Effect of genotype x alcoholism interaction on linkage analysis of an alcoholism-related quantitative phenotype

Rector Arya, Thomas D. Dyer, Diane M. Warren, Christopher P. Jenkinson, Ravindranath Duggirala, Laura Almasy

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Studies have shown that genetic and environmental factors and their interactions affect several alcoholism phenotypes. Genotype x alcoholism (GxA) interaction refers to the environmental (alcoholic and non-alcoholic) influences on the autosomal genes contributing to variation in an alcoholism-related quantitative phenotype. The purpose of this study was to examine the effects of GxA interaction on the detection of linkage for alcoholism-related phenotypes. We used phenotypic and genotypic data from the Collaborative Study on the Genetics of Alcoholism relating to 1,388 subjects as part of Genetic Analysis Workshop 14 problem 1. We analyzed the MXDRNK phenotype to detect GxA interaction using SOLAR. Upon detecting significant interaction, we conducted variance-component linkage analyses using microsatellite marker data. For maximum number of drinks per a 24 hour period, the highest LODs were observed on chromosomes 1, 4, and 13 without GxA interaction. Interaction analysis yielded four regions on chromosomes 1, 4, 13, and 15. On chromosome 4, a maximum LOD of 1.5 at the same location as the initial analysis was obtained after incorporating GxA interaction effects. However, after correcting for extra parameters, the LOD score was reduced to a corrected LOD of 1.1, which is similar to the LOD observed in the non-interaction analysis. Thus, we see little differences in LOD scores, while some linkage regions showed large differences in the magnitudes of estimated quantitative trait loci heritabilities between the alcoholic and non-alcoholic groups. These potential hints of differences in genetic effect may influence future analyses of variants under these linkage peaks.

Original languageEnglish (US)
Article numberS120
JournalBMC Genetics
Volume6
Issue numberSUPPL.1
DOIs
StatePublished - Dec 30 2005

Fingerprint

Alcoholism
Genotype
Phenotype
Chromosomes, Human, Pair 4
Chromosomes, Human, Pair 1
Chromosomes, Human, Pair 13
Quantitative Trait Loci
Microsatellite Repeats
Education
Genes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Arya, R., Dyer, T. D., Warren, D. M., Jenkinson, C. P., Duggirala, R., & Almasy, L. (2005). Effect of genotype x alcoholism interaction on linkage analysis of an alcoholism-related quantitative phenotype. BMC Genetics, 6(SUPPL.1), [S120]. https://doi.org/10.1186/1471-2156-6-S1-S120

Effect of genotype x alcoholism interaction on linkage analysis of an alcoholism-related quantitative phenotype. / Arya, Rector; Dyer, Thomas D.; Warren, Diane M.; Jenkinson, Christopher P.; Duggirala, Ravindranath; Almasy, Laura.

In: BMC Genetics, Vol. 6, No. SUPPL.1, S120, 30.12.2005.

Research output: Contribution to journalArticle

Arya, Rector ; Dyer, Thomas D. ; Warren, Diane M. ; Jenkinson, Christopher P. ; Duggirala, Ravindranath ; Almasy, Laura. / Effect of genotype x alcoholism interaction on linkage analysis of an alcoholism-related quantitative phenotype. In: BMC Genetics. 2005 ; Vol. 6, No. SUPPL.1.
@article{676dd5e5db174c7589ff114b41f79d11,
title = "Effect of genotype x alcoholism interaction on linkage analysis of an alcoholism-related quantitative phenotype",
abstract = "Studies have shown that genetic and environmental factors and their interactions affect several alcoholism phenotypes. Genotype x alcoholism (GxA) interaction refers to the environmental (alcoholic and non-alcoholic) influences on the autosomal genes contributing to variation in an alcoholism-related quantitative phenotype. The purpose of this study was to examine the effects of GxA interaction on the detection of linkage for alcoholism-related phenotypes. We used phenotypic and genotypic data from the Collaborative Study on the Genetics of Alcoholism relating to 1,388 subjects as part of Genetic Analysis Workshop 14 problem 1. We analyzed the MXDRNK phenotype to detect GxA interaction using SOLAR. Upon detecting significant interaction, we conducted variance-component linkage analyses using microsatellite marker data. For maximum number of drinks per a 24 hour period, the highest LODs were observed on chromosomes 1, 4, and 13 without GxA interaction. Interaction analysis yielded four regions on chromosomes 1, 4, 13, and 15. On chromosome 4, a maximum LOD of 1.5 at the same location as the initial analysis was obtained after incorporating GxA interaction effects. However, after correcting for extra parameters, the LOD score was reduced to a corrected LOD of 1.1, which is similar to the LOD observed in the non-interaction analysis. Thus, we see little differences in LOD scores, while some linkage regions showed large differences in the magnitudes of estimated quantitative trait loci heritabilities between the alcoholic and non-alcoholic groups. These potential hints of differences in genetic effect may influence future analyses of variants under these linkage peaks.",
author = "Rector Arya and Dyer, {Thomas D.} and Warren, {Diane M.} and Jenkinson, {Christopher P.} and Ravindranath Duggirala and Laura Almasy",
year = "2005",
month = "12",
day = "30",
doi = "10.1186/1471-2156-6-S1-S120",
language = "English (US)",
volume = "6",
journal = "BMC Genetics",
issn = "1471-2156",
publisher = "BioMed Central",
number = "SUPPL.1",

}

TY - JOUR

T1 - Effect of genotype x alcoholism interaction on linkage analysis of an alcoholism-related quantitative phenotype

AU - Arya, Rector

AU - Dyer, Thomas D.

AU - Warren, Diane M.

AU - Jenkinson, Christopher P.

AU - Duggirala, Ravindranath

AU - Almasy, Laura

PY - 2005/12/30

Y1 - 2005/12/30

N2 - Studies have shown that genetic and environmental factors and their interactions affect several alcoholism phenotypes. Genotype x alcoholism (GxA) interaction refers to the environmental (alcoholic and non-alcoholic) influences on the autosomal genes contributing to variation in an alcoholism-related quantitative phenotype. The purpose of this study was to examine the effects of GxA interaction on the detection of linkage for alcoholism-related phenotypes. We used phenotypic and genotypic data from the Collaborative Study on the Genetics of Alcoholism relating to 1,388 subjects as part of Genetic Analysis Workshop 14 problem 1. We analyzed the MXDRNK phenotype to detect GxA interaction using SOLAR. Upon detecting significant interaction, we conducted variance-component linkage analyses using microsatellite marker data. For maximum number of drinks per a 24 hour period, the highest LODs were observed on chromosomes 1, 4, and 13 without GxA interaction. Interaction analysis yielded four regions on chromosomes 1, 4, 13, and 15. On chromosome 4, a maximum LOD of 1.5 at the same location as the initial analysis was obtained after incorporating GxA interaction effects. However, after correcting for extra parameters, the LOD score was reduced to a corrected LOD of 1.1, which is similar to the LOD observed in the non-interaction analysis. Thus, we see little differences in LOD scores, while some linkage regions showed large differences in the magnitudes of estimated quantitative trait loci heritabilities between the alcoholic and non-alcoholic groups. These potential hints of differences in genetic effect may influence future analyses of variants under these linkage peaks.

AB - Studies have shown that genetic and environmental factors and their interactions affect several alcoholism phenotypes. Genotype x alcoholism (GxA) interaction refers to the environmental (alcoholic and non-alcoholic) influences on the autosomal genes contributing to variation in an alcoholism-related quantitative phenotype. The purpose of this study was to examine the effects of GxA interaction on the detection of linkage for alcoholism-related phenotypes. We used phenotypic and genotypic data from the Collaborative Study on the Genetics of Alcoholism relating to 1,388 subjects as part of Genetic Analysis Workshop 14 problem 1. We analyzed the MXDRNK phenotype to detect GxA interaction using SOLAR. Upon detecting significant interaction, we conducted variance-component linkage analyses using microsatellite marker data. For maximum number of drinks per a 24 hour period, the highest LODs were observed on chromosomes 1, 4, and 13 without GxA interaction. Interaction analysis yielded four regions on chromosomes 1, 4, 13, and 15. On chromosome 4, a maximum LOD of 1.5 at the same location as the initial analysis was obtained after incorporating GxA interaction effects. However, after correcting for extra parameters, the LOD score was reduced to a corrected LOD of 1.1, which is similar to the LOD observed in the non-interaction analysis. Thus, we see little differences in LOD scores, while some linkage regions showed large differences in the magnitudes of estimated quantitative trait loci heritabilities between the alcoholic and non-alcoholic groups. These potential hints of differences in genetic effect may influence future analyses of variants under these linkage peaks.

UR - http://www.scopus.com/inward/record.url?scp=30344470664&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=30344470664&partnerID=8YFLogxK

U2 - 10.1186/1471-2156-6-S1-S120

DO - 10.1186/1471-2156-6-S1-S120

M3 - Article

VL - 6

JO - BMC Genetics

JF - BMC Genetics

SN - 1471-2156

IS - SUPPL.1

M1 - S120

ER -