Haplo2Ped, a new tool using haplotypes as markers for linkage analysis, was recently developed by Professor ZENG Changqing’s group at the Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics (BIG).

Haplo2Ped is an effective tool for linkage analysis. It is developed to automatically transform single nucleotide polymorphism (SNP) data into haplotype markers and then to compute the logarithm (base 10) of odds (LOD) scores of regional haplotypes that are homozygous within the disease co-segregation haploid group. The results are reported as a hypertext file and a 3D figure to help users to obtain the candidate regions. The hypertext file contains parameters of the disease linked regions, candidate genes, and their links to public databases. The 3D figure clearly displays the linkage signals in each chromosome.

Haplo2Ped takes haplotype fragments as mapping markers in whole genome linkage analysis, which would largely overcome the low heterozygosity of individual SNPs. The advantages of this software also include straightforward output files, increased accuracy, and improved capacity to deal with pedigrees showing incomplete penetrance.

Tested with simulated SNP datasets, Haplo2Ped is proved to be a reliable and sensitive tool for linkage analysis with SNP data. In a study of a digital-anomaly family, researchers conducted linkage analysis with Haplo2Ped, and successfully located the disease linkage region. Further study determined the causative mutation in candidate gene.

The research results were published in BMC Bioinformatics on August 22, 2011. Researchers can download haplo2Ped directly at http://bighapmap.big.ac.cn/software.html.

Graphical report of the Haplo2Ped application with simulated dataset (Image by CHENG Feng )

Paper link: http://www.biomedcentral.com/1471-2105/12/350.

Contact: Prof. ZENG Changqing czeng@big.ac.cn