Abstract
Population admixture (or ancestry) is used as an approach to gene discovery in complex diseases, particularly when the disease prevalence varies widely across geographic populations. Admixture analysis could be useful for forensics because an indication of a perpetrator's ancestry would narrow the pool of suspects for a particular crime. The purpose of this study was to use Fisher's information to identify informative sets of markers for admixture analysis. Using published founding population allele frequencies we test three marker sets for efficacy for estimating admixture: the FBI CODIS Core STR loci, the HGDP-CEPH Human Genome Diversity Cell Line Panel and the set of 39 ancestry informative SNPS from the Shriver lab at Pennsylvania State University. We conclude that the FBI CODIS Core STR set is valid for admixture analysis, but not the most precise. We recommend using a combination of the most informative markers from the HGDP-CEPH and Shriver loci sets.
Issue Section:
Research Papers
References
1.
Cavalli-Sforza
LL
, Menozzi
P
, Piazza
A
. The history and geography of human genes
. Princeton, NJ
: Princeton University Press
, 1994
.2.
Roychoudhury
AK
, Nei
M
. Human polymorphic genes: world distribution
. New York
: Oxford University Press
, 1988
.3.
Parra
EJ
, Kittles
RA
, Argyropoulos
G
, Pfaff
CL
, Hiester
K
, Bonilla
C
, et al. Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina
. Am J Phys Anthropol
0002-9483 2001
;114
(1
):18
–29
.4.
Rosenberg
NA
, Pritchard
JK
, Weber
JL
, Cann
HM
, Kidd
KK
, Zhivotovsky
LA
, et al. Genetic structure of human populations
. Science
1095-9203 2002
;298
(5602
):2381
–5
.5.
Chakraborty
R
, Weiss
KM
. Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci
. Proc Natl Acad Sci USA
0027-8424 1988
;85
(23
):9119
–23
.6.
Pritchard
JK
, Rosenberg
NA
. Use of unlinked genetic markers to detect population stratification in association studies
. Am J Hum Genet
0002-9297 1999
;65
(1
):220
–8
.7.
Pritchard
JK
, Stephens
M
, Rosenberg
NA
, Donnelly
P
. Association mapping in structured populations
. Am J Hum Genet
0002-9297 2000
;67
(1
):170
–81
.8.
Lowe
AL
, Urquhart
A
, Foreman
LA
, Evett
IW
. Inferring ethnic origin by means of an STR profile
. Forensic Sci Int
0379-0738 2001
;119
(1
):17
–22
.9.
Rosenberg
NA
, Li
LM
, Ward
R
, Pritchard
JK
. Informativeness of genetic markers for inference of ancestry
. Am J Hum Genet
0002-9297 2003
;73
(6
):1402
–22
.10.
Pfaff
CL
, Barnholtz-Sloan
J
, Wagner
JK
, Long
JC
. Information on ancestry from genetic markers
. Genet Epidemiol
0016-6758 2004
;26
(1
):305
–15
.11.
Edwards
AWF
. Likelihood
. Expanded ed. Baltimore
: Johns Hopkins University Press
, 1992
.12.
Weir
BS
. Genetic data analysis II: methods for discrete population genetic data
. Sunderland, MA
: Sinauer Associates
, 1996
.13.
Chakraborty
R
. Gene admixture in human populations: models and predictions
. Yearbook of Phys Anthropol
1986
;29
:17
–22
.14.
Parra
EJ
, Marcini
A
, Akey
J
, Martinson
J
, Batzer
MA
, Cooper
R
, et al. Estimating African American admixture proportions by use of populationspecific alleles
. Am J Hum Genet
0002-9297 1998
;63
(6
):1839
–51
.15.
Shriver
MD
, Parra
EJ
, Dios
S
, Bonilla
C
, Norton
H
, Jovel
C
, et al. Skin pigmentation, biogeographical ancestry and admixture mapping
. Hum Genet
0340-6717 2003
;112
(4
):387
–99
.16.
Shriver
MD
, Smith
MW
, Jin
L
, Marcini
A
, Akey
JM
, Deka
R
, et al. Ethnic-affiliation estimation by use of population-specific DNA markers
. Am J Hum Genet
0002-9297 1997
;60
(4
):957
–64
.17.
Cann
HM
, de Toma
C
, Cazes
L
, Legrand
MF
, Morel
V
, Piouffre
L
, et al. A human genome diversity cell line panel
. Science
1095-9203 2002
;296
(5566
):261
–2
.18.
Weber
JL
, Broman
KW
. Genotyping for human whole-genome scans:past, present, and future
. Adv Genet
0065-2660 2001
;42
:77
–96
.19.
Smith
MW
, Lautenberger
JA
, Shin
HD
, Chretien
JP
, Shrestha
S
, Gilbert
DA
, et al. Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations
. Am J Hum Genet
0002-9297 2001
;69
(5
):1080
–94
.20.
Collins-Schramm
HE
, Phillips
CM
, Operario
DJ
, Lee
JS
, Weber
JL
, Hanson
RL
, et al. Ethnic-difference markers for use in mapping by admixture linkage disequilibrium
. Am J Hum Genet
0002-9297 2002
;70
(3
):737
–50
.21.
Reich
DE
, Goldstein
DB
. Detecting association in a case-control study while correcting for population stratification
. Genet Epidemiol
0741-0395 2001
;20
(1
):4
–16
.22.
Cardon
LR
, Palmer
LJ
. Population stratification and spurious allelic association
. Lancet
0140-6736 2003
;361
(9357
):598
–604
.23.
Council
NR
. The evaluation of forensic DNA evidence
. Washington, DC
: National Academy Press
, 1996
.24.
Chakraborty
R
, Jin
L
. Heterozygote deficiency, population substructure and their implications in DNA fingerprinting
. Hum Genet
0340-6717 1992
;88
(3
): 267–72.25.
Hanis
CL
, Chakraborty
R
, Ferrell
RE
, Schull
WJ
. Individual admixture estimates: disease associations and individual risk of diabetes and gallbladder disease among Mexican-Americans in Starr County, Texas
. Am J Phys Anthropol
0002-9483 1986
;70
(4
):433
–41
.
This content is only available via PDF.
Copyright © 2005 by ASTM
You do not currently have access to this content.
