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Global haplotype partitioning for maximal associated SNP pairs
Ali Katanforoush1, Mehdi Sadeghi, Hamid Pezeshk
1Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. katanfor@ibb.ut.ac.ir
BMC Bioinformatics
|August 29, 2009
Summary
This study introduces a novel method for genome partitioning using pairwise SNP associations to define haplotype blocks. The algorithm maximizes allelic associations, improving dimension reduction in genome-wide association studies and identifying recombination hotspots.
Area of Science:
- Genomics
- Population Genetics
- Bioinformatics
Background:
- Global genome partitioning using pairwise SNP associations for haplotype block definition is novel.
- Linkage Disequilibrium (LD) between SNP pairs is quantified using an association index.
- Fisher's exact test assesses the statistical significance of LD estimates.
Purpose of the Study:
- To develop a new method for defining haplotype blocks based on maximizing pairwise SNP associations.
- To apply this method for dimension reduction in genome-wide association studies (GWAS).
- To identify genomic features, such as recombination hotspots, using pairwise SNP allelic associations.
Main Methods:
- An association index based on LD between SNP pairs was defined.
- Fisher's exact test was used to characterize SNP pairs as associated, independent, or not statistically significant.
- A dynamic programming algorithm solved a constrained optimization problem to find partitions with maximal associated SNP pairs.
Main Results:
- The algorithm generates larger haplotype blocks compared to existing methods.
- Haplotype diversity within blocks is efficiently represented by a small number of tagSNPs.
- The method demonstrated robustness in reproducing partitioning and outperformed previous models in simulated association studies for mapping traits, excelling in recombination hotspot detection.
Conclusions:
- The proposed method effectively partitions chromosomes into regions of maximized pairwise SNP allelic associations.
- This approach offers a native design for dimension reduction in genome-wide association studies.
- Pairwise SNP allelic associations are valuable for describing genomic variation, particularly recombination hotspots.
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