Most Parsimonious Haplotype Allele Sharing Determination
- Zhipeng Cai
- Hadi Sabaa
- Yining Wang
- Randy Goebel
- Zhiquan Wang
- Jiaofen Xu
- Paul Stothard, Department of Agricultural, Food and Nutritional Science (AFNS)
- Guohui Lin
Background The "common disease – common variant" hypothesis and genome-wide association studies have achieved numerous successes in the last three years, particularly in genetic mapping in human diseases. Nevertheless, the power of the association study methods are still low, in particular on quantitative traits, and the description of the full allelic spectrum is deemed still far from reach. Given increasing density of single nucleotide polymorphisms available and suggested by the block-like structure of the human genome, a popular and prosperous strategy is to use haplotypes to try to capture the correlation structure of SNPs in regions of little recombination. The key to the success of this strategy is thus the ability to unambiguously determine the haplotype allele sharing status among the members. The association studies based on haplotype sharing status would have significantly reduced degrees of freedom and be able to capture the combined effects of tightly linked causal variants. Results For pedigree genotype datasets of medium density of SNPs, we present two methods for haplotype allele sharing status determination among the pedigree members. Extensive simulation study showed that both methods performed nearly perfectly on breakpoint discovery, mutation haplotype allele discovery, and shared chromosomal region discovery. Conclusion For pedigree genotype datasets, the haplotype allele sharing status among the members can be deterministically, efficiently, and accurately determined, even for very small pedigrees. Given their excellent performance, the presented haplotype allele sharing status determination programs can be useful in many downstream applications including haplotype based association studies.
Citation
Z. Cai, H. Sabaa, Y. Wang, R. Goebel, Z. Wang, J. Xu, P. Stothard, G. Lin. "Most Parsimonious Haplotype Allele Sharing Determination". BMC Bioinformatics, 10, pp n/a, April 2009.| Keywords: | |
| Category: | In Journal |
| Web Links: | DOI |
| BMC |
BibTeX
@article{Cai+al:09,
author = {Zhipeng Cai and Hadi Sabaa and Yining Wang and Randy Goebel and
Zhiquan Wang and Jiaofen Xu and Paul Stothard and Guohui Lin},
title = {Most Parsimonious Haplotype Allele Sharing Determination},
Volume = "10",
Pages = {n/a},
journal = {BMC Bioinformatics},
year = 2009,
}Last Updated: February 13, 2020Submitted by Sabina P
