iPat: intelligent prediction and association tool for genomic research

被引:28
作者
Chen, Chunpeng James [1 ]
Zhang, Zhiwu [1 ]
机构
[1] Washington State Univ, Dept Crop & Soil Sci, Pullman, WA 99164 USA
基金
美国食品与农业研究所;
关键词
REGRESSION;
D O I
10.1093/bioinformatics/bty015
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The Summary: The ultimate goal of genomic research is to effectively predict phenotypes from genotypes so that medical management can improve human health and molecular breeding can increase agricultural production. Genomic prediction or selection (GS) plays a complementary role to genome-wide association studies (GWAS), which is the primary method to identify genes underlying phenotypes. Unfortunately, most computing tools cannot perform data analyses for both GWAS and GS. Furthermore, the majority of these tools are executed through a command-line interface (CLI), which requires programming skills. Non-programmers struggle to use them efficiently because of the steep learning curves and zero tolerance for data formats and mistakes when inputting keywords and parameters. To address these problems, this study developed a software package, named the Intelligent Prediction and Association Tool (iPat), with a user-friendly graphical user interface. With iPat, GWAS or GS can be performed using a pointing device to simply drag and/or click on graphical elements to specify input data files, choose input parameters and select analytical models. Models available to users include those implemented in third party CLI packages such as GAPIT, PLINK, FarmCPU, BLINK, rrBLUP and BGLR. Users can choose any data format and conduct analyses with any of these packages. File conversions are automatically conducted for specified input data and selected packages. A GWAS-assisted genomic prediction method was implemented to perform genomic prediction using any GWAS method such as FarmCPU. iPat was written in Java for adaptation to multiple operating systems including Windows, Mac and Linux.
引用
收藏
页码:1925 / 1927
页数:3
相关论文
共 9 条
[1]   TASSEL: software for association mapping of complex traits in diverse samples [J].
Bradbury, Peter J. ;
Zhang, Zhiwu ;
Kroon, Dallas E. ;
Casstevens, Terry M. ;
Ramdoss, Yogesh ;
Buckler, Edward S. .
BIOINFORMATICS, 2007, 23 (19) :2633-2635
[2]   Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP [J].
Endelman, Jeffrey B. .
PLANT GENOME, 2011, 4 (03) :250-255
[3]   Efficient control of population structure in model organism association mapping [J].
Kang, Hyun Min ;
Zaitlen, Noah A. ;
Wade, Claire M. ;
Kirby, Andrew ;
Heckerman, David ;
Daly, Mark J. ;
Eskin, Eleazar .
GENETICS, 2008, 178 (03) :1709-1723
[4]   GAPIT: genome association and prediction integrated tool [J].
Lipka, Alexander E. ;
Tian, Feng ;
Wang, Qishan ;
Peiffer, Jason ;
Li, Meng ;
Bradbury, Peter J. ;
Gore, Michael A. ;
Buckler, Edward S. ;
Zhang, Zhiwu .
BIOINFORMATICS, 2012, 28 (18) :2397-2399
[5]   Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies [J].
Liu, Xiaolei ;
Huang, Meng ;
Fan, Bin ;
Buckler, Edward S. ;
Zhang, Zhiwu .
PLOS GENETICS, 2016, 12 (02)
[6]   Genome-Wide Regression and Prediction with the BGLR Statistical Package [J].
Perez, Paulino ;
de los Campos, Gustavo .
GENETICS, 2014, 198 (02) :483-U63
[7]   PLINK: A tool set for whole-genome association and population-based linkage analyses [J].
Purcell, Shaun ;
Neale, Benjamin ;
Todd-Brown, Kathe ;
Thomas, Lori ;
Ferreira, Manuel A. R. ;
Bender, David ;
Maller, Julian ;
Sklar, Pamela ;
de Bakker, Paul I. W. ;
Daly, Mark J. ;
Sham, Pak C. .
AMERICAN JOURNAL OF HUMAN GENETICS, 2007, 81 (03) :559-575
[8]   Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement [J].
Spindel, J. E. ;
Begum, H. ;
Akdemir, D. ;
Collard, B. ;
Redona, E. ;
Jannink, J-L ;
McCouch, S. .
HEREDITY, 2016, 116 (04) :395-408
[9]   GAPIT Version 2: An Enhanced Integrated Tool for Genomic Association and Prediction [J].
Tang, You ;
Liu, Xiaolei ;
Wang, Jiabo ;
Li, Meng ;
Wang, Qishan ;
Tian, Feng ;
Su, Zhongbin ;
Pan, Yuchun ;
Liu, Di ;
Lipka, Alexander E. ;
Buckler, Edward S. ;
Zhang, Zhiwu .
PLANT GENOME, 2016, 9 (02)