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

被引：4
作者：
Hernandez-Ferrer, Carles [1 ,2 ,3 ]
Quintela Garcia, Ines [4 ,5 ]
Danielski, Katharina [6 ]
Carracedo, Angel [4 ,7 ,8 ,9 ]
Perez-Jurado, Luis A. [7 ,10 ,11 ]
Gonzalez, Juan R. [1 ,2 ,3 ]
机构：
[1] Ctr Res Environm Epidemiol CREAL, Doctor Aiguader 88, Barcelona 08003, Spain
[2] Univ Pompeu Fabra, Barcelona, Spain
[3] CIBER Epidemiol & Salud Publ CIBERESP, Madrid, Spain
[4] Univ Santiago de Compostela, Grp Med Xenom, Santiago De Compostela, Spain
[5] Inst Salud Carlos III, Ctr Nacl Genotipado, Santiago De Compostela, Spain
[6] Affymetrix UK Ltd, High Wycombe, Bucks, England
[7] CIBER Enfermedades Raras CIBERER, Madrid, Spain
[8] Fdn Publ Galega Med Xenom SERGAS, Santiago De Compostela, Spain
[9] King Abdulaziz Univ, Ctr Excellence Genom Med Res, Jeddah 21413, Saudi Arabia
[10] Univ Pompeu Fabra, Dept Ciencies Expt & Salut, Barcelona, Spain
[11] Hosp del Mar Med Res Inst IMIM, Barcelona, Spain
来源：
BMC BIOINFORMATICS | 2015年 / 16卷
关键词：
Affymetrix; CytoScan; CytoScan HD; 750k; CNV; Inversion; Mosaicism; Structural variants;
D O I：
10.1186/s12859-015-0608-y
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
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.
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页数：11
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