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Genetic population structure analysis in New Hampshire reveals Eastern European ancestry.

Sloan CD, Andrew AD, Duell EJ, Williams SM, Karagas MR, Moore JH - PLoS ONE (2009)

Bottom Line: Using Bayesian clustering with a set of 960 single nucleotide polymorphisms (SNPs) we found evidence of population stratification in 864 individuals from New Hampshire that can be used to differentiate the population into six distinct genetic subgroups.We then correlated self-reported ancestry of the individuals with the Bayesian clustering results.Finnish and Russian/Polish/Lithuanian ancestries were most notably found to be associated with genetic substructure.

View Article: PubMed Central - PubMed

Affiliation: Computational Genetics Laboratory, Department of Genetics, Dartmouth Medical School, Lebanon, New Hampshire, United States of America.

ABSTRACT
Genetic structure due to ancestry has been well documented among many divergent human populations. However, the ability to associate ancestry with genetic substructure without using supervised clustering has not been explored in more presumably homogeneous and admixed US populations. The goal of this study was to determine if genetic structure could be detected in a United States population from a single state where the individuals have mixed European ancestry. Using Bayesian clustering with a set of 960 single nucleotide polymorphisms (SNPs) we found evidence of population stratification in 864 individuals from New Hampshire that can be used to differentiate the population into six distinct genetic subgroups. We then correlated self-reported ancestry of the individuals with the Bayesian clustering results. Finnish and Russian/Polish/Lithuanian ancestries were most notably found to be associated with genetic substructure. The ancestral results were further explained and substantiated using New Hampshire census data from 1870 to 1930 when the largest waves of European immigrants came to the area. We also discerned distinct patterns of linkage disequilibrium (LD) between the genetic groups in the growth hormone receptor gene (GHR). To our knowledge, this is the first time such an investigation has uncovered a strong link between genetic structure and ancestry in what would otherwise be considered a homogenous US population.

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D' values using 18 SNPs from the GHR gene for K = 4 population clusters.
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pone-0006928-g003: D' values using 18 SNPs from the GHR gene for K = 4 population clusters.

Mentions: Plots of D′ revealed different LD patterns among the genetic population subgroups in the growth hormone receptor (GHR) gene at K = 4 (Figure 3). For K = 4 the LD plots shows visual differences especially between population 3 and the other populations. This population corresponds to the Finland/Switzerland ancestry group. Plots above K = 4 are difficult to compare due to missing data, as we restricted the analysis to those individuals that could be absolutely placed in one population (q> = 0.5001). Statistical haplotype comparisons determined that there is statistically significant association between haplotypes and population membership between populations one and two, corresponding with the Poland/Russia/UK group and the Canadian Indian/Jewish group (Table 2). Other comparisons were not significant when corrected for multiple testing.


Genetic population structure analysis in New Hampshire reveals Eastern European ancestry.

Sloan CD, Andrew AD, Duell EJ, Williams SM, Karagas MR, Moore JH - PLoS ONE (2009)

D' values using 18 SNPs from the GHR gene for K = 4 population clusters.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2734429&req=5

pone-0006928-g003: D' values using 18 SNPs from the GHR gene for K = 4 population clusters.
Mentions: Plots of D′ revealed different LD patterns among the genetic population subgroups in the growth hormone receptor (GHR) gene at K = 4 (Figure 3). For K = 4 the LD plots shows visual differences especially between population 3 and the other populations. This population corresponds to the Finland/Switzerland ancestry group. Plots above K = 4 are difficult to compare due to missing data, as we restricted the analysis to those individuals that could be absolutely placed in one population (q> = 0.5001). Statistical haplotype comparisons determined that there is statistically significant association between haplotypes and population membership between populations one and two, corresponding with the Poland/Russia/UK group and the Canadian Indian/Jewish group (Table 2). Other comparisons were not significant when corrected for multiple testing.

Bottom Line: Using Bayesian clustering with a set of 960 single nucleotide polymorphisms (SNPs) we found evidence of population stratification in 864 individuals from New Hampshire that can be used to differentiate the population into six distinct genetic subgroups.We then correlated self-reported ancestry of the individuals with the Bayesian clustering results.Finnish and Russian/Polish/Lithuanian ancestries were most notably found to be associated with genetic substructure.

View Article: PubMed Central - PubMed

Affiliation: Computational Genetics Laboratory, Department of Genetics, Dartmouth Medical School, Lebanon, New Hampshire, United States of America.

ABSTRACT
Genetic structure due to ancestry has been well documented among many divergent human populations. However, the ability to associate ancestry with genetic substructure without using supervised clustering has not been explored in more presumably homogeneous and admixed US populations. The goal of this study was to determine if genetic structure could be detected in a United States population from a single state where the individuals have mixed European ancestry. Using Bayesian clustering with a set of 960 single nucleotide polymorphisms (SNPs) we found evidence of population stratification in 864 individuals from New Hampshire that can be used to differentiate the population into six distinct genetic subgroups. We then correlated self-reported ancestry of the individuals with the Bayesian clustering results. Finnish and Russian/Polish/Lithuanian ancestries were most notably found to be associated with genetic substructure. The ancestral results were further explained and substantiated using New Hampshire census data from 1870 to 1930 when the largest waves of European immigrants came to the area. We also discerned distinct patterns of linkage disequilibrium (LD) between the genetic groups in the growth hormone receptor gene (GHR). To our knowledge, this is the first time such an investigation has uncovered a strong link between genetic structure and ancestry in what would otherwise be considered a homogenous US population.

Show MeSH