Abstract
The study of a complex disease requires careful characterization of the clinical phenotypes for study. Linkage studies, which can detect relative risks of four or greater, apply stringent diagnostic criteria and restrictive rules for family selection to assure a maximally informative collection of subjects. Clinical characterizations that are adopted for association studies must be precise and should be widely accepted to facilitate large studies. The presence of linkage disequilibrium among tightly linked loci provides a basis for genome-wide association studies. A subset of “tagging” markers that maximally characterize interindividual variability can be sought to minimize genotyping costs. Association studies can detect lower relative risks than linkage methods provided there are a limited number of causal variants at each locus and linkage disequilibrium is present (or one directly studies the causal variant). For some complex diseases there may be multiple disease variants and only moderate risks from any single locus. For these complex diseases alternative strategies using comparative genomics and animal models may be required. Admixture linkage mapping may also permit the study of larger collections of patients than is feasible using traditional linkage methods. Finally, once causal loci are identified, further genotype-phenotype studies will allow the disease to be further delineated. Such studies may also identify subsets of patients with varying responsiveness to treatments.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Selected References
Ahmad T, Armuzzi A, Bunce M, et al. The molecular classification of the clinical manifestations of Crohn’s disease. Gastroenterology 2002; 122:854–866.
Amos CI, Rubin LA. Major gene analysis for diseases and disorders of complex etiology. Exp Clin Immunogenet 1995;12:141–155.
Cavanaugh J. International collaboration provides convincing linkage replication in complex disease through analysis of a large pooled dat set: Crohn disease and chromosome 16. Am J Hum Genet 2001;68: 1165–1171.
Cuthbert AP, Fisher SA, Mirza MM, et al. The contribution of NOD2 gene mutations to the risk and site of disease in inflammatory bowel disease. Gastroenterology 2002;122:867–874.
Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. High-resolution haplotype structure in the human genome. Nat Genet 2001;29: 229–232.
Davies JL, Kawaguchi Y, Bennett ST, et al. A genome-wide search for human type 1 diabetes susceptibility genes. Nature 1994;371:130–136.
Devlin B, Roeder K, Bacanu SA. Unbiased methods for population-based association studies. Genet Epidemiol 2001;21:273–284.
Gu C, Province MA, Rao DC. Meta-analysis for model-free methods. Adv Genet 2001;42:255–272.
Hugot JP, Chamaillard M, Zouali H, et al. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn’s disease. Nature 2001;411:599–603.
Hugot JP, Laurent-Puig P, Gower-Rousseau C, et al. Mapping of a susceptibility locus for Crohn’s disease on chromosome 16. Nature 1996;379:821–823.
King RA, Rotter JI, Motulsky AG. Approach to genetic basis of common diseases. In: King RA, Rotter JI, Motulsky AG, eds. The Genetic Basis of Common Diseases. New York: Oxford University Press, 2002; pp. 3–17.
Lander ES, Schork NJ. Genetic dissection of complex traits. Science 1994;265:2037–2048.
Lesage S, Zouali H, Cezard JP, et al. CARD15/NOD2 mutational analysis and genotype-phenotype correlation in 612 patients with inflammatory bowel disease. Am J Hum Genet 2002;70:845–857.
Newman B, Silverberg MS, Gu X, et al. CARD15 and HLA DRB1 alleles influence susceptibility and disease localization in Crohn’s disease. Am J Gastroenterol 2004;99:306–315.
Ogura Y, Bonen DK, InO’Hara N, et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn’s disease. Nature 2001;411: 603–606.
Orholm M, Binder V, Sorensen TI, Rasmussen LP, Kyvik KO. Concordance of inflammatory bowel disease among Danish twins. Results of a nationwide study. Scand J Gastroenterol 2000;35:1075–1081.
Ott J. Analysis of Human Genetic Linkage. Baltimore: Johns Hopkins University Press, 1999.
Rahman P, Bartlett S, Siannis F, et al. CARD 15: A pleiotropic autoimmune gene that confers susceptibility to psoriatic arthritis. Am J Hum Genet 2003;73:677–681.
Rich SS, Sellers TA. Genetic epidemiologic methods. In: Richard A King, Jerome I Rotter, Arno G Motulsky, eds. The Genetic Basis of Common Diseases. Oxford University Press, 2002; pp. 39–49.
Rioux JD, Daly MJ, Silverberg MS, et al. Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease. Nat Genet 2001;29:223–228.
Slager SL, Huang J, Vieland VJ. Effect of allelic heterogeneity on the power of the transmission disequilibrium test. Genet Epidemiol 2000;18:143–156.
Terwilliger JD and Ott J.Handbook of Human Genetic Linkage. Baltimore: Johns Hopkins University Press, 1994.
Thompson D, Goldgar D, Stram D, Witte JS. Design issues in using haplo-type tagging SNPs for association studies. Hum Hered 2003;56:48–55.
Vermeire S, Satsangi J, Peeters M, et al. Evidence for inflammatory bowel disease of a susceptibility locus on the X chromosome. Gastroenterology 2001;120:834–840.
Witte JS, Gauderman WJ, Thomas DC. Asymptotic bias and efficiency in case-control studies of candidate genes and gene-environment interactions: basic family designs. Am J Epideminol 1999;149: 693–705.
Zhang K, Sun F, Waterman S, Chen T. Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data. Am J Hum Genet 2003;73:63–73.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Humana Press Inc.
About this chapter
Cite this chapter
Amos, C.I., Witte, J.S., Newman, W.G. (2006). Identifying Causal Genetic Factors. In: Runge, M.S., Patterson, C. (eds) Principles of Molecular Medicine. Humana Press. https://doi.org/10.1007/978-1-59259-963-9_3
Download citation
DOI: https://doi.org/10.1007/978-1-59259-963-9_3
Publisher Name: Humana Press
Print ISBN: 978-1-58829-202-5
Online ISBN: 978-1-59259-963-9
eBook Packages: MedicineMedicine (R0)