title: affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Center for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, 08003, Barcelona, Spain. chernandez@creal.cat.|Universitat Pompeu Fabra (UPF), Barcelona, Spain. chernandez@creal.cat.|CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. chernandez@creal.cat.
authors.forename: Carles
authors.initials: C
authors.lastname: Hernandez-Ferrer
authors.affiliation: Grupo de Medicina Xenómica - Universidade de Santiago de Compostela, Santiago de Compostela, Spain. ines.quintela@usc.es.|Centro Nacional de Genotipado - Instituto Carlos III, Santiago de Compostela, Spain. ines.quintela@usc.es.
authors.forename: Ines
authors.initials: I
authors.lastname: Quintela Garcia
authors.affiliation: Affymetrix, UK Ltd, High Wycombe, UK. katharina_danielski@affymetrix.com.
authors.forename: Katharina
authors.initials: K
authors.lastname: Danielski
authors.affiliation: Grupo de Medicina Xenómica - Universidade de Santiago de Compostela, Santiago de Compostela, Spain. angel.carracedo@usc.es.|CIBER Enfermedades Raras (CIBERER), Madrid, Spain. angel.carracedo@usc.es.|Fundación Pública Galega de Medicina Xenómica (SERGAS), Santiago de Compostela, Spain. angel.carracedo@usc.es.|King Abdulaziz University, Center of Excellence in Genomic Medicine Research, Jeddah, Saudi Arabia. angel.carracedo@usc.es.
authors.forename: Ángel
authors.initials: Á
authors.lastname: Carracedo
authors.affiliation: CIBER Enfermedades Raras (CIBERER), Madrid, Spain. luis.perez@upf.edu.|Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain. luis.perez@upf.edu.|IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain. luis.perez@upf.edu.
authors.forename: Luis A
authors.initials: LA
authors.lastname: Pérez-Jurado
authors.affiliation: Center for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, 08003, Barcelona, Spain. jrgonzalez@creal.cat.|Universitat Pompeu Fabra (UPF), Barcelona, Spain. jrgonzalez@creal.cat.|CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. jrgonzalez@creal.cat.
authors.forename: Juan R
authors.initials: JR
authors.lastname: González
mesh_terms: D000465:Algorithms; D007446:Chromosome Inversion / Q000235:genetics*; D056915:DNA Copy Number Variations / Q000235:genetics*; D056726:Genetic Association Studies; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D009030:Mosaicism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016612:Paraffin Embedding; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012984:Software