title: High-density single-nucleotide polymorphism maps of the human genome.
abstract: 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.
authors.affiliation: Washington University, Division of Dermatology, St. Louis, MO, USA.
authors.forename: Raymond D
authors.initials: RD
authors.lastname: Miller
authors.forename: Michael S
authors.initials: MS
authors.lastname: Phillips
authors.forename: Inho
authors.initials: I
authors.lastname: Jo
authors.forename: Miriam A
authors.initials: MA
authors.lastname: Donaldson
authors.forename: Joel F
authors.initials: JF
authors.lastname: Studebaker
authors.forename: Nicholas
authors.initials: N
authors.lastname: Addleman
authors.forename: Steven V
authors.initials: SV
authors.lastname: Alfisi
authors.forename: Wendy M
authors.initials: WM
authors.lastname: Ankener
authors.forename: Hamid A
authors.initials: HA
authors.lastname: Bhatti
authors.forename: Chad E
authors.initials: CE
authors.lastname: Callahan
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Carey
authors.forename: Cheryl L
authors.initials: CL
authors.lastname: Conley
authors.forename: Justin M
authors.initials: JM
authors.lastname: Cyr
authors.forename: Vram
authors.initials: V
authors.lastname: Derohannessian
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Donaldson
authors.forename: Carolina
authors.initials: C
authors.lastname: Elosua
authors.forename: Stacey E
authors.initials: SE
authors.lastname: Ford
authors.forename: Angela M
authors.initials: AM
authors.lastname: Forman
authors.forename: Craig A
authors.initials: CA
authors.lastname: Gelfand
authors.forename: Nicole M
authors.initials: NM
authors.lastname: Grecco
authors.forename: Susan M
authors.initials: SM
authors.lastname: Gutendorf
authors.forename: Cricket R
authors.initials: CR
authors.lastname: Hock
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Hozza
authors.forename: Soyoung
authors.initials: S
authors.lastname: Hur
authors.forename: Sun Mi
authors.initials: SM
authors.lastname: In
authors.forename: Diana L
authors.initials: DL
authors.lastname: Jackson
authors.forename: Sangmee Ahn
authors.initials: SA
authors.lastname: Jo
authors.forename: Sung-Chul
authors.initials: SC
authors.lastname: Jung
authors.forename: Sook
authors.initials: S
authors.lastname: Kim
authors.forename: Kuchan
authors.initials: K
authors.lastname: Kimm
authors.forename: Ellen F
authors.initials: EF
authors.lastname: Kloss
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Koboldt
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Kuebler
authors.forename: Feng-Shen
authors.initials: FS
authors.lastname: Kuo
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Lathrop
authors.forename: Jong-Keuk
authors.initials: JK
authors.lastname: Lee
authors.forename: Kathy L
authors.initials: KL
authors.lastname: Leis
authors.forename: Stephanie A
authors.initials: SA
authors.lastname: Livingston
authors.forename: Elizabeth G
authors.initials: EG
authors.lastname: Lovins
authors.forename: Maria L
authors.initials: ML
authors.lastname: Lundy
authors.forename: Sima
authors.initials: S
authors.lastname: Maggan
authors.forename: Matthew
authors.initials: M
authors.lastname: Minton
authors.forename: Michael A
authors.initials: MA
authors.lastname: Mockler
authors.forename: David W
authors.initials: DW
authors.lastname: Morris
authors.forename: Eric P
authors.initials: EP
authors.lastname: Nachtman
authors.forename: Bermseok
authors.initials: B
authors.lastname: Oh
authors.forename: Chan
authors.initials: C
authors.lastname: Park
authors.forename: Chang-Wook
authors.initials: CW
authors.lastname: Park
authors.forename: Nicholas
authors.initials: N
authors.lastname: Pavelka
authors.forename: Adrienne B
authors.initials: AB
authors.lastname: Perkins
authors.forename: Stephanie L
authors.initials: SL
authors.lastname: Restine
authors.forename: Ravi
authors.initials: R
authors.lastname: Sachidanandam
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Reinhart
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Scott
authors.forename: Gira J
authors.initials: GJ
authors.lastname: Shah
authors.forename: Jatana M
authors.initials: JM
authors.lastname: Tate
authors.forename: Shobha A
authors.initials: SA
authors.lastname: Varde
authors.forename: Amy
authors.initials: A
authors.lastname: Walters
authors.forename: J Rebecca
authors.initials: JR
authors.lastname: White
authors.forename: Yeon-Kyeong
authors.initials: YK
authors.lastname: Yoo
authors.forename: Jong-Eun
authors.initials: JE
authors.lastname: Lee
authors.forename: Michael T
authors.initials: MT
authors.lastname: Boyce-Jacino
authors.forename: Pui-Yan
authors.initials: PY
authors.lastname: Kwok
mesh_terms: 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