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

Carles Hernandez-Ferrer, Ines Quintela Garcia, Katharina Danielski, Ángel Carracedo, Luis Perez-Jurado, Juan R. González

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

LanguageEnglish
Article number167
JournalBMC Bioinformatics
Volume16
Issue number1
DOIs
Publication statusPublished - 20 May 2015
Externally publishedYes

Keywords

  • Affymetrix
  • CNV
  • CytoScan
  • CytoScan 750k
  • CytoScan HD
  • Inversion
  • Mosaicism
  • Structural variants

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Hernandez-Ferrer, Carles ; Quintela Garcia, Ines ; Danielski, Katharina ; Carracedo, Ángel ; Perez-Jurado, Luis ; González, Juan R. / affy2sv : An R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling. In: BMC Bioinformatics. 2015 ; Vol. 16, No. 1.
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affy2sv : An R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling. / Hernandez-Ferrer, Carles; Quintela Garcia, Ines; Danielski, Katharina; Carracedo, Ángel; Perez-Jurado, Luis; González, Juan R.

In: BMC Bioinformatics, Vol. 16, No. 1, 167, 20.05.2015.

Research output: Contribution to journalArticle

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AU - González, Juan R.

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