Genomic screening and replication using the same data set in family-based association testing (original) (raw)
References
Sherry, S.T., Ward, M. & Sirotkin, K. dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res.9, 677–679 (1999). CASPubMed Google Scholar
International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature409, 928–933 (2001).
Marnellos, G. High-throughput SNP analysis for genetic association studies. Curr. Opin. Drug Discov. Devel.6, 317–321 (2003). CASPubMed Google Scholar
Bonferroni, C.E. Teoria statistica delle classi e calcolo delle probabilita. In Volume in Onore di Ricarrdo dalla Volta, Universita di Firenza, 1–62 (1937). Google Scholar
Hochberg, Y. A sharper Bonferroni procedure for multiple tests of significance. Biometrika75, 800–802 (1988). Article Google Scholar
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B57, 289–300 (1995). Google Scholar
Benjamini, Y. & Yekutieli, D. The control of the false discovery rate in multiple testing under dependency. Ann. Stat.29, 1165–1188 (2001). Article Google Scholar
Lange, C., DeMeo, D.L., Silverman, E., Weiss, S. & Laird, N.M. Using the noninformative families in family-based association tests: a powerful new testing strategy. Am. J. Hum. Genet.73, 801–811 (2003). ArticleCASPubMedPubMed Central Google Scholar
Lange, C. et al. A new powerful non-parametric two-stage approach for testing multiple phenotypes in family-based association studies. Hum. Hered.56, 10–17 (2003). ArticlePubMed Google Scholar
Lange, C., DeMeo, D.L., Silverman, E.K., Weiss, S.T. & Laird, N.M. PBAT: Tools for family-based association studies. Am. J. Hum. Genet.74, 367–369 (2004). ArticlePubMedPubMed Central Google Scholar
Van Steen, K. & Lange, C. PBAT: a comprehensive software package for genome-wide association analysis of complex family-based studies. Hum. Genomics2, 70–74 (2005). Article Google Scholar
Childhood Asthma Management Program Research Group. The childhood asthma management program (CAMP): design, rationale, and methods. Control. Clin. Trials20, 91–120 (1999).
Lyon, H. et al. IL10 gene polymorphisms are associated with asthma phenotypes in children. Genet. Epidemiol.26, 155–165 (2004). ArticlePubMedPubMed Central Google Scholar
Lange, C. & Laird, N.M. On a general class of conditional tests for family-based association studies in genetics: the asymptotic distribution, the conditional power, and optimality considerations. Genet. Epidemiol.23, 165–180 (2002). ArticlePubMed Google Scholar
Laird, N., Horvath, S. & Xu, X. Implementing a unified approach to family based tests of association. Genet. Epidemiol.19 Suppl 1, S36–S42 (2000). ArticlePubMed Google Scholar
Kennedy, G.C. et al. Large-scale genotyping of complex DNA. Nat. Biotechnol.21, 1233–1237 (2003). ArticleCASPubMed Google Scholar
Schaid, D.J. et al. Comparison of microsatellites versus single nucleotide polymorphisms by a genome linkage screen for prostate cancer susceptibility loci. Am. J. Hum. Genet.75, 948–965 (2004). ArticleCASPubMedPubMed Central Google Scholar
Lange, C. & Laird, N.M. Power calculations for a general class of family-based association tests: Dichotomous traits. Am. J. Hum. Genet.71, 575–584 (2002). ArticleCASPubMedPubMed Central Google Scholar
Lange, C., DeMeo, D.L. & Laird, N.M. Power calculations for a general class of family-based association tests: Quantitative traits. Am. J. Hum. Genet.71, 1330–1341 (2002). ArticleCASPubMedPubMed Central Google Scholar
Devlin, B. & Roeder, K. Genomic control for association studies. Biometrics55, 997–1004 (1999). ArticleCASPubMed Google Scholar
Duffy, D.L., Martin, N.G., Battistutta, D., Hopper, J.L. & Mathews, J.D. Genetics of asthma and hay fever in Australian twins. Am. Rev. Respir. Dis.142, 1351–1358 (1990). ArticleCASPubMed Google Scholar
Lange, C. et al. A family-based association test for repeatedly measured quantitative traits adjusting for unknown environmental and/or polygenic effects. Statistical Applications in Genetics and Molecular Biology [online]3, Article 17 (2004).
Holm, S. A simple sequentially rejective multiple testing procedure. Scand. J. Stat.6, 65–70 (1979). Google Scholar
Sidak, Z. On probabilities of rectangles in multivariate Student distributions: their dependence on correlations. Ann. Math. Statist.42, 169–175 (1971). Article Google Scholar
Satagopan, J.M., Venkatraman, E.S. & Begg, C.B. Two-stage designs for gene-disease association studies with sample size constraints. Biometrics60, 589–597 (2004). ArticlePubMedPubMed Central Google Scholar
International HapMap Consortium. The International HapMap Project. Nature426, 789–796 (2003).
Zhai, W., Todd, M.J. & Nielsen, R. Is haplotype block identification useful for association mapping studies? Genet. Epidemiol.27, 80–83 (2004). ArticlePubMed Google Scholar
Churchill, G.A. & Doerge, R.W. Empirical threshold values for quantitative trait mapping. Genetics138, 963–971 (1994). CASPubMedPubMed Central Google Scholar
Churchill, G.A. & Doerge, R.W. Permutation tests for multiple loci affecting a quantitative character. Genetics142, 285–294 (1996). PubMedPubMed Central Google Scholar
Lin, S., Chakravarti, A. & Cutler, D.J. Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies. Nat. Genet.36, 1181–1188 (2004). ArticleCASPubMed Google Scholar
Spielman, R.S., McGinnis, R.E. & Ewens, W.J. Transmission test for linkage disequilibrium: the insuline gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet.52, 506–516 (1993). CASPubMedPubMed Central Google Scholar
Lange, C., Silverman, E., Weiss, S.T., Xu, X. & Laird, N.M. A multivariate family-based test using generalized estimating equations: FBAT-GEE. Biostatistics4, 195–206 (2003). ArticlePubMed Google Scholar
Rabinowitz, D. & Laird, N.M. A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information. Hum. Hered.50, 211–223 (2000). ArticleCASPubMed Google Scholar