COGA phenotypes and linkages on chromosome 2.
- Authors
- Wiener, Howard W; Go, Rodney C P; Tiwari, Hemant; George, Varghese; Page, Grier P
- Year
- 2005
- Journal
- BMC genetics
- PMID
- 16451583
- DOI
- 10.1186/1471-2156-6-S1-S125
- PMCID
- PMC1866812
An initial linkage analysis of the alcoholism phenotype as defined by DSM-III-R criteria and alcoholism defined by DSM-IV criteria showed many, sometimes striking, inconsistencies. These inconsistencies are greatly reduced by making the definition of alcoholism more specific. We defined new phenotypes combining the alcoholism definitions and the latent variables, defining an individual as affected if that individual is alcoholic under one of the definitions (either DSM-III-R or DSM-IV), and indicated having a symptom defined by one of the latent variables. This was done for each of the two alcoholism definitions and five latent variables, selected from a canonical discriminant analyses indicating they formed significant groupings using the electrophysiological variables. We found that linkage analyses utilizing these latent variables were much more robust and consistent than the linkage results based on DSM-III-R or DSM-IV criteria for definition of alcoholism. We also performed linkage analyses on two first principal components derived phenotypes, one derived from the electrophysiological variables, and the other derived from the latent variables. A region on chromosome 2 at 250 cM was found to be linked to both of these derived phenotypes. Further examination of the SNPs in this region identified several haplotypes strongly associated with these derived phenotypes.
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| Name | Type |
|---|---|
| 220 cM region local | variant |
| 250 cM region local | variant |
| 5-SNP haplotype 234.0-234.5 cM local | variant |
| A1_1 local | phenotype |
| A1_11 local | phenotype |
| A1_2 local | phenotype |
| A1_7 local | phenotype |
| A1_9 local | phenotype |
| A2_1 local | phenotype |
| A2_11 local | phenotype |
| A2_2 local | phenotype |
| A2_7 local | phenotype |
| A2_9 local | phenotype |
| Affymetrix SNP data local | variant |
| age of onset | phenotype |
| Alc1 local | phenotype |
| Alc2 local | phenotype |
| alcohol | phenotype |
| alcohol dependence | phenotype |
| alcoholism | phenotype |
| Alcoholism (DSM-III-R) local | phenotype |
| Alcoholism (DSM-IV) local | phenotype |
| alcoholism/latent local | phenotype |
| Alcoholism latent variable principal component phenotype local | phenotype |
| Alzheimer's disease | phenotype |
| APP | gene |
| Chromosome 2 region 100 cM local | anatomy |
| Chromosome 2 region 250 cM local | anatomy |
| COGA dataset | cohort |
| Collaborative Study on the Genetics of Alcoholism (COGA) | cohort |
| complex traits | phenotype |
| derived phenotype Ai_j local | phenotype |
| DSM-IV | phenotype |
| early-onset Alzheimer's disease local | phenotype |
| EEG | phenotype |
| EEG phenotypes (Porjesz et al.) local | phenotype |
| EEG principal component local | phenotype |
| EEG principal component 1 local | phenotype |
| EEG principal component outcome local | phenotype |
| EEG principal component phenotype local | phenotype |
| EEG variable local | phenotype |
| EEG variables local | phenotype |
| Electrophysiological variables local | phenotype |
| habitual smoking | phenotype |
| Habitual smoking local | drug |
| latent variable local | phenotype |
| Latent variable local | phenotype |
| Latent Variable 11 (emotional psychological problems from drinking) local | phenotype |
| Latent Variable 1 (persistent desire to stop drinking) local | phenotype |
| Latent Variable 2 (morning drinking) local | phenotype |
| Latent Variable 7 (gave up activities to drink) local | phenotype |
| Latent Variable 9 (withdrawal symptoms) local | phenotype |
| latent variable principal component local | phenotype |
| latent variables local | phenotype |
| late-onset Alzheimer's disease | phenotype |
| Mendelian dominant trait local | phenotype |
| Platelet monoamine oxidase activity local | phenotype |
| principal component derived phenotypes local | phenotype |
| PS1 | gene |
| PSEN2 | gene |
| short tandem repeat local | variant |
| SNP | cohort |
| SNP haplotype 206 cM local | variant |
| SNP haplotype 210 cM local | variant |
| SNP haplotype 228 cM local | variant |
| STR markers local | variant |
| tsc0045051|tsc0620679|tsc0620681|tsc1612284|tsc0524593 local | variant |
| tsc0052569|tsc0530060 local | variant |
| tsc0548180|tsc0512074 local | variant |
| tsc0675766|tsc0040071 local | variant |
| tsc0977679|tsc0977680 local | variant |
| tsc1282391|tsc0539848 local | variant |
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In this knowledge base
| Title | Year | PMID |
|---|---|---|
| Evidence for genes on chromosome 2 contributing to alcohol dependence with conduct disorder and suicide attempts. | 2010 | 20468071 |
External
| Title | Authors | Journal | Year | Link |
|---|---|---|---|---|
| Using an Event-History with Risk-Free Model to Study the Genetics of Alcoholism. | Yang HC et al. | — | 2017 | → |
| Evidence for genes on chromosome 2 contributing to alcohol dependence with conduct disorder and suicide attempts. | Dick DM et al. | — | 2010 | → |
| Genes and alcohol. | Osby U et al. | — | 2010 | → |
| NK1 (TACR1) receptor gene 'knockout' mouse phenotype predicts genetic association with ADHD. | Yan TC et al. | — | 2010 | → |
| A genomic imprinting test for ordinal traits in pedigree data. | Feng R et al. | — | 2008 | → |
| A score test for linkage analysis of ordinal traits based on IBD sharing. | Feng R et al. | — | 2008 | → |
| Linkage and association analyses of principal components in expression data. | Hinrichs AL et al. | — | 2007 | → |
| Alcoholism and related traits: a summary of Group 13 contributions. | Rice JP et al. | — | 2005 | → |