| Linear Reduction Method for Predictive and Informative Tag SNP (2005) | |||||||||||||||||
Abstract | |||||||||||||||||
| Constructing a complete human haplotype map is helpful when associating complex dis-eases with their related SNPs. Unfortunately, the number of SNPs is very large and it is costly to sequence many individuals. Therefore, it is desirable to reduce the number of SNPs that should be sequenced to a small number of informative representatives called tag SNPs. In this paper, we propose a new linear algebra-based method for selecting and using tag SNPs. Our method is purely combinatorial and can be combined with linkage disequilibrium (LD) and block based methods. We measure the quality of our tag SNP selection algorithm by com-paring actual SNPs with SNPs predicted from selected linearly independent tag SNPs. For example, our experiments show that for long haplotypes (> 25000 SNPs), knowing only 0.4% of all SNPs our method predicts an unknown haplotype with 98 % accuracy while the predic-tion is based on 10 % of the sample population. Comparison with existing predictive tagging ∗ Preliminary version of paper has appeared in He et al. (2004). 1 methods of Halldorsson et al. (2004) and Zhang et al. (2004) shows that our method achieves | |||||||||||||||||
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