Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies (original) (raw)
Risch, N. & Merikangas, K. The future of genetic studies of complex human diseases. Science273, 1516–1517 (1996). ArticleCASPubMed Google Scholar
Collins, F.S., Guyer, M.S. & Chakravarti, A. Variations on a theme: cataloging human DNA sequence variation. Science278, 1580–1581 (1997). ArticleCASPubMed Google Scholar
Thomas, J.W. et al. Comparative analyses of multi-species sequences from targeted genomic regions. Nature424, 788–793 (2003). ArticleCASPubMed Google Scholar
Watterson, G.A. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol.7, 256–276 (1975). ArticleCASPubMed Google Scholar
Kruglyak, L. & Nickerson, D.A. Variation is the spice of life. Nat. Genet.27, 234–236 (2001). ArticleCASPubMed Google Scholar
Sachidanandam, R. et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature409, 928–933 (2001). ArticleCASPubMed Google Scholar
Patil, N. et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science294, 1719–1723 (2001). ArticleCASPubMed Google Scholar
Chapman, J.M., Cooper, J.D., Todd, J.A. & Clayton, D.G. Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power. Hum. Hered.56, 18–31 (2003). ArticlePubMed Google Scholar
Long, A.D. & Langley, C.H. The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res.9, 720–731 (1999). CASPubMedPubMed Central Google Scholar
Churchill, G.A. & Doerge, R.W. Empirical threshold values for quantitative trait mapping. Genetics138, 963–971 (1994). CASPubMedPubMed Central Google Scholar
Kennedy, G.C. et al. Large-scale genotyping of complex DNA. Nat. Biotechnol.21, 1233–1237 (2003). ArticleCASPubMed Google Scholar
Hudson, R.R. Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol.23, 183–201 (1983). ArticleCASPubMed Google Scholar
Morton, N.E. & MacLean, C.J. Analysis of family resemblance. 3. Complex segregation of quantitative traits. Am. J. Hum. Genet.26, 489–503 (1974). CASPubMedPubMed Central Google Scholar
Hudson, R.R. The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Genetics109, 611–631 (1985). CASPubMedPubMed Central Google Scholar
de la Chapelle, A. & Wright, F.A. Linkage disequilibrium mapping in isolated populations: the example of Finland revisited. Proc. Natl. Acad. Sci. USA95, 12416–12423 (1998). ArticleCASPubMedPubMed Central Google Scholar
Terwilliger, J.D. & Weiss, K.M. Linkage disequilibrium mapping of complex disease: fantasy or reality? Curr. Opin. Biotechnol.9, 578–594 (1998). ArticleCASPubMed Google Scholar
Liang, K.Y., Hsu, F.C., Beaty, T.H. & Barnes, K.C. Multipoint linkage-disequilibrium-mapping approach based on the case-parent trio design. Am. J. Hum. Genet.68, 937–950 (2001). ArticleCASPubMedPubMed Central Google Scholar
McPeek, M.S. & Strahs, A. Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping. Am. J. Hum. Genet.65, 858–875 (1999). ArticleCASPubMedPubMed Central Google Scholar
Service, S.K., Lang, D.W., Freimer, N.B. & Sandkuijl, L.A. Linkage-disequilibrium mapping of disease genes by reconstruction of ancestral haplotypes in founder populations. Am. J. Hum. Genet.64, 1728–1738 (1999). ArticleCASPubMedPubMed Central Google Scholar
Morris, A.P., Whittaker, J.C. & Balding, D.J. Bayesian fine-scale mapping of disease loci, by hidden Markov models. Am. J. Hum. Genet.67, 155–169 (2000). ArticleCASPubMedPubMed Central Google Scholar
Liu, J.S., Sabatti, C., Teng, J., Keats, BJ. & Risch, N. Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Res.11, 1716–1724 (2001). ArticleCASPubMedPubMed Central Google Scholar
McCallion, A.S. et al. Genomic variation in multigenic traits: Hirschsprung disease. Cold Spring Harb. Symp. Quant. Biol.68, 373–381 (2003). ArticleCASPubMed Google Scholar
Puffenberger, E.G. et al. Identity-by-descent and association mapping of a recessive gene for Hirschsprung disease on human chromosome 13q22. Hum. Mol. Genet.3, 1217–1225 (1994). ArticleCASPubMed Google Scholar
Chakravarti, A. & Lyonnet, S. Hirschsprung disease. in The Metabolic and Molecular Bases of Inherited Disease (ed. Charles R.S.) (McGraw-Hill, New York, 2001). Google Scholar
Edery, P. et al. Mutations of the RET proto-oncogene in Hirschsprung's disease. Nature367, 378–380 (1994). ArticleCASPubMed Google Scholar
Romeo, G. et al. Point mutations affecting the tyrosine kinase domain of the RET proto-oncogene in Hirschsprung's disease. Nature367, 377–378 (1994). ArticleCASPubMed Google Scholar
Jeffreys, A.J., Kauppi, L. & Neumann, R. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet.29, 217–222 (2001). ArticleCASPubMed Google Scholar
Puffenberger, E.G. et al. A missense mutation of the endothelin-B receptor gene in multigenic Hirschsprung's disease. Cell79, 1257–1266 (1994). ArticleCASPubMed Google Scholar
Jannot, A.S., Essioux, L., Reese, M.G. & Clerget-Darpoux, F. Improved use of SNP information to detect the role of genes. Genet. Epidemiol.25, 158–167 (2003). ArticlePubMed Google Scholar
Lander, E.S. & Schork, N.J. Genetic dissection of complex traits. Science265, 2037–2048 (1994). ArticleCASPubMed Google Scholar
Weiss, K.M. & Terwilliger, J.D. How many diseases does it take to map a gene with SNPs? Nat. Genet.26, 151–157 (2000). ArticleCASPubMed Google Scholar
Watterson, G.A. On the number of segregating sites in genetic models without recombination. Theor. Popul. Biol.7, 256–276 (1975). ArticleCASPubMed Google Scholar
Hudson, R.R. Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol.23, 183–201 (1983). ArticleCASPubMed Google Scholar
Halushka, M.K. et al. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet.22, 239–247 (1999). ArticleCASPubMed Google Scholar
Falconer, D.S. The inheritance of liability to certain diseases, estimated from the incidence among relatives. Ann. Hum. Genet.29, 51–76 (1965). Article Google Scholar
Falconer, D.S. & Mackay, T.F.C. Introduction to Quantitative Genetics (Longman, Essex, 1996). Google Scholar
Risch, N. Assessing the role of HLA-linked and unlinked determinants of disease. Am. J. Hum. Genet.40, 1–14 (1987). CASPubMedPubMed Central Google Scholar
Davison, A.C. & Hinkley, D.B. Bootstrap Methods and Their Application (Cambridge University Press, Cambridge, 1997). Book Google Scholar
Sidak, Z. Rectangular Confidence Regions for the Means of Multvariate Normal Distributions. J. Am. Stat. Assoc.62, 626–633 (1967). Google Scholar