Abstract
BackgroundGenerally, 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.ResultsHere 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.ConclusionsHaplo2Ped 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: http://bighapmap.big.ac.cn/software.html.
Highlights
SNPs are abundant in the genome; they display low power in linkage analysis because of their limited heterozygosity
Linkage mapping of complex traits was made feasible for experimental organisms, such as animals and plants, through the use of genetic mapping in large crosses [3,4]
It still lacks a tool for considering haplotype fragments as genomic markers for linkage research [7,8,9,10]
Summary
SNPs are abundant in the genome; they display low power in linkage analysis because of their limited heterozygosity. Along with the achievement of high-throughput SNP genotyping, using whole genome SNP data for linkage analysis has been shown to be an efficient strategy [5,6]. Because of their two-allele character, the Software packages have been developed to carry out multi-point analysis. The application of these two algorithms is limited, either by the number of markers or by the size of the pedigrees Another program, SNP4Linkage, is based on allele sharing determination and is better adapted to high-density SNP genotyping data. An auto-generated 3D picture allows users to visualize the linking signals clearly on a genomic scale
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