Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs.
Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs.
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DOI：
10.1186/1471-2105-9-s6-s10
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发表时间：
2008-05-28
影响因子：
3
通讯作者：
Ni J
中科院分区：
文献类型：
--
作者：
Mishima H;Lidral AC;Ni J
遗传关联研究已被用来绘制致病基因图谱。一种新引入的统计方法，称为穷举单倍型关联研究，分析由沿染色体的不同数量和组合的 DNA 序列变异组成的遗传信息。此类研究涉及大量统计计算以及随之而来的高计算能力。可以开发并行算法和代码来在高性能计算 (HPC) 系统上执行计算。然而，大多数现有的常用遗传研究统计包都是非并行版本。或者，可以利用网格计算及其软件包这一前沿技术，在集中式HPC系统或分布式计算系统上进行非并行遗传统计软件包。在本文中，我们报告了如何利用基于 Grid Engine 构建并在 Rocks Linux 集群上运行的排队调度程序来进行遗传统计研究。 FBAT (Laird et al., 2000) 和 Unphased (Dudbridge, 2003) 程序对连续和组合窗口单倍型进行了分析。该数据集包含来自 277 个大家庭（1484 人）的 26 个位点。使用具有 22 个计算节点的 Rocks Linux 集群，FBAT 作业的执行速度比累积计算持续时间快约 14.4–15.9 倍，而 Unphased 作业的执行速度比累积计算持续时间快 1.1–18.6 倍。在基于 Linux 的系统上使用非并行软件包执行详尽的单倍型分析在成本和性能方面是一种有效且高效的方法。
Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of different numbers and combinations of DNA sequence variations along a chromosome. Such studies involve a large number of statistical calculations and subsequently high computing power. It is possible to develop parallel algorithms and codes to perform the calculations on a high performance computing (HPC) system. However, most existing commonly-used statistic packages for genetic studies are non-parallel versions. Alternatively, one may use the cutting-edge technology of grid computing and its packages to conduct non-parallel genetic statistical packages on a centralized HPC system or distributed computing systems. In this paper, we report the utilization of a queuing scheduler built on the Grid Engine and run on a Rocks Linux cluster for our genetic statistical studies. Analysis of both consecutive and combinational window haplotypes was conducted by the FBAT (Laird et al., 2000) and Unphased (Dudbridge, 2003) programs. The dataset consisted of 26 loci from 277 extended families (1484 persons). Using the Rocks Linux cluster with 22 compute-nodes, FBAT jobs performed about 14.4–15.9 times faster, while Unphased jobs performed 1.1–18.6 times faster compared to the accumulated computation duration. Execution of exhaustive haplotype analysis using non-parallel software packages on a Linux-based system is an effective and efficient approach in terms of cost and performance.