Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis

Abstract It is well known that conventional association tests can lead to excessive false positives when there is population stratification. We propose a new test for detecting genetic association with a case-control study design. Unlike some other methods for handling population stratification, we...
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Autor*in:	Zhang, Yufang [verfasserIn] Xiao, Xiangjun Wang, Kai

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2009

Schlagwörter:	Population Stratification Genetic Association Study Likelihood Ratio Test Statistic Genetic Analysis Workshop Structure Association

Anmerkung:	© Zhang et al; licensee BioMed Central Ltd. 2009. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (

Übergeordnetes Werk:	Enthalten in: BMC proceedings - London : BioMed Central, 2007, 3(2009), Suppl 7 vom: 15. Dez.
Übergeordnetes Werk:	volume:3 ; year:2009 ; number:Suppl 7 ; day:15 ; month:12

Links:	Volltext

DOI / URN:	10.1186/1753-6561-3-S7-S111

Katalog-ID:	SPR028431383

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spelling	10.1186/1753-6561-3-S7-S111 doi (DE-627)SPR028431383 (SPR)1753-6561-3-S7-S111-e DE-627 ger DE-627 rakwb eng Zhang, Yufang verfasserin aut Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Zhang et al; licensee BioMed Central Ltd. 2009. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( Abstract It is well known that conventional association tests can lead to excessive false positives when there is population stratification. We propose a new test for detecting genetic association with a case-control study design. Unlike some other methods for handling population stratification, we treat the cases as a population and the controls as another one even though each of them may be a mixture of several sub-populations. A likelihood-ratio test is used to test whether the allele frequency of a testing single-nucleotide polymorphism in the case population is the same as that in the control population. This new test is applied to the Genetic Analysis Workshop 16 Problem 1 data on rheumatoid arthritis. Compared with the Pearson chi-square genotype test, the association strength of many single-nucleotide polymorphisms is decreased while the signal at the HLA region on 6p21 is maintained. Population Stratification (dpeaa)DE-He213 Genetic Association Study (dpeaa)DE-He213 Likelihood Ratio Test Statistic (dpeaa)DE-He213 Genetic Analysis Workshop (dpeaa)DE-He213 Structure Association (dpeaa)DE-He213 Xiao, Xiangjun aut Wang, Kai aut Enthalten in BMC proceedings London : BioMed Central, 2007 3(2009), Suppl 7 vom: 15. Dez. (DE-627)559080840 (DE-600)2411867-9 1753-6561 nnns volume:3 year:2009 number:Suppl 7 day:15 month:12 https://dx.doi.org/10.1186/1753-6561-3-S7-S111 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2027 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 3 2009 Suppl 7 15 12
allfields_unstemmed	10.1186/1753-6561-3-S7-S111 doi (DE-627)SPR028431383 (SPR)1753-6561-3-S7-S111-e DE-627 ger DE-627 rakwb eng Zhang, Yufang verfasserin aut Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Zhang et al; licensee BioMed Central Ltd. 2009. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( Abstract It is well known that conventional association tests can lead to excessive false positives when there is population stratification. We propose a new test for detecting genetic association with a case-control study design. Unlike some other methods for handling population stratification, we treat the cases as a population and the controls as another one even though each of them may be a mixture of several sub-populations. A likelihood-ratio test is used to test whether the allele frequency of a testing single-nucleotide polymorphism in the case population is the same as that in the control population. This new test is applied to the Genetic Analysis Workshop 16 Problem 1 data on rheumatoid arthritis. Compared with the Pearson chi-square genotype test, the association strength of many single-nucleotide polymorphisms is decreased while the signal at the HLA region on 6p21 is maintained. Population Stratification (dpeaa)DE-He213 Genetic Association Study (dpeaa)DE-He213 Likelihood Ratio Test Statistic (dpeaa)DE-He213 Genetic Analysis Workshop (dpeaa)DE-He213 Structure Association (dpeaa)DE-He213 Xiao, Xiangjun aut Wang, Kai aut Enthalten in BMC proceedings London : BioMed Central, 2007 3(2009), Suppl 7 vom: 15. Dez. (DE-627)559080840 (DE-600)2411867-9 1753-6561 nnns volume:3 year:2009 number:Suppl 7 day:15 month:12 https://dx.doi.org/10.1186/1753-6561-3-S7-S111 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2027 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 3 2009 Suppl 7 15 12
allfieldsGer	10.1186/1753-6561-3-S7-S111 doi (DE-627)SPR028431383 (SPR)1753-6561-3-S7-S111-e DE-627 ger DE-627 rakwb eng Zhang, Yufang verfasserin aut Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Zhang et al; licensee BioMed Central Ltd. 2009. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( Abstract It is well known that conventional association tests can lead to excessive false positives when there is population stratification. We propose a new test for detecting genetic association with a case-control study design. Unlike some other methods for handling population stratification, we treat the cases as a population and the controls as another one even though each of them may be a mixture of several sub-populations. A likelihood-ratio test is used to test whether the allele frequency of a testing single-nucleotide polymorphism in the case population is the same as that in the control population. This new test is applied to the Genetic Analysis Workshop 16 Problem 1 data on rheumatoid arthritis. Compared with the Pearson chi-square genotype test, the association strength of many single-nucleotide polymorphisms is decreased while the signal at the HLA region on 6p21 is maintained. Population Stratification (dpeaa)DE-He213 Genetic Association Study (dpeaa)DE-He213 Likelihood Ratio Test Statistic (dpeaa)DE-He213 Genetic Analysis Workshop (dpeaa)DE-He213 Structure Association (dpeaa)DE-He213 Xiao, Xiangjun aut Wang, Kai aut Enthalten in BMC proceedings London : BioMed Central, 2007 3(2009), Suppl 7 vom: 15. Dez. (DE-627)559080840 (DE-600)2411867-9 1753-6561 nnns volume:3 year:2009 number:Suppl 7 day:15 month:12 https://dx.doi.org/10.1186/1753-6561-3-S7-S111 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2027 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 3 2009 Suppl 7 15 12
allfieldsSound	10.1186/1753-6561-3-S7-S111 doi (DE-627)SPR028431383 (SPR)1753-6561-3-S7-S111-e DE-627 ger DE-627 rakwb eng Zhang, Yufang verfasserin aut Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Zhang et al; licensee BioMed Central Ltd. 2009. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License ( Abstract It is well known that conventional association tests can lead to excessive false positives when there is population stratification. We propose a new test for detecting genetic association with a case-control study design. Unlike some other methods for handling population stratification, we treat the cases as a population and the controls as another one even though each of them may be a mixture of several sub-populations. A likelihood-ratio test is used to test whether the allele frequency of a testing single-nucleotide polymorphism in the case population is the same as that in the control population. This new test is applied to the Genetic Analysis Workshop 16 Problem 1 data on rheumatoid arthritis. Compared with the Pearson chi-square genotype test, the association strength of many single-nucleotide polymorphisms is decreased while the signal at the HLA region on 6p21 is maintained. Population Stratification (dpeaa)DE-He213 Genetic Association Study (dpeaa)DE-He213 Likelihood Ratio Test Statistic (dpeaa)DE-He213 Genetic Analysis Workshop (dpeaa)DE-He213 Structure Association (dpeaa)DE-He213 Xiao, Xiangjun aut Wang, Kai aut Enthalten in BMC proceedings London : BioMed Central, 2007 3(2009), Suppl 7 vom: 15. Dez. (DE-627)559080840 (DE-600)2411867-9 1753-6561 nnns volume:3 year:2009 number:Suppl 7 day:15 month:12 https://dx.doi.org/10.1186/1753-6561-3-S7-S111 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2027 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 3 2009 Suppl 7 15 12
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author	Zhang, Yufang
spellingShingle	Zhang, Yufang misc Population Stratification misc Genetic Association Study misc Likelihood Ratio Test Statistic misc Genetic Analysis Workshop misc Structure Association Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis
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topic_title	Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis Population Stratification (dpeaa)DE-He213 Genetic Association Study (dpeaa)DE-He213 Likelihood Ratio Test Statistic (dpeaa)DE-He213 Genetic Analysis Workshop (dpeaa)DE-He213 Structure Association (dpeaa)DE-He213
topic	misc Population Stratification misc Genetic Association Study misc Likelihood Ratio Test Statistic misc Genetic Analysis Workshop misc Structure Association
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title	Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis
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title_full	Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis
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title_sort	accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis
title_auth	Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis
abstract	Abstract It is well known that conventional association tests can lead to excessive false positives when there is population stratification. We propose a new test for detecting genetic association with a case-control study design. Unlike some other methods for handling population stratification, we treat the cases as a population and the controls as another one even though each of them may be a mixture of several sub-populations. A likelihood-ratio test is used to test whether the allele frequency of a testing single-nucleotide polymorphism in the case population is the same as that in the control population. This new test is applied to the Genetic Analysis Workshop 16 Problem 1 data on rheumatoid arthritis. Compared with the Pearson chi-square genotype test, the association strength of many single-nucleotide polymorphisms is decreased while the signal at the HLA region on 6p21 is maintained. © Zhang et al; licensee BioMed Central Ltd. 2009. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (
abstractGer	Abstract It is well known that conventional association tests can lead to excessive false positives when there is population stratification. We propose a new test for detecting genetic association with a case-control study design. Unlike some other methods for handling population stratification, we treat the cases as a population and the controls as another one even though each of them may be a mixture of several sub-populations. A likelihood-ratio test is used to test whether the allele frequency of a testing single-nucleotide polymorphism in the case population is the same as that in the control population. This new test is applied to the Genetic Analysis Workshop 16 Problem 1 data on rheumatoid arthritis. Compared with the Pearson chi-square genotype test, the association strength of many single-nucleotide polymorphisms is decreased while the signal at the HLA region on 6p21 is maintained. © Zhang et al; licensee BioMed Central Ltd. 2009. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (
abstract_unstemmed	Abstract It is well known that conventional association tests can lead to excessive false positives when there is population stratification. We propose a new test for detecting genetic association with a case-control study design. Unlike some other methods for handling population stratification, we treat the cases as a population and the controls as another one even though each of them may be a mixture of several sub-populations. A likelihood-ratio test is used to test whether the allele frequency of a testing single-nucleotide polymorphism in the case population is the same as that in the control population. This new test is applied to the Genetic Analysis Workshop 16 Problem 1 data on rheumatoid arthritis. Compared with the Pearson chi-square genotype test, the association strength of many single-nucleotide polymorphisms is decreased while the signal at the HLA region on 6p21 is maintained. © Zhang et al; licensee BioMed Central Ltd. 2009. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (
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title_short	Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis
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Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis

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