Comparison of statistical methods for estimating genetic admixture in a lung cancer study of African Americans and Latinos.
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.
Aldrich
Melinda C
MC
University of California, San Francisco, Box 2911 Rock Hall, Mission Bay 582, 1550 4th Street, San Francisco, CA 94143-2911, USA. melinda.aldrich@ucsf.edu
Selvin
Steve
S
Hansen
Helen M
HM
Barcellos
Lisa F
LF
Wrensch
Margaret R
MR
Sison
Jennette D
JD
Quesenberry
Charles P
CP
Kittles
Rick A
RA
Silva
Gabriel
G
Buffler
Patricia A
PA
Seldin
Michael F
MF
Wiencke
John K
JK
D001741:Black or African American / Q000235:genetics*; D000368:Aged; D000369:Aged, 80 and over; D001499:Bayes Theorem; D016022:Case-Control Studies; D004812:Epidemiologic Methods; D005260:Female; D005838:Genotype; D006630:Hispanic or Latino / Q000235:genetics*; D006801:Humans; D008175:Lung Neoplasms / Q000453:epidemiology* / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D012495:San Francisco / Q000453:epidemiology
Am J Hum Genet. 2007 Jun;80(6):1014-23
17557415
Ann Hum Genet. 2000 Mar;64(Pt 2):171-86
11246470
Am J Public Health. 2005 Dec;95(12):2155-60
16257941
Genet Epidemiol. 2005 Jul;29(1):76-86
15918156
Int J Cancer. 2005 Jan 1;113(1):141-7
15386428
Bioinformatics. 2004 Oct 12;20(15):2363-9
15073024
Hum Genet. 2004 Feb;114(3):263-71
14628215
Am J Phys Anthropol. 1986 Aug;70(4):433-41
3766713
Hum Genet. 2006 Aug;120(1):69-76
16733712
J Am Soc Nephrol. 2006 Dec;17(12):3491-6
17082243
Diabetes. 2003 Apr;52(4):1047-51
12663479
Am J Hum Genet. 1999 Jul;65(1):220-8
10364535
Ann Hum Genet. 2004 Mar;68(Pt 2):139-53
15008793
Cancer Epidemiol Biomarkers Prev. 2007 Jan;16(1):142-50
17220343
Am J Hum Genet. 2005 Feb;76(2):268-75
15625622
Osteoporos Int. 2007 Jun;18(6):733-41
17235662
Pharmacogenomics. 2003 Jul;4(4):431-41
12831322
Mol Genet Metab. 2007 Sep-Oct;92(1-2):145-50
17618154
Genet Epidemiol. 1986;3(6):435-54
3803913
Hum Genet. 2005 Dec;118(3-4):424-33
16208514
N Engl J Med. 2003 Mar 20;348(12):1170-5
12646676
Am J Hum Genet. 2005 Mar;76(3):463-77
15660291
BMC Bioinformatics. 2006 Jun 22;7:317
16792813
J Natl Cancer Inst. 2007 Dec 19;99(24):1836-44
18073375
Lupus. 2006;15(1):26-31
16482742
Am J Hum Genet. 2006 Oct;79(4):640-9
16960800
Am J Hum Genet. 2004 May;74(5):965-78
15088268
Cancer Epidemiol Biomarkers Prev. 2007 Jun;16(6):1229-35
17548690
Hum Genet. 2007 Jun;121(5):615-24
17390149
Genetics. 1991 Feb;127(2):417-28
2004712
Cancer Epidemiol Biomarkers Prev. 2007 Aug;16(8):1686-90
17684147
Hum Hered. 2004;58(2):93-107
15711089
Am J Hum Genet. 2002 Mar;70(3):737-50
11845411
Pediatr Res. 2005 Nov;58(5):850-4
16183814
Hum Genet. 2006 Jun;119(5):547-57
16596417
Biol Psychiatry. 2007 Sep 15;62(6):616-26
17509535
Theor Popul Biol. 2001 Nov;60(3):227-37
11855957
Am J Hum Genet. 2003 Jun;72(6):1492-1504
12817591
Am J Hum Genet. 2005 Oct;77(4):519-32
16175499
Cancer Epidemiol Biomarkers Prev. 2005 Jun;14(6):1545-51
15941970
Nat Genet. 2004 Nov;36(11 Suppl):S43-7
15508002
Nat Genet. 2004 Nov;36(11 Suppl):S48-53
15508003
Am J Public Health. 2005 Dec;95(12):2125-8
16257933
Genetics. 2003 Jun;164(2):747-65
12807794
Science. 1969 Aug 22;165(3895):762-8
4894336
Genetics. 2007 Apr;175(4):1787-802
17237522
Genome Biol. 2002 Jul 1;3(7):comment2007
12184798
Carcinogenesis. 2007 Oct;28(10):2154-9
17724372
Biometrics. 1999 Dec;55(4):997-1004
11315092
Hum Genet. 2007 Jun;121(5):565-75
17356887
Cancer Epidemiol Biomarkers Prev. 2006 Oct;15(10):1878-85
17035394
Genetics. 2000 Jun;155(2):945-59
10835412
Evolution. 1984 Nov;38(6):1358-1370
28563791
Genet Res. 2001 Aug;78(1):59-77
11556138
Am J Respir Crit Care Med. 2005 Mar 15;171(6):563-70
15557128
Genet Epidemiol. 2005 May;28(4):289-301
15712363
Am J Epidemiol. 2003 Aug 1;158(3):272-9
12882950
Obes Res. 2003 Jul;11(7):904-11
12855761
Ethn Dis. 1991 Summer;1(3):245-56
1842537
Mol Ecol Notes. 2007 Jul 1;7(4):574-578
18784791
Diabetes. 2007 Mar;56(3):675-84
17327435
Prostate Cancer Prostatic Dis. 2008;11(4):349-56
18026184
Nat Genet. 2004 Nov;36(11 Suppl):S21-7
15507999
Am J Respir Crit Care Med. 2007 Dec 1;176(11):1129-37
17761618
Nat Genet. 2004 May;36(5):512-7
15052271
Am J Respir Crit Care Med. 2006 Nov 15;174(10):1088-93
16973984
Am J Phys Anthropol. 2001 Jan;114(1):18-29
11150049
Am J Phys Anthropol. 1986 Aug;70(4):489-503
3766715
Genetics. 2003 Aug;164(4):1567-87
12930761