GAW14 Workshop Summary
Linkage mapping methods applied to the COGA data set: Presentation Group 4 of Genetic Analysis Workshop 14
Article first published online: 8 DEC 2005
© 2005 Wiley-Liss, Inc.
Supplement: Summarizing Analyses Comparing Microsatellite and SNP Marker Loci for Genome-Wide Scans
Volume 29, Issue S1, pages S29–S34, 2005
How to Cite
Daw, E. W., Doan, B. Q. and Elston, R. C. (2005), Linkage mapping methods applied to the COGA data set: Presentation Group 4 of Genetic Analysis Workshop 14. Genet. Epidemiol., 29: S29–S34. doi: 10.1002/gepi.20107
- Issue published online: 8 DEC 2005
- Article first published online: 8 DEC 2005
- linkage analysis;
- affected-relative-pair linkage;
- SNP markers
Presentation Group 4 participants analyzed the Collaborative Study on the Genetics of Alcoholism data provided for Genetic Analysis Workshop 14. This group examined various aspects of linkage analysis and related issues. Seven papers included linkage analyses, while the eighth calculated identity-by-descent (IBD) probabilities. Six papers analyzed linkage to an alcoholism phenotype: ALDX1 (four papers), ALDX2 (one paper), or a combination both (one paper). Methods used included Bayesian variable selection coupled with Haseman-Elston regression, recursive partitioning to identify phenotype and covariate groupings that interact with evidence for linkage, nonparametric linkage regression modeling, affected sib-pair linkage analysis with discordant sib-pair controls, simulation-based homozygosity mapping in a single pedigree, and application of a propensity score to collapse covariates in a general conditional logistic model. Alcoholism linkage was found with ≥2 of these approaches on chromosomes 2, 4, 6, 7, 9, 14, and 21. The remaining linkage paper compared the utility of several single-nucleotide polymorphism (SNP) and microsatellite marker maps for Monte Carlo Markov chain combined oligogenic segregation and linkage analysis, and analyzed one of the electrophysiological endophenotypes, ttth1, on chromosome 7. Linkage was found with all marker sets. The last paper compared the multipoint IBD information content of several SNP sets and the microsatellite set, and found that while all SNP sets examined contained more information than the microsatellite set, most of the information contained in the SNP sets was captured by a subset of the SNP markers with ∼1-cM marker spacing. From these papers, we highlight three points: a 1-cM SNP map seems to capture most of the linkage information, so denser maps do not appear necessary; careful and appropriate use of covariates can aid linkage analysis; and sources of increased gene-sharing between relatives should be accounted for in analyses. Genet. Epidemiol. 29(Suppl. 1):S29–S34, 2005. © 2005 Wiley-Liss, Inc.