Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies.
Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies.
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DOI：
10.1186/1471-2105-9-315
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发表时间：
2008-07-21
影响因子：
3
通讯作者：
Da, Yang
中科院分区：
文献类型：
--
作者：
Ma, Li;Runesha, H. Birali;Dvorkin, Daniel;Garbe, John R.;Da, Yang
使用单核苷酸多态(SNP)标记的全基因组关联研究(GWAS)提供了检测与数量性状相关的上位性SNPs和检测上位性效应的确切模式的机会。计算难度是大范围上位性检验的主要瓶颈。在扩展Kempthorne模型的基础上，编制了EPISNPmpi和EPISNP计算机程序，用于检验单基因座和上位性SNP对数量性状的效应，包括每个SNP的3个单基因座效应(SNP基因效应、加性和显性效应)和每对SNP的5个上位性效应(两个座位互作、加性×加性、加性×显性、显性×加性和显性×显性)。EPISNPmpi是一种用于大规模上位性测试的并行计算程序，具有良好的大规模分析可扩展性和对各种并行计算平台的可移植性。EPISNP是基于EPISNPmpi代码的串口计算程序，用于使用常用的操作系统和计算机硬件进行小规模GWAS的上位性测试。开发了三个串行计算实用程序，用于以图形方式查看测试结果和上位机网络，并用于估计CPU时间和磁盘空间需求。EPISNPmpi并行计算程序为大规模GWAS的上位性检验提供了一个有效的计算工具，而EPSNP系列计算程序则是利用现有计算机硬件进行小规模GWAS上位性分析的便捷工具。
Genome-wide association studies (GWAS) using single nucleotide polymorphism (SNP) markers provide opportunities to detect epistatic SNPs associated with quantitative traits and to detect the exact mode of an epistasis effect. Computational difficulty is the main bottleneck for epistasis testing in large scale GWAS. The EPISNPmpi and EPISNP computer programs were developed for testing single-locus and epistatic SNP effects on quantitative traits in GWAS, including tests of three single-locus effects for each SNP (SNP genotypic effect, additive and dominance effects) and five epistasis effects for each pair of SNPs (two-locus interaction, additive × additive, additive × dominance, dominance × additive, and dominance × dominance) based on the extended Kempthorne model. EPISNPmpi is the parallel computing program for epistasis testing in large scale GWAS and achieved excellent scalability for large scale analysis and portability for various parallel computing platforms. EPISNP is the serial computing program based on the EPISNPmpi code for epistasis testing in small scale GWAS using commonly available operating systems and computer hardware. Three serial computing utility programs were developed for graphical viewing of test results and epistasis networks, and for estimating CPU time and disk space requirements. The EPISNPmpi parallel computing program provides an effective computing tool for epistasis testing in large scale GWAS, and the epiSNP serial computing programs are convenient tools for epistasis analysis in small scale GWAS using commonly available computer hardware.
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影响因子：
1.8
作者：
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通讯作者：
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影响因子：
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作者：
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