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SNP haplotype tagging from DNA pools of two individuals
Josephine Hoh1, Fumihiko Matsuda, Xu Peng
1Laboratory of Statistical Genetics, Rockefeller University, New York, NY 10021, USA. jhoh@linkage.rockefeller.edu
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.