On the complexity of SNP block partitioning under the perfect phylogeny model

  • Authors:

  • Jens Gramm;Tzvika Hartman;Till Nierhoff;Roded Sharan;Till Tantau

  • Affiliations:

  • Wilhelm-Schickard-Institut für Informatik, Universität Tübingen, Germany;Dept. of Computer Science, Bar-Ilan University, Ramat-Gan, Israel;International Computer Science Institute, Berkeley;School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel;Institut für Theoretische Informatik, Universität zu Lübeck, Germany

  • Venue:
  • WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
  • Year:
  • 2006

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Abstract

Recent technologies for typing single nucleotide polymorphisms (SNPs) across a population are producing genome-wide genotype data for tens of thousands of SNP sites. The emergence of such large data sets underscores the importance of algorithms for large-scale haplotyping. Common haplotyping approaches first partition the SNPs into blocks of high linkage-disequilibrium, and then infer haplotypes for each block separately. We investigate an integrated haplotyping approach where a partition of the SNPs into a minimum number of non-contiguous subsets is sought, such that each subset can be haplotyped under the perfect phylogeny model. We show that finding an optimum partition is NP-hard even if we are guaranteed that two subsets suffice. On the positive side, we show that a variant of the problem, in which each subset is required to admit a perfect path phylogeny haplotyping, is solvable in polynomial time.