Complex diseases involve multiple genes with low penetration.
EditBy: Complex diseases involve multiple genes with low penetration which may be distributed over the genome. Most of the current haplotype association methods are typically restricted in length and consist of alleles from contiguous SNPs. These approaches have limited Capacity to Detect epistasis from multiple gene-gene interactions. Recent evidence has shown that the 3-D structure of chromosomes can play a role in allowing SNPs to interact with genetic elements which are physically separated by great distances. We hypothesize that interactions Between different chromosomes may play a role in disease susceptibility. Thus we have developed a cooperative coevolutionary Algorithm (CCA) to detect gene-gene interactions from case-control haplotype data; moreover, this algorithm can tolerate up to 15% missing/ambiguous positions in haplotype data arising during haplotype phasing from genotypes. Further, the algorithm can compute epistatic associations from genes spanning multiple chromosomes.

Input Format:

* Haplotype Files
This program takes two input files which contains the same set of SNP genotypes for cases and controls. Below is a sample case and control phased haplotype files for 3 SNPs.

* Map File:
The first column of the map file is the Chromosome number, the second column represents the rs# of each SNP and the third column is the chromosomal position of the SNP.

Example Files:
* Cases.txt
* Controls.txt
* Map.txt you can free download HapEvolution now.