SNP haplotype tagging from DNA pools of two individuals

Background: DNA pooling is a technique to reduce genotyping effort while incurring only minor losses in accuracy of allele frequency estimates for single nucleotide polymorphism (SNP) markers. Results: We present an algorithm for reconstructing haplotypes (alleles for multiple SNPs on same chromosome) from pools of two individual DNAs, in which Hardy-Weinberg equilibrium conditions or other assumptions are not required. The program outputs, in addition to inferred haplotypes, a minimal number of haplotype-tagging SNPs that are identified after an exhaustive search procedure. Conclusion: Our method and algorithms lead to a significant reduction in genotyping effort, for example, in case-control disease association studies while maintaining the possibility of reconstructing haplotypes under very general conditions.