BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies.
BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies.
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DOI：
10.1093/nar/gks550
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发表时间：
2012-07
影响因子：
14.9
通讯作者：
Wei WH
中科院分区：
文献类型：
--
作者：
Gyenesei A;Moody J;Laiho A;Semple CA;Haley CS;Wei WH
全基因组关联研究（GWAS）发现了许多与常见疾病和数量性状相关的基因座。然而，大多数GWAS没有研究基因-基因相互作用（上位性），这可能是重要的复杂性状遗传学。在GWAS中分析上位性的一个主要挑战是分析数十亿SNP组合的巨大计算需求。最近已经开发了几种方法来解决这个问题，其中一些使用配备了特定图形处理单元的计算机，大多数仅限于二进制疾病特征，并且都不适合在最广泛使用的操作系统上的一般使用。我们开发了BiForce分析仪，以满足所有常用计算机系统中定量和疾病性状GWAS中成对上位性的高通量分析需求。BiForceTM是一个独立的Java程序，它集成了按位计算和多线程并行化，因此可以通过图形用户界面或命令行进行快速的全成对基因组扫描。此外，BiForceTM还结合了涉及SNP的相互作用的额外测试，这些SNP具有显著的边际效应，可能会增加上位性的检测能力。BiForceTM易于使用，并已应用于大型GWAS数据集中的上位性研究，识别有趣的相互作用信号和途径。
Genome-wide association studies (GWAS) have discovered many loci associated with common disease and quantitative traits. However, most GWAS have not studied the gene–gene interactions (epistasis) that could be important in complex trait genetics. A major challenge in analysing epistasis in GWAS is the enormous computational demands of analysing billions of SNP combinations. Several methods have been developed recently to address this, some using computers equipped with particular graphical processing units, most restricted to binary disease traits and all poorly suited to general usage on the most widely used operating systems. We have developed the BiForce Toolbox to address the demand for high-throughput analysis of pairwise epistasis in GWAS of quantitative and disease traits across all commonly used computer systems. BiForce Toolbox is a stand-alone Java program that integrates bitwise computing with multithreaded parallelization and thus allows rapid full pairwise genome scans via a graphical user interface or the command line. Furthermore, BiForce Toolbox incorporates additional tests of interactions involving SNPs with significant marginal effects, potentially increasing the power of detection of epistasis. BiForce Toolbox is easy to use and has been applied in multiple studies of epistasis in large GWAS data sets, identifying interesting interaction signals and pathways.
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DOI：
10.1038/nrg2579
发表时间：
2009-06
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
Cordell HJ
通讯作者：
Cordell HJ
影响因子：
3.8
作者：
Wei, W-H;Knott, S.;de Koning, D-J
通讯作者：
de Koning, D-J
DOI：
10.1038/ejhg.2010.196
发表时间：
2011-04-01
期刊：
European journal of human genetics : EJHG
影响因子：
--
作者：
Kam-Thong, Tony;Czamara, Darina;Muller-Myhsok, Bertram
通讯作者：
Muller-Myhsok, Bertram
影响因子：
3.7
作者：
Wei W;Hemani G;Hicks AA;Vitart V;Cabrera-Cardenas C;Navarro P;Huffman J;Hayward C;Knott SA;Rudan I;Pramstaller PP;Wild SH;Wilson JF;Campbell H;Dunlop MG;Hastie N;Wright AF;Haley CS
通讯作者：
Haley CS
影响因子：
9.8
作者：
Wan, Xiang;Yang, Can;Yu, Weichuan
通讯作者：
Yu, Weichuan