Analysis of Sequence Data Under Multivariate Trait-Dependent Sampling

REFERENCES

• Allison, D. B. (1997), “Transmission-Disequilibrium Tests for Quantitative Traits,” American Journal of Human Genetics, 60, 676–690.
   PubMed Web of Science ®Google Scholar
• Bild, D. E., Bluemke, D. A., Burke, G. L., Detrano, R., Roux, A. V., Folsom, A. R., Greenland, P., Jacobs, Jr, D. R., Kronmal, R., Liu, K., Nelson, J. C., OLeary, D., Saad, M. F., Shea, S., Szklo, M., and Tracy, R. P. (2002), “Multi-Ethnic Study of Atherosclerosis: Objectives and Design,” American Journal of Epidemiology, 156, 871–881.
   PubMed Web of Science ®Google Scholar
• Chen, Z., Zheng, G., Ghosh, K., and Li, Z. (2005), “Linkage Disequilibrium Mapping of Quantitative-Trait Loci by Selective Genotyping,” American Journal of Human Genetics, 77, 661–669.
   PubMed Web of Science ®Google Scholar
• Dawber, T. R., Meadors, G. F., and Jr, F. E. (1951), “Epidemiological Approaches to Heart Disease: The Framingham Study,” American Journal of Public Health and the Nation’s Health, 41, 279–286.
   PubMed Web of Science ®Google Scholar
• Dempster, A. P., Laird, N. M., and Rubin, D. B. (1977), “Maximum Likelihood From Incomplete Data via the EM Algorithm,” Journal of the Royal Statistical Society, Series B, 39, 1–38.
   Google Scholar
• Fried, L. P., Borhani, N. O., Enright, P., Furberg, C. D., Gardin, J. M., Kronmal, R. A., Kuller, L. H., Manolio, T. A., Mittelmark, M. B., Newman, A., O’Leary, D. H., Psaty, B., Rautaharju, P., Tracy, R. P., and Weiler, P. G. (1991), “The Cardiovascular Health Study: Design and Rationale,” Annals of Epidemiology, 1, 263–276.
   PubMedGoogle Scholar
• Friedman, G. D., Cutter, G. R., Donahue, R. P., Hughes, G. H., Hulley, S. B., Jr, D. R. J., Liu, K., and Savage, P. J. (1988), “CARDIA: Study Design, Recruitment, and Some Characteristics of the Examined Subjects,” Journal of Clinical Epidemiology, 41, 1105–1116.
   PubMed Web of Science ®Google Scholar
• Hu, Y. J., Lin, D. Y., and Zeng, D. (2010), “A General Framework for Studying Genetic Effects and Gene-Environment Interactions with Missing Data,” Biostatistics, 11, 583–598.
   PubMed Web of Science ®Google Scholar
• Huang, B. E., and Lin, D. Y. (2007), “Efficient Association Mapping of Quantitative Trait Loci With Selective Genotyping,” American Journal of Human Genetics, 80, 567–576.
   PubMed Web of Science ®Google Scholar
• Li, B., and Leal, S. M. (2008), “Methods for Detecting Associations With Rare Variants for Common Diseases: Application to Analysis of Sequence Data,” American Journal of Human Genetics, 83, 311–321.
   PubMed Web of Science ®Google Scholar
• Lin, D. Y., and Tang, Z. Z. (2011), “A General Framework for Detecting Disease Associations With Rare Variants in Sequencing Studies,” American Journal of Human Genetics, 89, 354–367.
   PubMed Web of Science ®Google Scholar
• Lin, D. Y., and Zeng, D. (2006), “Likelihood-Based Inference on Haplotype Effects in Genetic Association Studies,” Journal of the American Statistical Association, 101, 89–104.
   Web of Science ®Google Scholar
• ——— (2009), “Proper Analysis of Secondary Phenotype Data in Case-Control Association Studies,” Genetic Epidemiology, 33, 256–265.
   PubMed Web of Science ®Google Scholar
• Lin, D. Y., Zeng, D., and Tang, Z. Z. (2013), “Quantitative Trait Analysis in Sequencing Studies Under Trait-Dependent Sampling,” Proceedings of the National Academy of Sciences, 110, 12247–12252.
   PubMed Web of Science ®Google Scholar
• Lin, H., Wang, M., Brody, J. A., Bis, J. C., Dupuis, J., Lumley, T., McKnight, B., Rice, K. M., Sitlani, C. M., Reid, J. G., Bressler, J., Liu, X., Davis, B. C., Johnson, A. D., O’Donnell, C. J., Kovar, C. L., Dinh, H., Wu, Y., Newsham, I., Chen, H., Broka, A., DeStefano, A. L., Gupta, M., Lunetta, K. L., Liu, C.-T., White, C. C., Xing, C., Zhou, Y., Benjamin, E. J., Schnabel, R. B., Heckbert, S. R., Psaty, B. M., Muzny, D. M., Cupples, L. A., Morrison, A. C., and Boerwinkle, E. (2014), “Strategies to Design and Analyze Targeted Sequencing Data: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study,” Circulation: Cardiovascular Genetics, 7, 335–343.
   PubMed Web of Science ®Google Scholar
• Louis, T. A. (1982), “Finding the Observed Information Matrix When Using the EM Algorithm,” Journal of the Royal Statistical Society, Series B, 44, 226–233.
   Web of Science ®Google Scholar
• Madsen, B. E., and Browning, S. R. (2009), “A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic,” PLoS Genetics [online], 5, e1000384. Available at http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000384
   PubMed Web of Science ®Google Scholar
• Page, G. P., and Amos, C. I. (1999), “Comparison of Linkage-Disequilibrium Methods for Localization of Genes Influencing Quantitative Traits in Humans,” American Journal of Human Genetics, 64, 1194–1205.
   PubMed Web of Science ®Google Scholar
• Price, A. L., Kryukov, G. V., Bakker, P. I., Purcell, S. M., Staples, J., Wei, L.-J., and Sunyaev, S. R. (2010), “Pooled Association Tests for Rare Variants in Exon-Resequencing Studies,” The American Journal of Human Genetics, 86, 832–838.
   PubMed Web of Science ®Google Scholar
• Slatkin, M. (1999), “Disequilibrium Mapping of a Quantitative-Trait Locus in an Expanding Population,” American Journal of Human Genetics, 64, 1765–1773.
   Web of Science ®Google Scholar
• Tang, Z. Z., and Lin, D. Y. (2013), “MASS: Meta-Analysis of Score Statistics for Sequencing Studies,” Bioinformatics, 29, 1803–1805.
   PubMed Web of Science ®Google Scholar
• (1989), “The Atherosclerosis Risk in Communities (ARIC) Study: Design and Objectives,” American Journal of Epidemiology, 129, 687–702.
   PubMed Web of Science ®Google Scholar
• (1998), “Design of the Women’s Health Initiative Clinical Trial and Observational Study-Examples from the Women’s Health Initiative,” Controlled Clinical Trials, 19, 61–109.
   PubMedGoogle Scholar
• Wu, M. C., Lee, S., Cai, T., Li, Y., Boehnke, M., and Lin, X. (2011), “Rare-Variant Association Testing for Sequencing Data With the Sequence Kernel Association Test,” American Journal of Human Genetics, 89, 82–93.
   PubMed Web of Science ®Google Scholar