Linkage analysis and association analysis in the presence of linkage using age at onset of COGA alcoholism data.
- Authors
- Zhong, Xiaoyun; Zhang, Heping
- Year
- 2005
- Journal
- BMC genetics
- PMID
- 16451641
- DOI
- 10.1186/1471-2156-6-S1-S31
- PMCID
- PMC1866754
Complex disease mapping usually involves a combination of linkage and association techniques. Linkage analysis can scan the entire genome in a few hundred tests. Association tests may involve an even greater number of tests. However, association tests can localize the susceptibility genes more accurately. Using a recently developed combined linkage and association strategy, we analyzed a subset of the Collaborative Study on the Genetics of Alcoholism (COGA) data for the Genetic Analysis Workshop 14 (GAW14). In this analysis, we first employed linkage analysis based on frailty models that take into account age of onset information to establish which regions along the chromosome are likely to harbor disease susceptibility genes for alcohol dependence. Second, we used an association analysis by exploiting linkage disequilibrium to narrow down the peak regions. We also compare the methods with mean identity-by-descent tests and transmission/disequilibrium tests that do not use age of onset information.
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| Name | Type |
|---|---|
| age of onset | phenotype |
| alcohol dependence | phenotype |
| alcoholism | phenotype |
| ALDX1 local | phenotype |
| ALDX2 local | phenotype |
| candidate chromosomal locus local | cohort |
| candidate genes | cohort |
| Collaborative Study on the Genetics of Alcoholism (COGA) | cohort |
| disease | phenotype |
| hazard function local | drug |
| marker locus d local | variant |
| nonsmoker | cohort |
| proportional hazards model local | drug |
| related phenotypes local | phenotype |
| rs1039559 local | variant |
| rs12142 local | variant |
| rs1224438 local | variant |
| rs1444588 local | variant |
| rs1495042 local | variant |
| rs1565933 local | variant |
| rs1705748 local | variant |
| rs1705772 local | variant |
| rs1820545 local | variant |
| rs1843910 local | variant |
| rs1846629 local | variant |
| rs1848125 local | variant |
| rs1867299 local | variant |
| rs1978161 local | variant |
| rs2279400 local | variant |
| rs273954 local | variant |
| rs700273 local | variant |
| rs710411 local | variant |
| rs727714 local | variant |
| rs951149 local | variant |
| rs965125 local | variant |
| sex | phenotype |
| sibship local | cohort |
| smoking | phenotype |
| test chromosomal region local | cohort |
| testing allele local | variant |
| Tj local | phenotype |
| Zj local | variant |
| Ξ΄j local | phenotype |
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In this knowledge base
External
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| Molecular genetics of addiction and related heritable phenotypes: genome-wide association approaches identify "connectivity constellation" and drug target genes with pleiotropic effects. | Uhl GR et al. | β | 2008 | β |
| Testing association in the presence of linkage--a powerful score for binary traits. | Jonasdottir G et al. | β | 2007 | β |
| Comparison of single-nucleotide polymorphisms and microsatellite markers for linkage analysis in the COGA and simulated data sets for Genetic Analysis Workshop 14: Presentation Groups 1, 2, and 3. | Wilcox MA et al. | β | 2005 | β |