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Pathway-PDT: a flexible pathway analysis tool for nuclear families

Yo Son Park12, Michael Schmidt12, Eden R Martin12, Margaret A Pericak-Vance12 and Ren-Hua Chung3*

Author Affiliations

1 John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA

2 Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FLUSA

3 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli, Taiwan

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BMC Bioinformatics 2013, 14:267  doi:10.1186/1471-2105-14-267

Published: 4 September 2013

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/ webcite.

Keywords:
Pathway; GWAS; PDT; GSEA; Kolmogorov-Smirnov-like running sum statistic; Pedigree GWAS