez@creal.cat.
2
Universitat Pompeu Fabra (UPF), Barcelona, Spain. chernandez@creal.cat.
3
CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. chernandez@creal.cat.
4
Grupo de Medicina Xenómica - Universidade de Santiago de Compostela, Santiago de Compostela, Spain. ines.quintela@usc.es.
5
Centro Nacional de Genotipado - Instituto Carlos III, Santiago de Compostela, Spain. ines.quintela@usc.es.
6
Affymetrix, UK Ltd, High Wycombe, UK. katharina_danielski@affymetrix.com.
7
Grupo de Medicina Xenómica - Universidade de Santiago de Compostela, Santiago de Compostela, Spain. angel.carracedo@usc.es.
8
CIBER Enfermedades Raras (CIBERER), Madrid, Spain. angel.carracedo@usc.es.
9
Fundación Pública Galega de Medicina Xenómica (SERGAS), Santiago de Compostela, Spain. angel.carracedo@usc.es.
10
King Abdulaziz University, Center of Excellence in Genomic Medicine Research, Jeddah, Saudi Arabia. angel.carracedo@usc.es.
11
CIBER Enfermedades Raras (CIBERER), Madrid, Spain. luis.perez@upf.edu.
12
Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain. luis.perez@upf.edu.
13
IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain. luis.perez@upf.edu.
14
Center for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, 08003, Barcelona, Spain. jrgonzalez@creal.cat.
15
Universitat Pompeu Fabra (UPF), Barcelona, Spain. jrgonzalez@creal.cat.
16
CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. jrgonzalez@creal.cat.

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.

PMID:
25991004
PMCID:
PMC4438530
DOI:
10.1186/s12859-015-0608-y
[Indexed for MEDLINE]
Free PMC Article

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