Introduction

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.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.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.

Publications

  1. affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling.
    Cite this
    Hernandez-Ferrer C, Quintela Garcia I, Danielski K, Carracedo Á, Pérez-Jurado LA, González JR, 2015-05-01 - BMC Bioinformatics

Credits

  1. Carles Hernandez-Ferrer
    Developer

    CIBER Epidemiología y Salud Pública (CIBERESP), Madrid

  2. Ines Quintela Garcia
    Developer

    Centro Nacional de Genotipado - Instituto Carlos III, Santiago de Compostela

  3. Katharina Danielski
    Developer

    Affymetrix, UK Ltd

  4. Ángel Carracedo
    Developer

    King Abdulaziz University, Center of Excellence in Genomic Medicine Research

  5. Luis A Pérez-Jurado
    Developer

    IMIM (Hospital del Mar Medical Research Institute), Barcelona

  6. Juan R Gonzalez
    Investigator

    CIBER Epidemiología y Salud Pública (CIBERESP), Madrid

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Summary
AccessionBT005791
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++, R
User InterfaceTerminal Command Line
Download Count0
Submitted ByJuan R Gonzalez