GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores.
GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores.
复制标题
DOI：
10.1186/1756-0500-4-158
复制
发表时间：
2011-05-26
影响因子：
1.8
通讯作者：
Li, Mingyao
中科院分区：
文献类型：
--
作者：
Chikkagoudar, Satish;Wang, Kai;Li, Mingyao
背景：当涉及大量SNP时，遗传关联研究中的基因-基因相互作用是计算密集型的。大多数最新的中央处理器（CPU）都有多个核心，而图形处理器（GPU）也有数百个核心，最近被用来实现更快的科学软件。然而，目前还没有遗传分析软件包，允许用户充分利用这些多核设备的计算能力的遗传交互分析二进制traits.FINDINGS：在这里，我们提出了一种新的软件包GENIE，它利用多个GPU或CPU处理器核心的并行化的相互作用分析。GENIE将整个遗传关联研究数据集读取到内存中，并将数据集划分为具有非重叠SNP集的片段。对于每个片段，GENIE分析：1）其中SNP的相互作用，以及2）当前片段的SNP与其他片段之间的相互作用。我们在高密度脂蛋白胆固醇的大规模候选基因研究中测试了GENIE。使用NVIDIA Tesla C1060显卡，GENIE的GPU模式比单核CPU模式运行时获得了27倍的加速比。结论：GENIE是一个开源的、经济的、用户友好的、可扩展的软件。由于图形卡的计算能力和内存容量正在迅速增加，而其成本正在下降，我们预计GENIE将通过更快的GPU卡实现更大的加速。文档、源代码和预编译的二进制文件可以从http://www.cceb.upenn.edu/~mli/software/GENIE/下载。
BACKGROUND: Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs) have multiple cores, whereas Graphics Processing Units (GPUs) also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits.FINDINGS: Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. GENIE reads an entire genetic association study dataset into memory and partitions the dataset into fragments with non-overlapping sets of SNPs. For each fragment, GENIE analyzes: 1) the interaction of SNPs within it in parallel, and 2) the interaction between the SNPs of the current fragment and other fragments in parallel. We tested GENIE on a large-scale candidate gene study on high-density lipoprotein cholesterol. Using an NVIDIA Tesla C1060 graphics card, the GPU mode of GENIE achieves a speedup of 27 times over its single-core CPU mode run.CONCLUSIONS: GENIE is open-source, economical, user-friendly, and scalable. Since the computing power and memory capacity of graphics cards are increasing rapidly while their cost is going down, we anticipate that GENIE will achieve greater speedups with faster GPU cards. Documentation, source code, and precompiled binaries can be downloaded from http://www.cceb.upenn.edu/~mli/software/GENIE/.