HAPGEN2: simulation of multiple disease SNPs
HAPGEN2: simulation of multiple disease SNPs
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DOI：
10.1093/bioinformatics/btr341
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发表时间：
2011-08-15
期刊：
影响因子：
5.8
通讯作者：
Donnelly, Peter
中科院分区：
文献类型：
--
作者：
Su, Zhan;Marchini, Jonathan;Donnelly, Peter
动机：使用模拟数据进行实验是一种评估全基因组关联研究中竞争实验设计和分析方法的廉价方法。基于重新采样的已知单倍型的仿真是快速有效的，可以生成具有连锁不平衡（LD）模式的样品，这些样本模仿了实际数据中的样本。但是，当前方法无法模拟同一染色体上的多个附近疾病SNP的方法可能会限制其应用。回报：我们基于成功的重新采样方法HAPGEN引入了一种新的模拟算法，可以在同一染色体上模拟附近的多个疾病SNP 。新方法HAPGEN2保留了重新采样方法的许多优势，并扩大了当前模拟器提供的疾病模型的范围。
Motivation: Performing experiments with simulated data is an inexpensive approach to evaluating competing experimental designs and analysis methods in genome-wide association studies. Simulation based on resampling known haplotypes is fast and efficient and can produce samples with patterns of linkage disequilibrium (LD), which mimic those in real data. However, the inability of current methods to simulate multiple nearby disease SNPs on the same chromosome can limit their application.Results: We introduce a new simulation algorithm based on a successful resampling method, HAPGEN, that can simulate multiple nearby disease SNPs on the same chromosome. The new method, HAPGEN2, retains many advantages of resampling methods and expands the range of disease models that current simulators offer.