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Evidence of admixture from haplotyping in an epidemiological study of UK Caucasian males: implications for association analyses

Evidence of admixture from haplotyping in an epidemiological study of UK Caucasian males: implications for association analyses
Evidence of admixture from haplotyping in an epidemiological study of UK Caucasian males: implications for association analyses
Objective: Cohort and case-control genetic association studies offer the greatest power to detect small genotypic influences on disease phenotypes, relative to family-based designs. However, genetic subdivisions could confound studies involving unrelated individuals, but the topic has been little investigated. We examined geographical and interallelic association of SNP and microsatellite haplotypes of the Y chromosome, of regions of chromosome 11, and of autosomal SNP genotypes relevant to cardiovascular risk traits in a UK-wide epidemiological survey. Results: We show evidence (p = 0.00001) of the Danelaw history of the UK, marked by a two-fold excess of a Viking Y haplotype in central England. We also found evidence for a (different) single-centre geographical over-representation of one haplotype, both for APOC3-A4-A5 and for IGF2. The basis of this remains obscure but neither reflect genotyping error nor correlate with the phenotypic associations by centre of these markers. A panel of SNPs relevant to cardiovascular risks traits showed neither association with geographical location nor with Y haplotypes. Conclusion: Combinations of Y haplotyping, autosomal haplotyping, and genome-wide SNP typing, taken together with phenotypic2 associations, should improve epidemiological recognition and interpretation of possible confounding by genetic subdivision.
genetic association studies, population subdivision, stratification, Y chromosome, autosomal SNPs, haplotypic analysis
142 - 155
Chen, X.H.
fe7ddffb-99db-4473-8d70-c9ecc07f2b16
Rodriguez, S.
b047a823-28c8-4043-8d4f-dc6b23f52e4e
Hawe, E.
04b00658-cb75-42fc-9213-9c3ba8372105
Talmud, P.J.
6921755a-49e5-4a12-b4b7-051c19091974
Miller, G.J.
c0be8252-47b0-4482-a977-25ac06cf59df
Underhill, P.
3c57b3ae-59af-4598-ba41-d9833767262c
Humphries, S.E.
ccc89458-fe7c-4cce-92a3-470dac1b33b6
Day, I.N.
e9cacaf7-f4c8-4ef0-82fa-b459ad683d50
Chen, X.H.
fe7ddffb-99db-4473-8d70-c9ecc07f2b16
Rodriguez, S.
b047a823-28c8-4043-8d4f-dc6b23f52e4e
Hawe, E.
04b00658-cb75-42fc-9213-9c3ba8372105
Talmud, P.J.
6921755a-49e5-4a12-b4b7-051c19091974
Miller, G.J.
c0be8252-47b0-4482-a977-25ac06cf59df
Underhill, P.
3c57b3ae-59af-4598-ba41-d9833767262c
Humphries, S.E.
ccc89458-fe7c-4cce-92a3-470dac1b33b6
Day, I.N.
e9cacaf7-f4c8-4ef0-82fa-b459ad683d50

Chen, X.H., Rodriguez, S., Hawe, E., Talmud, P.J., Miller, G.J., Underhill, P., Humphries, S.E. and Day, I.N. (2004) Evidence of admixture from haplotyping in an epidemiological study of UK Caucasian males: implications for association analyses. Human Heredity, 57 (3), 142 - 155. (doi:10.1159/000079245).

Record type: Article

Abstract

Objective: Cohort and case-control genetic association studies offer the greatest power to detect small genotypic influences on disease phenotypes, relative to family-based designs. However, genetic subdivisions could confound studies involving unrelated individuals, but the topic has been little investigated. We examined geographical and interallelic association of SNP and microsatellite haplotypes of the Y chromosome, of regions of chromosome 11, and of autosomal SNP genotypes relevant to cardiovascular risk traits in a UK-wide epidemiological survey. Results: We show evidence (p = 0.00001) of the Danelaw history of the UK, marked by a two-fold excess of a Viking Y haplotype in central England. We also found evidence for a (different) single-centre geographical over-representation of one haplotype, both for APOC3-A4-A5 and for IGF2. The basis of this remains obscure but neither reflect genotyping error nor correlate with the phenotypic associations by centre of these markers. A panel of SNPs relevant to cardiovascular risks traits showed neither association with geographical location nor with Y haplotypes. Conclusion: Combinations of Y haplotyping, autosomal haplotyping, and genome-wide SNP typing, taken together with phenotypic2 associations, should improve epidemiological recognition and interpretation of possible confounding by genetic subdivision.

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Published date: 2004
Keywords: genetic association studies, population subdivision, stratification, Y chromosome, autosomal SNPs, haplotypic analysis

Identifiers

Local EPrints ID: 24652
URI: https://eprints.soton.ac.uk/id/eprint/24652
PURE UUID: 6bd92723-616a-4678-b204-312f44f77848

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Date deposited: 04 Apr 2006
Last modified: 15 Jul 2019 19:17

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Contributors

Author: X.H. Chen
Author: S. Rodriguez
Author: E. Hawe
Author: P.J. Talmud
Author: G.J. Miller
Author: P. Underhill
Author: S.E. Humphries
Author: I.N. Day

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