R-Gada: a fast and flexible pipeline for copy number analysis in association studies.

BMC Bioinformatics
Roger Pique-RegiJuan R González

Abstract

Genome-wide association studies (GWAS) using Copy Number Variation (CNV) are becoming a central focus of genetic research. CNVs have successfully provided target genome regions for some disease conditions where simple genetic variation (i.e., SNPs) has previously failed to provide a clear association. Here we present a new R package, that integrates: (i) data import from most common formats of Affymetrix, Illumina and aCGH arrays; (ii) a fast and accurate segmentation algorithm to call CNVs based on Genome Alteration Detection Analysis (GADA); and (iii) functions for displaying and exporting the Copy Number calls, identification of recurrent CNVs, multivariate analysis of population structure, and tools for performing association studies. Using a large dataset containing 270 HapMap individuals (Affymetrix Human SNP Array 6.0 Sample Dataset) we demonstrate a flexible pipeline implemented with the package. It requires less than one minute per sample (3 million probe arrays) on a single core computer, and provides a flexible parallelization for very large datasets. Case-control data were generated from the HapMap dataset to demonstrate a GWAS analysis. The package provides the tools for creating a complete integrated pipeline from...Continue Reading

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Citations

Sep 21, 2013·Bioinformatics·Liangcai Zhang, Li Zhang
Nov 8, 2012·Physiological Genomics·Wenli Li, Michael Olivier
Dec 29, 2012·BMC Bioinformatics·Melissa PronoldShahab Asgharzadeh
Nov 20, 2013·Seminars in Hematology·Mitchell J Machiela, Stephen J Chanock
Sep 20, 2015·Genomics, Proteomics & Bioinformatics·Qiyan WangChangqing Zeng
Mar 13, 2012·British Journal of Haematology·Louise BorstKjeld Schmiegelow
Apr 21, 2016·European Journal of Human Genetics : EJHG·Kristina Magaard KoldbyLene Christiansen
Apr 19, 2015·BMC Genomics·Tamas RevayW Allan King
Feb 20, 2014·Proceedings of the National Academy of Sciences of the United States of America·Francesco GattoJens Nielsen
Jul 22, 2015·PloS One·Marcel Elie NutsuaMichael Nothnagel
Feb 11, 2015·Scientific Reports·Laura KasakMaris Laan
May 9, 2012·Nature Genetics·Kevin B JacobsStephen J Chanock
Sep 10, 2019·Inflammation and Regeneration·Masafumi UmekageNaoko Takasu
Jan 4, 2018·Blood Advances·Mitchell J MachielaStephen J Chanock
Jan 1, 2015·Microarrays·Logan C WalkerJohn F Pearson
Jun 14, 2015·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Rebeca Sanz-PamplonaVictor Moreno
Jan 13, 2021·Journal of Personalized Medicine·Nayoung HanIn-Wha Kim
Nov 17, 2017·G3 : Genes - Genomes - Genetics·Benjamin L Rambo-MartinMichael E Zwick

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Methods Mentioned

BETA
genotyping
PCA

Software Mentioned

ade4
UCSC
BeadStudio
parSBL
Rmpi
aroma
Multiple Correspondence Discriminant Analysis ( MCDA )
R
GadaModel
parBE

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