Haplotypes and informative SNP selection algorithms: don't block out information
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Phasing and missing data recovery in family trios
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
Fuzzy guided BPSO method for haplotype tag SNP selection
FUZZ-IEEE'09 Proceedings of the 18th international conference on Fuzzy Systems
Tag SNP selection based on multivariate linear regression
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
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Constructing a complete human haplotype map is helpful when associating complex diseases 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. We measure the quality of our tag SNP selection algorithm by comparing actual SNPs with SNPs predicted from selected linearly independent tag SNPs. Our experiments show that for sufficiently long haplotypes, knowing only 0.4% of all SNPs the proposed linear reduction method predicts an unknown haplotype with the error rate below 2% based on 10% of the population.