A genome-wide scanning and fine mapping study of COGA data

A thorough genetic mapping study was performed to identify predisposing genes for alcoholism dependence using the Collaborative Study on the Genetics of Alcoholism (COGA) data. The procedure comprised whole-genome linkage and confirmation analyses, single locus and haplotype fine mapping analyses, a...

Descripción completa

Detalles Bibliográficos
Autores principales: Yang, Hsin-Chou, Chang, Chien-Ching, Lin, Chin-Yu, Chen, Chun-Liang, Fann, Cathy SJ
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866755/
https://www.ncbi.nlm.nih.gov/pubmed/16451640
http://dx.doi.org/10.1186/1471-2156-6-S1-S30
_version_ 1782133319333314560
author Yang, Hsin-Chou
Chang, Chien-Ching
Lin, Chin-Yu
Chen, Chun-Liang
Lin, Chin-Yu
Fann, Cathy SJ
author_facet Yang, Hsin-Chou
Chang, Chien-Ching
Lin, Chin-Yu
Chen, Chun-Liang
Lin, Chin-Yu
Fann, Cathy SJ
author_sort Yang, Hsin-Chou
collection PubMed
description A thorough genetic mapping study was performed to identify predisposing genes for alcoholism dependence using the Collaborative Study on the Genetics of Alcoholism (COGA) data. The procedure comprised whole-genome linkage and confirmation analyses, single locus and haplotype fine mapping analyses, and gene × environment haplotype regression. Stratified analysis was considered to reduce the ethnic heterogeneity and simultaneously family-based and case-control study designs were applied to detect potential genetic signals. By using different methods and markers, we found high linkage signals at D1S225 (253.7 cM), D1S547 (279.2 cM), D2S1356 (64.6 cM), and D7S2846 (56.8 cM) with nonparametric linkage scores of 3.92, 4.10, 4.44, and 3.55, respectively. We also conducted haplotype and odds ratio analyses, where the response was the dichotomous status of alcohol dependence, explanatory variables were the inferred individual haplotypes and the three statistically significant covariates were age, gender, and max drink (the maximum number of drinks consumed in a 24-hr period). The final model identified important AD-related haplotypes within a candidate region of NRXN1 at 2p21 and a few others in the inter-gene regions. The relative magnitude of risks to the identified risky/protective haplotypes was elucidated.
format Text
id pubmed-1866755
institution National Center for Biotechnology Information
language English
publishDate 2005
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-18667552007-05-11 A genome-wide scanning and fine mapping study of COGA data Yang, Hsin-Chou Chang, Chien-Ching Lin, Chin-Yu Chen, Chun-Liang Lin, Chin-Yu Fann, Cathy SJ BMC Genet Proceedings A thorough genetic mapping study was performed to identify predisposing genes for alcoholism dependence using the Collaborative Study on the Genetics of Alcoholism (COGA) data. The procedure comprised whole-genome linkage and confirmation analyses, single locus and haplotype fine mapping analyses, and gene × environment haplotype regression. Stratified analysis was considered to reduce the ethnic heterogeneity and simultaneously family-based and case-control study designs were applied to detect potential genetic signals. By using different methods and markers, we found high linkage signals at D1S225 (253.7 cM), D1S547 (279.2 cM), D2S1356 (64.6 cM), and D7S2846 (56.8 cM) with nonparametric linkage scores of 3.92, 4.10, 4.44, and 3.55, respectively. We also conducted haplotype and odds ratio analyses, where the response was the dichotomous status of alcohol dependence, explanatory variables were the inferred individual haplotypes and the three statistically significant covariates were age, gender, and max drink (the maximum number of drinks consumed in a 24-hr period). The final model identified important AD-related haplotypes within a candidate region of NRXN1 at 2p21 and a few others in the inter-gene regions. The relative magnitude of risks to the identified risky/protective haplotypes was elucidated. BioMed Central 2005-12-30 /pmc/articles/PMC1866755/ /pubmed/16451640 http://dx.doi.org/10.1186/1471-2156-6-S1-S30 Text en Copyright © 2005 Yang et al; licensee BioMed Central Ltd http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Yang, Hsin-Chou
Chang, Chien-Ching
Lin, Chin-Yu
Chen, Chun-Liang
Lin, Chin-Yu
Fann, Cathy SJ
A genome-wide scanning and fine mapping study of COGA data
title A genome-wide scanning and fine mapping study of COGA data
title_full A genome-wide scanning and fine mapping study of COGA data
title_fullStr A genome-wide scanning and fine mapping study of COGA data
title_full_unstemmed A genome-wide scanning and fine mapping study of COGA data
title_short A genome-wide scanning and fine mapping study of COGA data
title_sort genome-wide scanning and fine mapping study of coga data
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866755/
https://www.ncbi.nlm.nih.gov/pubmed/16451640
http://dx.doi.org/10.1186/1471-2156-6-S1-S30
work_keys_str_mv AT yanghsinchou agenomewidescanningandfinemappingstudyofcogadata
AT changchienching agenomewidescanningandfinemappingstudyofcogadata
AT linchinyu agenomewidescanningandfinemappingstudyofcogadata
AT chenchunliang agenomewidescanningandfinemappingstudyofcogadata
AT linchinyu agenomewidescanningandfinemappingstudyofcogadata
AT fanncathysj agenomewidescanningandfinemappingstudyofcogadata
AT yanghsinchou genomewidescanningandfinemappingstudyofcogadata
AT changchienching genomewidescanningandfinemappingstudyofcogadata
AT linchinyu genomewidescanningandfinemappingstudyofcogadata
AT chenchunliang genomewidescanningandfinemappingstudyofcogadata
AT linchinyu genomewidescanningandfinemappingstudyofcogadata
AT fanncathysj genomewidescanningandfinemappingstudyofcogadata