affy2sv：一个用于预处理Affymetrix CytoScan HD和750K阵列以进行单核苷酸多态性（SNP）、拷贝数变异（CNV）、倒位和嵌合体检测的R软件包。
affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling.
作者信息
Hernandez-Ferrer Carles, Quintela Garcia Ines, Danielski Katharina, Carracedo Ángel, Pérez-Jurado Luis A, González Juan R
机构信息
Center for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, 08003, Barcelona, Spain.
Universitat Pompeu Fabra (UPF), Barcelona, Spain.
出版信息
BMC Bioinformatics. 2015 May 20;16:167. doi: 10.1186/s12859-015-0608-y.
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.
背景
著名的全基因组关联研究（GWAS）利用单核苷酸多态性（SNP）数据带来了许多科学发现。即便如此，它们仍无法解释复杂疾病的全部遗传力。如今，其他结构变异，如拷贝数变异或DNA倒位，无论是种系的还是嵌合事件中的，都正在被研究。我们展示了R包affy2sv，用于在结构变异研究中对Affymetrix CytoScan HD/750k阵列（也适用于全基因组SNP 5.0/6.0和Axiom）进行预处理。
结果
我们使用两个不同的完整流程在真实数据上展示了affy2sv的功能。第一个流程进行全基因组关联研究和嵌合改变检测研究，另一个流程检测拷贝数变异并进行倒位检测。
结论
本文给出的两个例子都展示了affy2sv如何作为更复杂流程的一部分，用于在遗传关联研究中分析Affymetrix SNP阵列数据，其中考虑了不同类型的结构变异。
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