Evaluation of HapMap data in six populations of European descent

Per E Lundmark, Ulrika Liljedahl, Dorret I Boomsma, Heikki Mannila, Nicholas G Martin, Aarno Palotie, Leena Peltonen, Markus Perola, Tim D Spector, Ann-Christine Syvänne

Tutkimustuotos: ArtikkelijulkaisuArtikkeliTieteellinenvertaisarvioitu

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We studied how well the European CEU samples used in the Haplotype Mapping Project (HapMap) represent five European populations by analyzing nuclear family samples from the Swedish, Finnish, Dutch, British and Australian (European ancestry) populations. The number of samples from each population (about 30 parent-offspring trios) was similar to that in the HapMap sample sets. A panel of 186 single nucleotide polymorphisms (SNPs) distributed over the 1.5 Mb region of the GRID2 gene on chromosome 4 was genotyped. The genotype data were compared pair-wise between the HapMap sample and the other population samples. Principal component analysis (PCA) was used to cluster the data from different populations with respect to allele frequencies and to define the markers responsible for observed variance. The only sample with detectable differences in allele frequencies was that from Kuusamo, Finland. This sample also separated from the others, including the other Finnish sample, in the PCA analysis. A set of tagSNPs was defined based on the HapMap data and applied to the samples. The tagSNPs were found to capture the genetic variation in the analyzed region at r(2) = 40.8 at levels ranging from 95% in the Kuusamo sample to 87% in the Australian sample. To capture the maximal genetic variation in the region, the Kuusamo, HapMap and Australian samples required 58, 63 and 73 native tagSNPs, respectively. The HapMap CEU sample represents the European samples well for tagSNP selection, with some caution regarding estimation of allele frequencies in the Finnish Kuusamo sample, and a slight reduction in tagging efficiency in the Australian sample.
Alkuperäiskielienglanti
LehtiEuropean Journal of Human Genetics
Vuosikerta16
Numero9
Sivut1142-1150
Sivumäärä9
ISSN1018-4813
DOI - pysyväislinkit
TilaJulkaistu - 2008
OKM-julkaisutyyppiA1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä, vertaisarvioitu

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Lundmark, P. E., Liljedahl, U., Boomsma, D. I., Mannila, H., Martin, N. G., Palotie, A., ... Syvänne, A-C. (2008). Evaluation of HapMap data in six populations of European descent. European Journal of Human Genetics, 16(9), 1142-1150. https://doi.org/10.1038/ejhg.2008.77
Lundmark, Per E ; Liljedahl, Ulrika ; Boomsma, Dorret I ; Mannila, Heikki ; Martin, Nicholas G ; Palotie, Aarno ; Peltonen, Leena ; Perola, Markus ; Spector, Tim D ; Syvänne, Ann-Christine. / Evaluation of HapMap data in six populations of European descent. Julkaisussa: European Journal of Human Genetics. 2008 ; Vuosikerta 16, Nro 9. Sivut 1142-1150.
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title = "Evaluation of HapMap data in six populations of European descent",
abstract = "We studied how well the European CEU samples used in the Haplotype Mapping Project (HapMap) represent five European populations by analyzing nuclear family samples from the Swedish, Finnish, Dutch, British and Australian (European ancestry) populations. The number of samples from each population (about 30 parent-offspring trios) was similar to that in the HapMap sample sets. A panel of 186 single nucleotide polymorphisms (SNPs) distributed over the 1.5 Mb region of the GRID2 gene on chromosome 4 was genotyped. The genotype data were compared pair-wise between the HapMap sample and the other population samples. Principal component analysis (PCA) was used to cluster the data from different populations with respect to allele frequencies and to define the markers responsible for observed variance. The only sample with detectable differences in allele frequencies was that from Kuusamo, Finland. This sample also separated from the others, including the other Finnish sample, in the PCA analysis. A set of tagSNPs was defined based on the HapMap data and applied to the samples. The tagSNPs were found to capture the genetic variation in the analyzed region at r(2) = 40.8 at levels ranging from 95{\%} in the Kuusamo sample to 87{\%} in the Australian sample. To capture the maximal genetic variation in the region, the Kuusamo, HapMap and Australian samples required 58, 63 and 73 native tagSNPs, respectively. The HapMap CEU sample represents the European samples well for tagSNP selection, with some caution regarding estimation of allele frequencies in the Finnish Kuusamo sample, and a slight reduction in tagging efficiency in the Australian sample.",
author = "Lundmark, {Per E} and Ulrika Liljedahl and Boomsma, {Dorret I} and Heikki Mannila and Martin, {Nicholas G} and Aarno Palotie and Leena Peltonen and Markus Perola and Spector, {Tim D} and Ann-Christine Syv{\"a}nne",
year = "2008",
doi = "10.1038/ejhg.2008.77",
language = "English",
volume = "16",
pages = "1142--1150",
journal = "European Journal of Human Genetics",
issn = "1018-4813",
publisher = "Nature Publishing Group",
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}

Lundmark, PE, Liljedahl, U, Boomsma, DI, Mannila, H, Martin, NG, Palotie, A, Peltonen, L, Perola, M, Spector, TD & Syvänne, A-C 2008, 'Evaluation of HapMap data in six populations of European descent', European Journal of Human Genetics, Vuosikerta 16, Nro 9, Sivut 1142-1150. https://doi.org/10.1038/ejhg.2008.77

Evaluation of HapMap data in six populations of European descent. / Lundmark, Per E; Liljedahl, Ulrika; Boomsma, Dorret I; Mannila, Heikki; Martin, Nicholas G; Palotie, Aarno; Peltonen, Leena; Perola, Markus; Spector, Tim D; Syvänne, Ann-Christine.

julkaisussa: European Journal of Human Genetics, Vuosikerta 16, Nro 9, 2008, s. 1142-1150.

Tutkimustuotos: ArtikkelijulkaisuArtikkeliTieteellinenvertaisarvioitu

TY - JOUR

T1 - Evaluation of HapMap data in six populations of European descent

AU - Lundmark, Per E

AU - Liljedahl, Ulrika

AU - Boomsma, Dorret I

AU - Mannila, Heikki

AU - Martin, Nicholas G

AU - Palotie, Aarno

AU - Peltonen, Leena

AU - Perola, Markus

AU - Spector, Tim D

AU - Syvänne, Ann-Christine

PY - 2008

Y1 - 2008

N2 - We studied how well the European CEU samples used in the Haplotype Mapping Project (HapMap) represent five European populations by analyzing nuclear family samples from the Swedish, Finnish, Dutch, British and Australian (European ancestry) populations. The number of samples from each population (about 30 parent-offspring trios) was similar to that in the HapMap sample sets. A panel of 186 single nucleotide polymorphisms (SNPs) distributed over the 1.5 Mb region of the GRID2 gene on chromosome 4 was genotyped. The genotype data were compared pair-wise between the HapMap sample and the other population samples. Principal component analysis (PCA) was used to cluster the data from different populations with respect to allele frequencies and to define the markers responsible for observed variance. The only sample with detectable differences in allele frequencies was that from Kuusamo, Finland. This sample also separated from the others, including the other Finnish sample, in the PCA analysis. A set of tagSNPs was defined based on the HapMap data and applied to the samples. The tagSNPs were found to capture the genetic variation in the analyzed region at r(2) = 40.8 at levels ranging from 95% in the Kuusamo sample to 87% in the Australian sample. To capture the maximal genetic variation in the region, the Kuusamo, HapMap and Australian samples required 58, 63 and 73 native tagSNPs, respectively. The HapMap CEU sample represents the European samples well for tagSNP selection, with some caution regarding estimation of allele frequencies in the Finnish Kuusamo sample, and a slight reduction in tagging efficiency in the Australian sample.

AB - We studied how well the European CEU samples used in the Haplotype Mapping Project (HapMap) represent five European populations by analyzing nuclear family samples from the Swedish, Finnish, Dutch, British and Australian (European ancestry) populations. The number of samples from each population (about 30 parent-offspring trios) was similar to that in the HapMap sample sets. A panel of 186 single nucleotide polymorphisms (SNPs) distributed over the 1.5 Mb region of the GRID2 gene on chromosome 4 was genotyped. The genotype data were compared pair-wise between the HapMap sample and the other population samples. Principal component analysis (PCA) was used to cluster the data from different populations with respect to allele frequencies and to define the markers responsible for observed variance. The only sample with detectable differences in allele frequencies was that from Kuusamo, Finland. This sample also separated from the others, including the other Finnish sample, in the PCA analysis. A set of tagSNPs was defined based on the HapMap data and applied to the samples. The tagSNPs were found to capture the genetic variation in the analyzed region at r(2) = 40.8 at levels ranging from 95% in the Kuusamo sample to 87% in the Australian sample. To capture the maximal genetic variation in the region, the Kuusamo, HapMap and Australian samples required 58, 63 and 73 native tagSNPs, respectively. The HapMap CEU sample represents the European samples well for tagSNP selection, with some caution regarding estimation of allele frequencies in the Finnish Kuusamo sample, and a slight reduction in tagging efficiency in the Australian sample.

U2 - 10.1038/ejhg.2008.77

DO - 10.1038/ejhg.2008.77

M3 - Article

VL - 16

SP - 1142

EP - 1150

JO - European Journal of Human Genetics

JF - European Journal of Human Genetics

SN - 1018-4813

IS - 9

ER -