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Haplo2Ped: a tool using haplotypes as markers for linkage analysis

Feng Cheng12, Xianglong Zhang13, Yinan Zhang1, Chaohua Li1 and Changqing Zeng1*

  • * Corresponding author: Changqing Zeng

  • † Equal contributors

Author Affiliations

1 Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, No.7 Beitucheng West Road, Beijing 100029, PR China

2 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing 100081, PR China

3 Graduate School of the Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, PR China

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BMC Bioinformatics 2011, 12:350  doi:10.1186/1471-2105-12-350

Published: 22 August 2011



Generally, SNPs are abundant in the genome; however, they display low power in linkage analysis because of their limited heterozygosity. Haplotype markers, on the other hand, which are composed of many SNPs, greatly increase heterozygosity and have superiority in linkage statistics.


Here we developed Haplo2Ped to automatically transform 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 linkage 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. We tested Haplo2Ped in a simulated SNP dataset and also applied it to data from a real study. It successfully and accurately located the causative genomic regions. Comparison of Haplo2Ped with other existing software for linkage analysis further indicated the high effectiveness of this software.


Haplo2Ped uses haplotype fragments as mapping markers in whole genome linkage analysis. The advantages of Haplo2Ped over other existing software include straightforward output files, increased accuracy and superior ability to deal with pedigrees showing incomplete penetrance. Haplo2Ped is freely available at: webcite.