Algorithm for haplotype resolution and block partitioning for partial XOR-genotype data

Journal of Biomedical Informatics

Volumn 43, Issue 1, 2010, Pages 51-59

  Sazonova, Nadezhda ^a   Sazonov, Edward ^a   Harner, E James ^b  

^a Wallace H Coulter School of Engineering   (United States)

^b WEST VIRGINIA UNIVERSITY   (United States)

Author keywords

Genetic algorithm; Haplotype; Haplotype block; XOR genotype; XOR haplotyping

Indexed keywords

BLOCK PARTITIONING; BLOCK STRUCTURES; COST-EFFICIENT; HAPLOTYPES; HAPLOTYPING; MISSING DATA; PRACTICAL ALGORITHMS; PREDICTION RATE; XOR-GENOTYPE;

ALGORITHMS;

ARTICLE; DATA ANALYSIS; DATA COLLECTION METHOD; GENE SEQUENCE; GENETIC ALGORITHM; GENOTYPE; HAPLOTYPE; HAPLOTYPE MAP; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; ALLELES; AUTOMATIC DATA PROCESSING; CHROMOSOME MAPPING; CHROMOSOMES; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; FEMALE; GENOME, HUMAN; GENOTYPE; HAPLOTYPES; HUMANS; MALE; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS;

EID: 74649083906     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2009.08.009     Document Type: Article

References (24)

1. Gusfield D. An overview of combinatorial methods for haplotype inference. In: Computational methods for SNPs and haplotype inference. Lecture Notes on Computer Science, vol. 2983. Berlin/Heidelberg: Springer; 2004. p. 599-600.
2. Gabriel S.B., Schaffner S.F., Nguyen H., Moore J.M., Roy J., Blumenstiel B., et al. The structure of haplotype blocks in the human genome. Science 296 (2002) 2225-2229
3. Zhang K., Deng M., Chen T., Waterman M.S., and Sun F. A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci USA 99 11 (2002) 7335-7339
4. Patil N., Berno A.J., Hinds D.A., Barret W.A., Doshi J.M., Hacker C.R., et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294 5547 (2001) 1719-1723
5. Daly M.J., Rioux J.D., Schaffner S.F., and Hudson T.J. Lander ES high-resolution haplotype structure in the human genome. Nat Genet 29 (2001) 229-232
6. Clark A. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol 7 2 (1990) 111-122
7. Excoffier L., and Slatkin M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12 5 (1995) 921-927
8. Stephens M., Smith N.J., and Donnelly P. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68 (2001) 978-989
9. Niu T., Qin Z.S., Xu W., and Liu J.S. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet 710 (2002) 157-169
10. Gusfield D. Haplotyping as perfect phylogeny: conceptual framework and efficient solutions. In: Proceedings of 6th annual conference on research in computational molecular biology (RECOMB'02). 2002. p. 166-75.
11. Halperin E., Eskin E., and Karp R.M. Efficient reconstruction of haplotype structure via perfect phylogeny. J Bioinform Comput Biol 1 1 (2003) 1-20
12. Koivisto M., Perola M., Varilo T., Hennah W., Ekelund J., Lukk M., et al. An MDL method for finding haplotype blocks and for estimating the strength of haplotype block boundaries. Pac Symp Biocomput (2003) 502-513
13. Kimmel G, Shamir R. Maximum likelihood resolution of multi-block genotypes. In: Proceedings of 8th annual conference on research in computational molecular biology (RECOMB'04). 2004. p. 2-9.
14. Greenspan G, Geiger D. Model-based inference of haplotype block variation. In: Proceedings of 8th annual conference on research in computational molecular biology (RECOMB'03). 2003. p. 131-7.
15. Scheet P., and Stephens M. A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78 (2006) 629-644
16. Xiao W., and Oefner P.J. Denaturing high-performance liquid chromatography: a review. Hum Mutat 17 6 (2001) 439-474
17. Barzuza T., Beckmann J.S., and Shamir R. Computational problems in perfect phylogeny haplotyping: typing without calling the allele. IEEE/ACM Trans Comput Biol Bioinform 5 1 (2008) 101-109
18. Barzuza T, Beckmann JS, Shamir R, Pe'er I. Computational problems in perfect phylogeny haplotyping: XOR-genotypes and tag SNPs. In: Proceedings of annual symposium in combinatorial pattern matching (CPM '04). 2004. p. 14-31.
19. Barzuza T., Beckmann J.S., Shamir R., and Pe'er I. Typing without calling the allele: a strategy for inferring SNP haplotypes. Eur J Hum Genet 13 (2005) 898-901
20. Sazonova N. Parsimony-based genetic algorithm for haplotyping and block partitioning. Dissertation. West Virginia University, Dec. 2007.
21. Nothnagel M., Furst R., and Ronde K. Entropy as a measure for linkage disequilibrium over multilocus haplotype blocks. Hum Hered 54 4 (2002) 186-198
22. Wang L., and Xu Y. Haplotype inference by maximum parsimony. Bioinformatics 19 14 (2003) 1773-1780
23. The International HapMap Consortium. The International HapMap Project. Nature 2003;426:789-96.
24. The International HapMap Consortium. A haplotype map of the human genome. Nature 2005;437:1299-320.