Robustness of inference of haplotype block structure

Journal of Computational Biology

Volumn 10, Issue 1, 2003, Pages 13-19

  Schwartz, Russell ^a,c   Halldórsson, Bjarni V ^a   Bafna, Vineet ^a,d   Clark, Andrew G ^b   Istrail, Sorin ^a  

^a CELERA GENOMICS   (United States)

^b Cornell University ^*  (United States)

^c CARNEGIE MELLON UNIVERSITY   (United States)

^d Center for Medical Genetics   (United States)

Author keywords

Diversity; Haplotype block; Linkage disequilibrium; Recombination; SNP

Indexed keywords

ALGORITHM; ARTICLE; COMPARATIVE STUDY; CONCEPT FORMATION; CORRELATION ANALYSIS; CRYSTAL STRUCTURE; DATA ANALYSIS; DECOMPOSITION; GAMETE; GENE LINKAGE DISEQUILIBRIUM; GENETIC RECOMBINATION; GENETIC VARIABILITY; HAPLOTYPE; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; TECHNIQUE; VALIDATION PROCESS;

ALGORITHMS; DATABASES, GENETIC; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

EID: 0037227781     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652703763255642     Document Type: Article

References (9)

1. Daly, M., Rioux, J., Schaffner, S., and Hudson, T. 2001. High-resolution haplotype structure in the human genome. Nat. Genet. 29, 229-232.
2. Gabriel, S., Schaffner, S., Nguyen, H., Moore, J., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S.N., Rotimi, C., Adeyemo, A., Cooper, R., Ward, R., Lander, E.S., Daly, M.J., and Altschuler, D. 2002. The structure of haplotype blocks in the human genome. Science 296, 2225-2229.
3. Hudson, R., Kaplan, N. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111, 147-164.
4. Jeffreys, A., Kauppi, L., Neumann, R. 2001. Intensely punctute meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29, 217-222.
5. Johnson, G.C., Esposito, L., Barratt, B.J., Smith, A.N., Heward, J., Di Genova, G., Ueda, H., Cordell, H.J., Eaves, I.A., Dudbridge, F., Twells, R.C., Payne, F., Hughes, W., Nutland, S., Stevens, H., Carr, P., Tuomilehto-Wolf, E., Tuomilehto, J., Gough, S.C., Clayton, D.G., and Todd, J.A. 2001. Haplotype tagging for the identification of common disease genes. Nat. Genet. 29, 233-237.
6. Nickerson, D.A., Taylor, S.L., Fullerton, S.M., Weiss, K.M., Clark, A.G., Stengaard, J.H., Salomaa, V., Boerwinkle, E., Sing, C.F. 2000. Sequence diversity and large-scale typing of SNPs in the human apolipoprotein E gene. Genome Res. 10, 1532-1545.
7. Patil, N., Berno, A.J., Hinds, D.A., Barrett, W.A., Doshi, J.M., Hacker, C.R., Kautzer, C.R., Lee, D.H., Marjoribanks, C., McDonough, D.P., Nguyen, B.T., Norris, M.C., Sheehan, J.B., Shen, N., Stern, D., Stokowski, R.P., Thomas, D.J., Trulson, M.O., Vyas, K.R., Frazer, K.A., Fodor, S.P., and Cox, D.R. 2001. Blocks of limited haplotype diversity revealed by high resolution scanning of human chromosome 21. Science 294, 1719-1722.
8. Schwartz, R., Clark, A.G., and Istrail, S. Methods for inferring block-wise ancestral history from haploid sequences. In Guigó, R., and Gusfield, D., eds., Algorithms in Bioinformatics. Lecture Notes in Computer Science 2452, 44-59, Springer, Berlin.
9. Zhang, K., Deng, M., Chen, T., Waterman, M., and Sun, F. 2002. A dynamic programming algorithm for haplotype block partitioning. Proc. Natl. Acad. Sci. USA 99, 7335-7339.