The HAPLOTYPE Procedure

Clayton, D. (2002), “Choosing a Set of Haplotype Tagging SNPs from a Larger Set of Diallelic Loci,” http://www-gene.cimr.cam.ac.uk/clayton/software/stata/htSNP/htsnp.pdf

Excoffier, L. and Slatkin, M. (1995), “Maximum-Likelihood Estimation of Molecular Haplotype Frequencies in a Diploid Population,” Molecular Biology and Evolution, 12, 921–927.

Fallin, D., Cohen, A., Essioux, L., Chumakov, I., Blumenfeld, M., Cohen, D., and Schork, N.J. (2001), “Genetic Analysis of Case/Control Data Using Estimated Haplotype Frequencies: Application to APOE Locus Variation and Alzheimer’s Disease,” Genome Research, 11, 143–151.

Fallin, D. and Schork, N.J. (2000), “Accuracy of Haplotype Frequency Estimation for Biallelic Loci, via the Expectation-Maximization Algorithm for Unphased Diploid Genotype Data,” American Journal of Human Genetics, 67, 947–959.

Hawley, M.E. and Kidd, K.K. (1995), “HAPLO: A Program Using the EM Algorithm to Estimate the Frequencies of Multi-site Haplotypes,” Journal of Heredity, 86, 409–411.

Lab of Statistical Genetics at Rockefeller University (2001), “User’s Guide to the EH Program” http://linkage.rockefeller.edu/ott/eh.htm.

Lin, S., Cutler, D.J., Zwick, M.E., Chakravarti, A. (2002), “Haplotype Inference in Random Population Samples,” American Journal of Human Genetics, 71, 1129–1137.

Long, J.C., Williams, R.C., and Urbanek, M. (1995), “An E-M Algorithm and Testing Strategy for Multiple-Locus Haplotypes,” American Journal of Human Genetics, 56, 799–810.

Schaid, D.J., Rowland, C.M., Tines, D.E., Jacobson, R.M., and Poland, G.A. (2002), “Score Tests for Association between Traits and Haplotypes When Linkage Phase Is Ambiguous,” American Journal of Human Genetics, 70, 425–434.

Stephens, M., Smith, N.J., Donnelly, P. (2001), “A New Statistical Method for Haplotype Reconstruction from Population Data,” American Journal of Human Genetics, 68, 978–989.

Wijsman, E.M., Almasy, L., Amos, C.I., Borecki, I., Falk, C.T., King, T.M., Martinez, M.M., Meyers, D., Neuman, R., Olson, J.M., Rich, S., Spence, M.A., Thomas, D.C., Vieland, V.J., Witte, J.S., and MacCluer, J.W. (2001), “Analysis of Complex Genetic Traits: Applications to Asthma and Simulated Data,” Genetic Epidemiology, 21, S1–S853.

Zaykin, D.V., Westfall, P.H., Young, S.S., Karnoub, M.A., Wagner, M.J., and Ehm, M.G. (2002), “Testing Association of Statistically Inferred Haplotypes with Discrete and Continuous Traits in Samples of Unrelated Individuals,” Human Heredity, 53, 79–91.

Zhao, J.H., Curtis, D., and Sham, P.C. (2000), “Model-Free Analysis and Permutation Tests for Allelic Associations,” Human Heredity, 50, 133–139.