High-density single-nucleotide polymorphism maps of the human genome.
Here we report a large, extensively characterized set of single-nucleotide polymorphisms (SNPs) covering the human genome. We determined the allele frequencies of 55,018 SNPs in African Americans, Asians (Japanese-Chinese), and European Americans as part of The SNP Consortium's Allele Frequency Project. A subset of 8333 SNPs was also characterized in Koreans. Because these SNPs were ascertained in the same way, the data set is particularly useful for modeling. Our results document that much genetic variation is shared among populations. For autosomes, some 44% of these SNPs have a minor allele frequency > or =10% in each population, and the average allele frequency differences between populations with different continental origins are less than 19%. However, the several percentage point allele frequency differences among the closely related Korean, Japanese, and Chinese populations suggest caution in using mixtures of well-established populations for case-control genetic studies of complex traits. We estimate that approximately 7% of these SNPs are private SNPs with minor allele frequencies <1%. A useful set of characterized SNPs with large allele frequency differences between populations (>60%) can be used for admixture studies. High-density maps of high-quality, characterized SNPs produced by this project are freely available.
Miller
Raymond D
RD
Washington University, Division of Dermatology, St. Louis, MO, USA.
Phillips
Michael S
MS
Jo
Inho
I
Donaldson
Miriam A
MA
Studebaker
Joel F
JF
Addleman
Nicholas
N
Alfisi
Steven V
SV
Ankener
Wendy M
WM
Bhatti
Hamid A
HA
Callahan
Chad E
CE
Carey
Benjamin J
BJ
Conley
Cheryl L
CL
Cyr
Justin M
JM
Derohannessian
Vram
V
Donaldson
Rachel A
RA
Elosua
Carolina
C
Ford
Stacey E
SE
Forman
Angela M
AM
Gelfand
Craig A
CA
Grecco
Nicole M
NM
Gutendorf
Susan M
SM
Hock
Cricket R
CR
Hozza
Mark J
MJ
Hur
Soyoung
S
In
Sun Mi
SM
Jackson
Diana L
DL
Jo
Sangmee Ahn
SA
Jung
Sung-Chul
SC
Kim
Sook
S
Kimm
Kuchan
K
Kloss
Ellen F
EF
Koboldt
Daniel C
DC
Kuebler
Jennifer M
JM
Kuo
Feng-Shen
FS
Lathrop
Jessica A
JA
Lee
Jong-Keuk
JK
Leis
Kathy L
KL
Livingston
Stephanie A
SA
Lovins
Elizabeth G
EG
Lundy
Maria L
ML
Maggan
Sima
S
Minton
Matthew
M
Mockler
Michael A
MA
Morris
David W
DW
Nachtman
Eric P
EP
Oh
Bermseok
B
Park
Chan
C
Park
Chang-Wook
CW
Pavelka
Nicholas
N
Perkins
Adrienne B
AB
Restine
Stephanie L
SL
Sachidanandam
Ravi
R
Reinhart
Andrew J
AJ
Scott
Kathryn E
KE
Shah
Gira J
GJ
Tate
Jatana M
JM
Varde
Shobha A
SA
Walters
Amy
A
White
J Rebecca
JR
Yoo
Yeon-Kyeong
YK
Lee
Jong-Eun
JE
Boyce-Jacino
Michael T
MT
Kwok
Pui-Yan
PY
D000483:Alleles; D002874:Chromosome Mapping; D030541:Databases, Genetic; D005787:Gene Frequency; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA