Comparison of statistical methods for estimating genetic admixture in a lung cancer study of African Americans and Latinos

Melinda C. Aldrich, Steve Selvin, Helen M. Hansen, Lisa F. Barcellos, Margaret R. Wrensch, Jennette D. Sison, Charles P. Quesenberry, Rick A. Kittles, Gabriel Silva, Patricia A. Buffler, Michael F Seldin, John K. Wiencke

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

A variety of methods are available for estimating genetic admixture proportions in populations; however, few investigators have conducted detailed comparisons using empirical data. The authors characterized admixture proportions among self-identified African Americans (n = 535) and Latinos (n = 412) living in the San Francisco Bay Area who participated in a lung cancer case-control study (1998-2003). Individual estimates of genetic ancestry based on 184 informative markers were obtained from a Bayesian approach and 2 maximum likelihood approaches and were compared using descriptive statistics, Pearson correlation coefficients, and Bland-Altman plots. Case-control differences in individual admixture proportions were assessed using 2-sample t tests and logistic regression analysis. Results indicated that Bayesian and frequentist approaches to estimating admixture provide similar estimates and inferences. No difference was observed in admixture proportions between African-American cases and controls, but Latino cases and controls significantly differed according to Amerindian and European genetic ancestry. Differences in admixture proportions between Latino cases and controls were not unexpected, since cases were more likely to have been born in the United States. Genetic admixture proportions provide a quantitative measure of ancestry differences among Latinos that can be used in analyses of genetic risk factors.

Original languageEnglish (US)
Pages (from-to)1035-1046
Number of pages12
JournalAmerican Journal of Epidemiology
Volume168
Issue number9
DOIs
StatePublished - Nov 2008

Fingerprint

Hispanic Americans
African Americans
Lung Neoplasms
Bayes Theorem
San Francisco
Individuality
Case-Control Studies
Logistic Models
Regression Analysis
Research Personnel
Population

Keywords

  • African Americans
  • Case-control studies
  • Epidemiologic methods
  • Genetics, population
  • Hispanic Americans
  • Linkage disequilibrium
  • Lung neoplasms
  • Statistics

ASJC Scopus subject areas

  • Epidemiology

Cite this

Aldrich, M. C., Selvin, S., Hansen, H. M., Barcellos, L. F., Wrensch, M. R., Sison, J. D., ... Wiencke, J. K. (2008). Comparison of statistical methods for estimating genetic admixture in a lung cancer study of African Americans and Latinos. American Journal of Epidemiology, 168(9), 1035-1046. https://doi.org/10.1093/aje/kwn224

Comparison of statistical methods for estimating genetic admixture in a lung cancer study of African Americans and Latinos. / Aldrich, Melinda C.; Selvin, Steve; Hansen, Helen M.; Barcellos, Lisa F.; Wrensch, Margaret R.; Sison, Jennette D.; Quesenberry, Charles P.; Kittles, Rick A.; Silva, Gabriel; Buffler, Patricia A.; Seldin, Michael F; Wiencke, John K.

In: American Journal of Epidemiology, Vol. 168, No. 9, 11.2008, p. 1035-1046.

Research output: Contribution to journalArticle

Aldrich, MC, Selvin, S, Hansen, HM, Barcellos, LF, Wrensch, MR, Sison, JD, Quesenberry, CP, Kittles, RA, Silva, G, Buffler, PA, Seldin, MF & Wiencke, JK 2008, 'Comparison of statistical methods for estimating genetic admixture in a lung cancer study of African Americans and Latinos', American Journal of Epidemiology, vol. 168, no. 9, pp. 1035-1046. https://doi.org/10.1093/aje/kwn224
Aldrich, Melinda C. ; Selvin, Steve ; Hansen, Helen M. ; Barcellos, Lisa F. ; Wrensch, Margaret R. ; Sison, Jennette D. ; Quesenberry, Charles P. ; Kittles, Rick A. ; Silva, Gabriel ; Buffler, Patricia A. ; Seldin, Michael F ; Wiencke, John K. / Comparison of statistical methods for estimating genetic admixture in a lung cancer study of African Americans and Latinos. In: American Journal of Epidemiology. 2008 ; Vol. 168, No. 9. pp. 1035-1046.
@article{4a615444e80d4e8d97aa160c19ba4f13,
title = "Comparison of statistical methods for estimating genetic admixture in a lung cancer study of African Americans and Latinos",
abstract = "A variety of methods are available for estimating genetic admixture proportions in populations; however, few investigators have conducted detailed comparisons using empirical data. The authors characterized admixture proportions among self-identified African Americans (n = 535) and Latinos (n = 412) living in the San Francisco Bay Area who participated in a lung cancer case-control study (1998-2003). Individual estimates of genetic ancestry based on 184 informative markers were obtained from a Bayesian approach and 2 maximum likelihood approaches and were compared using descriptive statistics, Pearson correlation coefficients, and Bland-Altman plots. Case-control differences in individual admixture proportions were assessed using 2-sample t tests and logistic regression analysis. Results indicated that Bayesian and frequentist approaches to estimating admixture provide similar estimates and inferences. No difference was observed in admixture proportions between African-American cases and controls, but Latino cases and controls significantly differed according to Amerindian and European genetic ancestry. Differences in admixture proportions between Latino cases and controls were not unexpected, since cases were more likely to have been born in the United States. Genetic admixture proportions provide a quantitative measure of ancestry differences among Latinos that can be used in analyses of genetic risk factors.",
keywords = "African Americans, Case-control studies, Epidemiologic methods, Genetics, population, Hispanic Americans, Linkage disequilibrium, Lung neoplasms, Statistics",
author = "Aldrich, {Melinda C.} and Steve Selvin and Hansen, {Helen M.} and Barcellos, {Lisa F.} and Wrensch, {Margaret R.} and Sison, {Jennette D.} and Quesenberry, {Charles P.} and Kittles, {Rick A.} and Gabriel Silva and Buffler, {Patricia A.} and Seldin, {Michael F} and Wiencke, {John K.}",
year = "2008",
month = "11",
doi = "10.1093/aje/kwn224",
language = "English (US)",
volume = "168",
pages = "1035--1046",
journal = "American Journal of Epidemiology",
issn = "0002-9262",
publisher = "Oxford University Press",
number = "9",

}

TY - JOUR

T1 - Comparison of statistical methods for estimating genetic admixture in a lung cancer study of African Americans and Latinos

AU - Aldrich, Melinda C.

AU - Selvin, Steve

AU - Hansen, Helen M.

AU - Barcellos, Lisa F.

AU - Wrensch, Margaret R.

AU - Sison, Jennette D.

AU - Quesenberry, Charles P.

AU - Kittles, Rick A.

AU - Silva, Gabriel

AU - Buffler, Patricia A.

AU - Seldin, Michael F

AU - Wiencke, John K.

PY - 2008/11

Y1 - 2008/11

N2 - A variety of methods are available for estimating genetic admixture proportions in populations; however, few investigators have conducted detailed comparisons using empirical data. The authors characterized admixture proportions among self-identified African Americans (n = 535) and Latinos (n = 412) living in the San Francisco Bay Area who participated in a lung cancer case-control study (1998-2003). Individual estimates of genetic ancestry based on 184 informative markers were obtained from a Bayesian approach and 2 maximum likelihood approaches and were compared using descriptive statistics, Pearson correlation coefficients, and Bland-Altman plots. Case-control differences in individual admixture proportions were assessed using 2-sample t tests and logistic regression analysis. Results indicated that Bayesian and frequentist approaches to estimating admixture provide similar estimates and inferences. No difference was observed in admixture proportions between African-American cases and controls, but Latino cases and controls significantly differed according to Amerindian and European genetic ancestry. Differences in admixture proportions between Latino cases and controls were not unexpected, since cases were more likely to have been born in the United States. Genetic admixture proportions provide a quantitative measure of ancestry differences among Latinos that can be used in analyses of genetic risk factors.

AB - A variety of methods are available for estimating genetic admixture proportions in populations; however, few investigators have conducted detailed comparisons using empirical data. The authors characterized admixture proportions among self-identified African Americans (n = 535) and Latinos (n = 412) living in the San Francisco Bay Area who participated in a lung cancer case-control study (1998-2003). Individual estimates of genetic ancestry based on 184 informative markers were obtained from a Bayesian approach and 2 maximum likelihood approaches and were compared using descriptive statistics, Pearson correlation coefficients, and Bland-Altman plots. Case-control differences in individual admixture proportions were assessed using 2-sample t tests and logistic regression analysis. Results indicated that Bayesian and frequentist approaches to estimating admixture provide similar estimates and inferences. No difference was observed in admixture proportions between African-American cases and controls, but Latino cases and controls significantly differed according to Amerindian and European genetic ancestry. Differences in admixture proportions between Latino cases and controls were not unexpected, since cases were more likely to have been born in the United States. Genetic admixture proportions provide a quantitative measure of ancestry differences among Latinos that can be used in analyses of genetic risk factors.

KW - African Americans

KW - Case-control studies

KW - Epidemiologic methods

KW - Genetics, population

KW - Hispanic Americans

KW - Linkage disequilibrium

KW - Lung neoplasms

KW - Statistics

UR - http://www.scopus.com/inward/record.url?scp=54949107881&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=54949107881&partnerID=8YFLogxK

U2 - 10.1093/aje/kwn224

DO - 10.1093/aje/kwn224

M3 - Article

C2 - 18791191

AN - SCOPUS:54949107881

VL - 168

SP - 1035

EP - 1046

JO - American Journal of Epidemiology

JF - American Journal of Epidemiology

SN - 0002-9262

IS - 9

ER -