TY - GEN
T1 - On the complexity of SNP block partitioning under the perfect phylogeny model
AU - Gramm, Qjens
AU - Hartman, Tzvika
AU - Nierhoff, Till
AU - Sharan, Roded
AU - Tantau, Till
N1 - Funding Information:
JG was supported by a grant for the DFG project Optimal solutions for hard problems in computational biology. JG, TN and TT were supported through a postdoc fellowship by the DAAD. TT was supported by a grant for the DFG project Complexity of haplotyping problems. RS was supported by an Alon Fellowship.
PY - 2006
Y1 - 2006
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=33750231156&partnerID=8YFLogxK
U2 - 10.1007/11851561_9
DO - 10.1007/11851561_9
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AN - SCOPUS:33750231156
SN - 3540395830
SN - 9783540395836
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 92
EP - 102
BT - Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings
PB - Springer Verlag
T2 - 6th International Workshop on Algorithms in Bioinformatics, WABI 2006
Y2 - 11 September 2006 through 13 September 2006
ER -