title: Pathway-PDT: a flexible pathway analysis tool for nuclear families.
abstract: BACKGROUND
  Pathway analysis based on Genome-Wide Association Studies (GWAS) data has become popular as a secondary analysis strategy. Although many pathway analysis tools have been developed for case-control studies, there is no tool that can use all information from raw genotypes in general nuclear families. We developed Pathway-PDT, which uses the framework of Pedigree Disequilibrium Test (PDT) for general family data, to perform pathway analysis based on raw genotypes in family-based GWAS.
  
  
  RESULTS
  Simulation results showed that Pathway-PDT is more powerful than the p-value based method, ALIGATOR. Pathway-PDT also can be more powerful than the PLINK set-based test when analyzing general nuclear families with multiple siblings or missing parents. Additionally, Pathway-PDT has a flexible and convenient user interface, which allows users to modify their analysis parameters as well as to apply various types of gene and pathway definitions.
  
  
  CONCLUSIONS
  The Pathway-PDT method is implemented in C++ with POSIX threads and is computationally feasible for pathway analysis with large scale family GWAS datasets. The Windows binary along with Makefile and source codes for the Linux are available at https://sourceforge.net/projects/pathway-pdt/.
authors.affiliation: Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli, Taiwan. rchung@nhri.org.tw.
authors.forename: Yo Son
authors.initials: YS
authors.lastname: Park
authors.forename: Michael
authors.initials: M
authors.lastname: Schmidt
authors.forename: Eden R
authors.initials: ER
authors.lastname: Martin
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Pericak-Vance
authors.forename: Ren-Hua
authors.initials: RH
authors.lastname: Chung
mesh_terms: D019295:Computational Biology / Q000379:methods*; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D006801:Humans; D009679:Nuclear Family; D010375:Pedigree; D012984:Software