SNP haplotype tagging from DNA pools of two individuals

doi:10.1186/1471-2105-4-14

BMC Bioinformatics

Volume 4

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Lathrop MG
Ott J

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Methodology article

SNP haplotype tagging from DNA pools of two individuals

Josephine Hoh¹ , Fumihiko Matsuda² , Xu Peng² , Daniela Markovic¹ , Mark G Lathrop² and Jurg Ott¹

¹Laboratory of Statistical Genetics, Rockefeller University, New York, NY 10021, USA

²Centre National de Génotypage, 91057 Evry, France

author email corresponding author email

BMC Bioinformatics 2003, 4:14doi:10.1186/1471-2105-4-14


Published:	22 April 2003

Abstract

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.