Analysis and application of European genetic substructure using 300 K SNP information.

paper Cited Public

Authors: Tian, Chao; Plenge, Robert M; Ransom, Michael; Lee, Annette; Villoslada, Pablo; Selmi, Carlo; Klareskog, Lars; Pulver, Ann E; Qi, Lihong; Gregersen, Peter K; Seldin, Michael F
Year: 2008
Journal: PLoS genetics
PMID: 18208329
DOI: 10.1371/journal.pgen.0040004
PMCID: PMC2211544

Figure 1

European Substructure Analysis of a Diverse Set of Individuals of European Descent(A) Graphic representation of the first two PCs for 952 individuals genotyped with 300K SNPs.(B) Color code shows subgroup of individuals with more detailed grandparental origin information. Each color-coded individual had 4GP of origin information with the exception of the AJA group. The individuals included 14 Spanish (SPN), 28 Italian (ITN), eight Greek (GRK), 11 German (GERM), 52 IRISH, five United Kingdom (UK), three Scandinavian (SCAN), and two Netherland (NETH). For the Ashkenazi Jewish individuals, 38 had 4GP information (AJA_4GP), and 220 participants were self identified as Ashkenazi Jewish (AJA) but without other information.(C) The STRUCTURE analyses shows results from the same participant set using three random sets of >3,500 SNPs for assessment of the number of population groups (K). The ordinate shows the Ln probability (mean +/− SD) corresponding to the number of clusters.(D) STRUCTURE results under the assumption of two population groups (K = 2). The proportion of each cluster group (population) for each individual is shown by the color code.

Figure 2

Comparison of Principal Component Analysis Excluding Different Individual GroupsColor key shows groups as defined in Figure 1.(A) All individuals with 4GP information.(B) Same individual set except exclusion of individuals of Irish descent.(C) Same individual set with exclusion of Ashkenazi Jewish individuals.

Figure 3

STRUCTURE Analysis Using 1,400 ESAIMs Selected for North/South InformationAnalysis was performed without any prior population assignment using STRUCTURE under the assumption of two population groups (K = 2). The results are shown for only individuals not used in selection of the north/south-ESIAMs. The individual individuals and 90% confidence limits are shown for selected groups with ethnic and grandparental origins (see Figure S1 for entire results). The individuals grouped by self identification included: Ashkenazi 4GP; Ashkenazi Jewish (without 4GP information) (AJA); Greek (GRK); Italian (ITN); Spanish (SPN); German (GERM); Scandinavian (SCAN); United Kingdom (UK); and Irish.

Figure 4

Analysis of European Substructure in Northern European Individuals(A) The first two PCs are depicted for RA cases and NYCP controls.(B) Color codes show the Irish contribution to each individual with at least two GP country of origin information in the sample set shown in (A), e.g., the 2GP Irish individuals have 2GP Irish origin and 2GP unknown or USA origin; Not Irish includes only individuals without known Irish ancestry and with at least 2GP information; mixed Irish are those individuals with at least one GP Irish and one GP non-Irish.(C) Analysis using 1,211 ESAIMs selected for differences along PC1 in northern European individuals (see Results).

Figure 5

Principal Component Analysis Shows Chromosome 8 InversionThe selected informative SNPs from a 3.8 Mb segment of Chromosome 8 shows the same PC score distribution as the entire SNP set for the second PC in analysis of “northern” European individuals. The graph shows the position of each of 382 tested individuals for the second axis in the PCA using 500K SNPs (ordinate) and the position based on analysis using 20 selected SNPs from the 3.8 Mb segment of Chromosome 8 (abscissa). The 20 selected SNPs were those with the highest In between the outer groups in an independent dataset separated by a minimum of 50 kb.

Figure 6

Graphic Display of Principal Components 3 and 4 after Deletion of Chromosome 8 InversionResults of individuals with 4GP information are shown.

#	Section	Preview
40	Methods — — Statistical analyses.	For initial STRUCTURE analyses we selected random SNPs based on a minimum inter-SNP distance 500 kb;…
41	Methods — — Statistical analyses.	PCA, PCA control for association testing, and determination of the genomic control parameter (λgc)…
42	Methods — — Statistical analyses.	alternate half chromosomes, and 3) half genome SNP sets. These sets were chosen to eliminate any…
43	Methods — — Statistical analyses.	PCA can be sensitive to quality control issues that can give rise to spurious clustering [43].…

Name	Type
1441 ESAIM set local	cohort
300K set local	cohort
384 ESAIM set local	cohort
5000 SNP panel local	cohort
500K SNP set local	cohort
ancestry	phenotype
ancestry groups	cohort
Ashkenazi Jewish local	cohort
Ashkenazi Jewish ancestry	cohort
Ashkenazi Jewish heritage local	cohort
Ashkenazi Jewish individuals local	cohort
Ashkenazi Jewish populations local	cohort
blood cell samples local	drug
cases	cohort
Celtic contributions local	cohort
Central Europe descent local	cohort
CEU	cohort
chromosomal inversion local	variant
Chromosome 17 inversion local	variant
Chromosome 8 inversion local	variant
Chromosome 8 inversion (8.135-11.936 Mb) local	variant
controls	cohort
Crohn's disease	phenotype
Eastern European local	cohort
Eastern European ancestry local	cohort
Eastern Europe descent local	cohort
EIGENSTRAT program local	drug
ESAIMs local	drug
ESAIMs local	variant
European American sample groups local	cohort
European American sample set local	cohort
European ancestry	cohort
European groups local	cohort
European only analysis local	cohort
European participant set local	cohort
European population	cohort
European population substructure cohort local	cohort
European set local	cohort
European substructure local	cohort
European substructure local	phenotype
European substructure ancestry informative markers local	cohort
False discovery rate statistics local	drug
Fst local	drug
Genetix software local	drug
German ancestry local	cohort
German cohort	cohort
Golden Helix local	drug
Greek local	cohort
Greek, Italian, or Spanish origin local	cohort
haplotype A local	variant
haplotype B local	variant
HelixTree 5.0.2 software local	drug
Iberian peninsular local	cohort
IBS	cohort
In local	drug
IRF4 local	gene
Irish local	cohort
Irish ancestry local	cohort
Irish descent local	cohort
Irish group local	cohort
Irish individuals local	cohort
Italian individuals local	cohort
Italy	cohort
Jewish ancestry individuals local	cohort
Lactose intolerance local	phenotype
LCT	gene
LCT-associated SNP local	variant
Linkage disequilibrium local	drug
Mesolithic contributions local	cohort
MHC	gene
more homogenous subgroup local	phenotype
NARAC local	cohort
NARAC case-control dataset local	cohort
NARAC cases local	cohort
NARAC controls local	cohort
NARAC RA study local	cohort
NARAC studies local	cohort
National Inception Cohort of Rheumatoid Arthritis Patients local	cohort
Neolithic contributions local	cohort
New York Cancer Project (NYCP) local	cohort
North American Rheumatoid Arthritis local	cohort
Northern and Western European ancestry	cohort
Northern European local	cohort
northern European axis local	phenotype
Northern European individuals local	cohort
Northern European subset local	cohort
Northern group local	cohort
Northern subcohort local	cohort
north-ESAIMs local	cohort
north-ESAIM set local	cohort
north/south-ESAIM local	cohort
north/south-ESAIMs local	cohort
north/south-ESAIM set local	cohort
north/south gradient local	phenotype
NYCP controls local	cohort
NYCP individuals local	cohort
PC1	phenotype
PC2	phenotype
population	cohort
population affiliation local	phenotype
principal component analysis (PCA) local	drug
prostate cancer	phenotype
PTPN22	gene
RA individuals local	cohort
random sets local	cohort
random sets >40K SNPs local	variant
rheumatoid arthritis	phenotype
Rheumatoid arthritis probands local	cohort
rs12203592 local	variant
rs1446585	variant
Scandinavian local	cohort
Scandinavian descent local	cohort
sets <11K SNPs local	variant
SNP	cohort
SNP set 10K local	variant
SNP set 300K local	drug
SNP set 300K local	variant
Southern group local	cohort
Southern Mediterranean local	cohort
Southern subcohort local	cohort
Spain	cohort
Spanish individuals local	cohort
Study Of New Onset Rheumatoid Arthritis local	cohort
subgroup outliers local	phenotype
substructure local	phenotype
Swedish individuals	cohort
TRAF1 local	gene
United Kingdom	cohort
United Kingdom ancestry local	cohort
Weir and Cockerham algorithm local	drug
Welcome Trust Case Control Consortium local	cohort
west-east gradient local	phenotype
Western, Northern or Central heritage local	cohort
WGA local	drug
Wichita Rheumatic Disease Data Bank local	cohort
δ local	drug

Citation	PMID	DOI	Status
Amos, CI et al., Genes Immun, 2006, High-density SNP analysis of 642 Caucasian families with rheumatoid arthritis identifies two new linkage regions on 11p12 and 2q33	16691188	10.1038/sj.gene.6364295	Cited
Barbujani, G et al., Proc Natl Acad Sci U S A, 2001, Genetics and the population history of Europe	11136246	10.1073/pnas.98.1.22	Cited
Bauchet, M et al., Am J Hum Genet, 2007, Measuring European population stratification with microarray genotype data	17436249	10.1086/513477	Cited
Belkhir, K et al., GENETIX, software under WindowsTM for the genetic of populations. 4.02 ed, 2001	—	—	—
Belle, EM et al., Proc Biol Sci, 2006, Origins and evolution of the Europeans' genome: evidence from multiple microsatellite loci	16769629	10.1098/rspb.2006.3494	Cited
Campbell, CD et al., Nat Genet, 2005, Demonstrating stratification in a European American population	16041375	10.1038/ng1607	Cited
Cavalli-Sforza, LL et al., Science, 1993, Demic expansions and human evolution	8430313	10.1126/science.8430313	Cited
Cavalli-Sforza, LL et al., The history and geography of human genes, 1996	—	—	—
Clayton, DG et al., Nat Genet, 2005, Population structure, differential bias and genomic control in a large-scale, case-control association study	16228001	10.1038/ng1653	Cited
Devlin, B et al., Biometrics, 1999, Genomic control for association studies	11315092	10.1111/j.0006-341x.1999.00997.x	Cited
Duerr, RH et al., Science, 2006, A genome-wide association study identifies IL23R as an inflammatory bowel disease gene	17068223	10.1126/science.1135245	Cited
Epstein, MP et al., Am J Hum Genet, 2007, A simple and improved correction for population stratification in case-control studies	17436246	10.1086/516842	Cited
Falush, D et al., Genetics, 2003, Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies	12930761	10.1093/genetics/164.4.1567	Cited
Freedman, ML et al., Nat Genet, 2004, Assessing the impact of population stratification on genetic association studies	15052270	10.1038/ng1333	Cited
Giglio, S et al., Am J Hum Genet, 2001, Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements	11231899	10.1086/319506	Cited
Helgason, A et al., Nat Genet, 2005, An Icelandic example of the impact of population structure on association studies	15608637	10.1038/ng1492	Cited
Herva, R et al., Am J Hum Genet, 1976, A large pericentric inversion of human chromosome 8	944528	—	Cited
Hoggart, CJ et al., Am J Hum Genet, 2003, Control of confounding of genetic associations in stratified populations	12817591	10.1086/375613	Cited
Klein, U et al., Nat Immunol, 2006, Transcription factor IRF4 controls plasma cell differentiation and class-switch recombination	16767092	10.1038/ni1357	Cited
Lohoff, M et al., J Exp Med, 2004, Enhanced TCR-induced apoptosis in interferon regulatory factor 4-deficient CD4(+) Th cells	15249594	10.1084/jem.20040182	Cited
Ma, S et al., J Immunol, 2006, IFN regulatory factor 4 and 8 promote Ig light chain kappa locus activation in pre-B cell development	17114461	10.4049/jimmunol.177.11.7898	Cited
Macalister, RAS, Ancient Ireland, 1935	—	—	—
Marchini, J et al., Nat Genet, 2004, The effects of human population structure on large genetic association studies	15052271	10.1038/ng1337	Cited
Menozzi, P et al., Science, 1978, Synthetic maps of human gene frequencies in Europeans	356262	10.1126/science.356262	Cited
Mitchell, MK et al., J Urban Health, 2004, The New York Cancer project: rationale, organization, design, and baseline characteristics	15136663	10.1093/jurban/jth116	Cited
Nature, 2007, Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls	17554300	10.1038/nature05911	Cited
Patterson, N et al., PLoS Genet, 2006, Population structure and Eigenanalysis	17194218	10.1371/journal.pgen.0020190	Cited
Plenge, RM et al., N Engl J Med, 2007, TRAF1-C5 as a risk locus for rheumatoid arthritis–a genomewide study	17804836	10.1056/NEJMoa073491	Cited
Price, AL et al., Nat Genet, 2006, Principal components analysis corrects for stratification in genome-wide association studies	16862161	10.1038/ng1847	Cited
Pritchard, JK et al., Am J Hum Genet, 2000, Association mapping in structured populations	10827107	10.1086/302959	Cited
Pritchard, JK et al., Genetics, 2000, Inference of population structure using multilocus genotype data	10835412	10.1093/genetics/155.2.945	Cited
Purcell, S et al., Am J Hum Genet, 2007, PLINK: a toolset for whole-genome association and population-based linkage analyses	17701901	10.1086/519795	Cited
Rosenberg, NA et al., Am J Hum Genet, 2003, Informativeness of genetic markers for inference of ancestry	14631557	10.1086/380416	Cited
Royston, P, Appl Stat, 1995, A remark on Algorithm AS 181: The W Test for normality	—	—	—
Satten, GA et al., Am J Hum Genet, 2001, Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model	11170894	10.1086/318195	Cited
Seldin, MF et al., PLoS Genetics, 2006, European population substructure: clustering of northern and southern populations	17044734	10.1371/journal.pgen.0020143	Cited
Snyder, HL, Irish history and culture, 1976, From the beginnings to the end of the middle ages	—	—	—
Sokal, RR et al., Nature, 1991, Genetic evidence for the spread of agriculture in Europe by demic diffusion	2030731	10.1038/351143a0	Cited
Spearman, C, Br J Psychol, 1910, Correlation calculated with faulty data	—	—	—
Stefansson, H et al., Nat Genet, 2005, A common inversion under selection in Europeans	15654335	10.1038/ng1508	Cited
Tailor, P et al., Cell Res, 2006, IRF family proteins and type I interferon induction in dendritic cells	16474425	10.1038/sj.cr.7310018	Cited
Weir, B et al., Evolution, 1984, Estimating F-statistics for the analysis of population structure	28563791	10.1111/j.1558-5646.1984.tb05657.x	Cited
Wolfe, F et al., Arthritis Rheum, 2003, Predicting mortality in patients with rheumatoid arthritis	12794820	10.1002/art.11024	Cited

In this knowledge base

Title	Year	PMID
Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses.	2016	27089181
New approaches to population stratification in genome-wide association studies.	2010	20548291
Quality control and quality assurance in genotypic data for genome-wide association studies.	2010	20718045
Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America.	2009	18683858
Genetic structure of Europeans: a view from the North-East.	2009	19424496
The impact of divergence time on the nature of population structure: an example from Iceland.	2009	19503599
Application of ancestry informative markers to association studies in European Americans.	2008	18208330
Genes mirror geography within Europe.	2008	18758442
Population substructure and control selection in genome-wide association studies.	2008	18596976

External

Title	Authors	Journal	Year	Link
A probabilistic approach to visualize the effect of missing data on PCA in ancient human genomics.	Zabel S et al.	—	2025	→
Comparative Whole Genome Phylogeography Reveals Genetic Distinctiveness of Appalachian Populations of Boreal Songbirds.	Kimmitt AA et al.	—	2025	→
Empowering canine genomics: design and validation of a high-density SNP array for Indian dogs.	Nachiappan R et al.	—	2025	→
Adjusting for principal components can induce collider bias in genome-wide association studies.	Grinde KE et al.	—	2024	→
Advancing equine genomics: the development of a high density Axiom_Ashwa SNP chip for Indian horses and ponies.	Ahlawat S et al.	—	2024	→
Linking the spatial and genomic structure of adaptive potential for conservation management: a review.	Chhina AK et al.	—	2024	→
Design and validation of high-density SNP array of goats and population stratification of Indian goat breeds.	Vijh RK et al.	—	2023	→
Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map.	Johansen M et al.	—	2023	→
Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated.	Elhaik E	—	2022	→
Genetic ancestry plays a central role in population pharmacogenomics.	Yang HC et al.	—	2021	→
PCAmatchR: a flexible R package for optimal case-control matching using weighted principal components.	Brown DW et al.	—	2021	→
The TRIB3 R84 variant is associated with increased left ventricular mass in a sample of 2426 White individuals.	Mannino GC et al.	—	2021	→
Differential admixture in Latin American populations and its impact on the study of colorectal cancer.	Colistro V et al.	—	2020	→
Exploring Population Structure with Admixture Models and Principal Component Analysis.	Liu CC et al.	—	2020	→
High-resolution inference of genetic relationships among Jewish populations.	Kopelman NM et al.	—	2020	→
Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon.	McKinney G et al.	—	2020	→
Scalable probabilistic PCA for large-scale genetic variation data.	Agrawal A et al.	—	2020	→
The Genetic Landscape of Dystrophin Mutations in Italy: A Nationwide Study.	Neri M et al.	—	2020	→
Distribution of local ancestry and evidence of adaptation in admixed populations.	Secolin R et al.	—	2019	→
Genetic history of the population of Crete.	Drineas P et al.	—	2019	→
Mitochondrial DNA variability of the Polish population.	Jarczak J et al.	—	2019	→
rs2572431 Polymorphism on Chromosome 8 Is Associated With Individual Differences in Anxiety Related Coping Modes.	Jung S et al.	—	2019	→
Implementation and Evaluation of an Algorithm for Cryptographically Private Principal Component Analysis on Genomic Data.	Bogdanov D et al.	—	2018	→
Improving ancestry distinctions among Southwest Asian populations.	Bulbul O et al.	—	2018	→
Item-level analyses reveal genetic heterogeneity in neuroticism.	Nagel M et al.	—	2018	→
Population structure in Argentina.	Muzzio M et al.	—	2018	→
A genome-wide association study identifies six novel risk loci for primary biliary cholangitis.	Qiu F et al.	—	2017	→
Aggressive medullary thyroid cancer, an analysis of the Irish National Cancer Registry.	Lennon P et al.	—	2017	→
Ancestry inference using principal component analysis and spatial analysis: a distance-based analysis to account for population substructure.	Byun J et al.	—	2017	→
Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe.	Triska P et al.	—	2017	→
Modeling prior information of common genetic variants improves gene discovery for neuroticism.	Lo MT et al.	—	2017	→
A comparison of DMET Plus microarray and genome-wide technologies by assessing population substructure.	Jackson JN et al.	—	2016	→
A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set.	Santos HC et al.	—	2016	→
Associations of Genetically Determined Continental Ancestry With CD4+ Count and Plasma HIV-1 RNA Beyond Self-Reported Race and Ethnicity.	Brummel SS et al.	—	2016	→
Common variants at PVT1, ATG13-AMBRA1, AHI1 and CLEC16A are associated with selective IgA deficiency.	Bronson PG et al.	—	2016	→
Differential burden of rare protein truncating variants in Alzheimer's disease patients compared to centenarians.	Freudenberg-Hua Y et al.	—	2016	→
Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia.	Galinsky KJ et al.	—	2016	→
Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses.	Okbay A et al.	—	2016	→
Power considerations for λ inflation factor in meta-analyses of genome-wide association studies.	Georgiopoulos G et al.	—	2016	→
Recent advances in the study of fine-scale population structure in humans.	Novembre J et al.	—	2016	→
Visualizing spatial population structure with estimated effective migration surfaces.	Petkova D et al.	—	2016	→
What Ancestry Can Tell Us About the Genetic Origins of Inter-Ethnic Differences in Asthma Expression.	Hernandez-Pacheco N et al.	—	2016	→
Characterization of the biological processes shaping the genetic structure of the Italian population.	Parolo S et al.	—	2015	→
Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort.	Banda Y et al.	—	2015	→
Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample.	Francalacci P et al.	—	2015	→
Genetic variants associated with susceptibility of Ashkenazi Jews to West Nile virus infection.	Danial-Farran N et al.	—	2015	→
Genomic architecture of human neuroanatomical diversity.	Toro R et al.	—	2015	→
Mapping the genetic diversity of HLA haplotypes in the Japanese populations.	Saw WY et al.	—	2015	→
A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese.	Qin P et al.	—	2014	→
Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations.	Yun L et al.	—	2014	→
Candidate gene approach for parasite resistance in sheep--variation in immune pathway genes and association with fecal egg count.	Periasamy K et al.	—	2014	→
Relationship estimation from whole-genome sequence data.	Li H et al.	—	2014	→
The peopling of the African continent and the diaspora into the new world.	Campbell MC et al.	—	2014	→
Using ancestry-informative markers to identify fine structure across 15 populations of European origin.	Huckins LM et al.	—	2014	→
Variation in oxytocin receptor gene (OXTR) polymorphisms is associated with emotional and behavioral reactions to betrayal.	Tabak BA et al.	—	2014	→
Visualizing spatial population structure with estimated effective migration surfaces	Petkova D et al.	—	2014	—
A genome-wide analysis of populations from European Russia reveals a new pole of genetic diversity in northern Europe.	Khrunin AV et al.	—	2013	→
Anisotropic isolation by distance: the main orientations of human genetic differentiation.	Jay F et al.	—	2013	→
An overview of STRUCTURE: applications, parameter settings, and supporting software.	Porras-Hurtado L et al.	—	2013	→
A small number of candidate gene SNPs reveal continental ancestry in African Americans.	Kodaman N et al.	—	2013	→
Confounding and heterogeneity in genetic association studies with admixed populations.	Liu J et al.	—	2013	→
Enhanced localization of genetic samples through linkage-disequilibrium correction.	Baran Y et al.	—	2013	→
ETHNOPRED: a novel machine learning method for accurate continental and sub-continental ancestry identification and population stratification correction.	Hajiloo M et al.	—	2013	→
Genomic architecture of heritability and genetic correlations for intramuscular and back fat contents in Duroc pigs.	Hernández-Sánchez J et al.	—	2013	→
High mammographic density in women of Ashkenazi Jewish descent.	Caswell JL et al.	—	2013	→
Improved ancestry inference using weights from external reference panels.	Chen CY et al.	—	2013	→
Inference of human continental origin and admixture proportions using a highly discriminative ancestry informative 41-SNP panel.	Nievergelt CM et al.	—	2013	→
Meta-analysis methods for genome-wide association studies and beyond.	Evangelou E et al.	—	2013	→
No evidence from genome-wide data of a Khazar origin for the Ashkenazi Jews.	Behar DM et al.	—	2013	→
North Africans traveling north.	Skorecki K et al.	—	2013	→
Selective estrogen receptor modulators and pharmacogenomic variation in ZNF423 regulation of BRCA1 expression: individualized breast cancer prevention.	Ingle JN et al.	—	2013	→
The GenoChip: a new tool for genetic anthropology.	Elhaik E et al.	—	2013	→
The missing link of Jewish European ancestry: contrasting the Rhineland and the Khazarian hypotheses.	Elhaik E	—	2013	→
5-HTTLPR polymorphism impacts task-evoked and resting-state activities of the amygdala in Han Chinese.	Li S et al.	—	2012	→
A comprehensive genetic approach for improving prediction of skin cancer risk in humans.	Vazquez AI et al.	—	2012	→
An overview of the genetic structure within the Italian population from genome-wide data.	Di Gaetano C et al.	—	2012	→
Bias in effect size of systemic lupus erythematosus susceptibility loci across Europe: a case-control study.	Alonso-Perez E et al.	—	2012	→
Common variants in FTO, MC4R, TMEM18, PRL, AIF1, and PCSK1 show evidence of association with adult obesity in the Greek population.	Rouskas K et al.	—	2012	→
Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L.	Allegre M et al.	—	2012	→
European American stratification in ovarian cancer case control data: the utility of genome-wide data for inferring ancestry.	Raska P et al.	—	2012	→
European ancestry decreases the risk of early onset, severe lupus nephritis in a single center, multiethnic pediatric lupus inception cohort.	Frankovich JD et al.	—	2012	→
Further evidence of subphenotype association with systemic lupus erythematosus susceptibility loci: a European cases only study.	Alonso-Perez E et al.	—	2012	→
Genetic clustering of European cancer patients indicates that opioid-mediated pain relief is independent of ancestry.	Galvan A et al.	—	2012	→
Genome-wide association studies of quantitatively measured skin, hair, and eye pigmentation in four European populations.	Candille SI et al.	—	2012	→
High-density SNP mapping of the HLA region identifies multiple independent susceptibility loci associated with selective IgA deficiency.	Ferreira RC et al.	—	2012	→
Human longevity and common variations in the LMNA gene: a meta-analysis.	Conneely KN et al.	—	2012	→
Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations.	Yang HC et al.	—	2012	→
Investigation of inversion polymorphisms in the human genome using principal components analysis.	Ma J et al.	—	2012	→
NetView: a high-definition network-visualization approach to detect fine-scale population structures from genome-wide patterns of variation.	Neuditschko M et al.	—	2012	→
Principal components analysis of population admixture.	Ma J et al.	—	2012	→
Rare and low frequency variant stratification in the UK population: description and impact on association tests.	Babron MC et al.	—	2012	→
Transancestral mapping of the MHC region in systemic lupus erythematosus identifies new independent and interacting loci at MSH5, HLA-DPB1 and HLA-G.	Fernando MM et al.	—	2012	→
Association of systemic lupus erythematosus clinical features with European population genetic substructure.	Alonso-Perez E et al.	—	2011	→
A test of the influence of continental axes of orientation on patterns of human gene flow.	Ramachandran S et al.	—	2011	→
CIITA is not associated with risk of developing rheumatoid arthritis.	Bronson PG et al.	—	2011	→
Genetic architecture of prostate cancer in the Ashkenazi Jewish population.	Vijai J et al.	—	2011	→
Genetic background of patients from a university medical center in Manhattan: implications for personalized medicine.	Tayo BO et al.	—	2011	→
hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets.	Johnson TA et al.	—	2011	→
Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy.	Höglinger GU et al.	—	2011	→
Including additional controls from public databases improves the power of a genome-wide association study.	Mukherjee S et al.	—	2011	→
Perspectives on human population structure at the cusp of the sequencing era.	Novembre J et al.	—	2011	→
Recommendations for publication of genetic association studies in Arthritis & Rheumatism.	Plenge RM et al.	—	2011	→
Relationship between ADIPOQ gene, circulating high molecular weight adiponectin and albuminuria in individuals with normal kidney function: evidence from a family-based study.	Menzaghi C et al.	—	2011	→
Study of large and highly stratified population datasets by combining iterative pruning principal component analysis and structure.	Limpiti T et al.	—	2011	→
The rs4774 CIITA missense variant is associated with risk of systemic lupus erythematosus.	Bronson PG et al.	—	2011	→
The type 2 diabetes and insulin-resistance locus near IRS1 is a determinant of HDL cholesterol and triglycerides levels among diabetic subjects.	Sharma R et al.	—	2011	→
Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry.	Atzmon G et al.	—	2010	→
A candidate gene study of CLEC16A does not provide evidence of association with risk for anti-CCP-positive rheumatoid arthritis.	Bronson PG et al.	—	2010	→
Ancestral informative marker selection and population structure visualization using sparse Laplacian eigenfunctions.	Zhang J	—	2010	→
Ancestry, ancestry-informative markers, asthma, and the quest for personalized medicine.	Barnes KC	—	2010	→
Ancestry informative markers for fine-scale individual assignment to worldwide populations.	Paschou P et al.	—	2010	→
An intronic polymorphism of IRF4 gene influences gene transcription in vitro and shows a risk association with childhood acute lymphoblastic leukemia in males.	Do TN et al.	—	2010	→
Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency.	Ferreira RC et al.	—	2010	→
A weighted false discovery rate control procedure reveals alleles at FOXA2 that influence fasting glucose levels.	Xing C et al.	—	2010	→
Characterizing allelic association in the genome era.	Weir BS et al.	—	2010	→
Circulating high molecular weight adiponectin isoform is heritable and shares a common genetic background with insulin resistance in nondiabetic White Caucasians from Italy: evidence from a family-based study.	Menzaghi C et al.	—	2010	→
Clustering by genetic ancestry using genome-wide SNP data.	Solovieff N et al.	—	2010	→
CoAIMs: a cost-effective panel of ancestry informative markers for determining continental origins.	Londin ER et al.	—	2010	→
European population substructure correlates with systemic lupus erythematosus endophenotypes in North Americans of European descent.	Richman IB et al.	—	2010	→
Examination of disease-based selection, demographic history and population structure in European Y-chromosome haplogroup I.	Sezgin E et al.	—	2010	→
Genetic differentiation of Jewish populations.	Klitz W et al.	—	2010	→
Genetic diversity in India and the inference of Eurasian population expansion.	Xing J et al.	—	2010	→
Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.	Hendrickson SL et al.	—	2010	→
Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration.	Chen W et al.	—	2010	→
Genomes, populations and diseases: ethnic genomics and personalized medicine.	Stepanov VA	—	2010	→
Genome-wide associations and functional genomic studies of musculoskeletal adverse events in women receiving aromatase inhibitors.	Ingle JN et al.	—	2010	→
Genomewide association studies in allergy and the influence of ethnicity.	Barnes KC	—	2010	→
Genome-wide association study of growth in crossbred beef cattle.	Snelling WM et al.	—	2010	→
Genome-wide patterns of population structure and admixture in West Africans and African Americans.	Bryc K et al.	—	2010	→
Identification of population substructure among Jews using STR markers and dependence on reference populations included.	Listman JB et al.	—	2010	→
Identifying candidate causal variants via trans-population fine-mapping.	Teo YY et al.	—	2010	→
Inferring geographic coordinates of origin for Europeans using small panels of ancestry informative markers.	Drineas P et al.	—	2010	→
Magnitude of stratification in human populations and impacts on genome wide association studies.	Hao K et al.	—	2010	→
New approaches to population stratification in genome-wide association studies.	Price AL et al.	—	2010	→
Population stratification in European South-American subjects and its importance to psychiatric genetics research in Brazil.	Cordeiro Q et al.	—	2010	→
Principal component analysis under population genetic models of range expansion and admixture.	François O et al.	—	2010	→
Quality control and quality assurance in genotypic data for genome-wide association studies.	Laurie CC et al.	—	2010	→
Quality control for genome-wide association studies.	Weale ME	—	2010	→
Refining the association of MHC with multiple sclerosis in African Americans.	McElroy JP et al.	—	2010	→
Replication of genetic association studies in asthma and related phenotypes.	Undarmaa S et al.	—	2010	→
Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population.	Bray SM et al.	—	2010	→
Susceptibility genes in common complex kidney disease.	Divers J et al.	—	2010	→
Testing for non-random mating: evidence for ancestry-related assortative mating in the Framingham heart study.	Sebro R et al.	—	2010	→
The genome-wide structure of the Jewish people.	Behar DM et al.	—	2010	→
Theoretical formulation of principal components analysis to detect and correct for population stratification.	Ma J et al.	—	2010	→
Toward a more uniform sampling of human genetic diversity: a survey of worldwide populations by high-density genotyping.	Xing J et al.	—	2010	→
Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies.	Hao K et al.	—	2009	→
A genomewide comparison of population structure at STRPs and nearby SNPs in humans.	Payseur BA et al.	—	2009	→
A genome wide survey of SNP variation reveals the genetic structure of sheep breeds.	Kijas JW et al.	—	2009	→
Allele-specific gene expression is widespread across the genome and biological processes.	Palacios R et al.	—	2009	→
An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels.	Nassir R et al.	—	2009	→
An assessment of the portability of ancestry informative markers between human populations.	Myles S et al.	—	2009	→
Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America.	Kosoy R et al.	—	2009	→
Data for Genetic Analysis Workshop 16 Problem 1, association analysis of rheumatoid arthritis data.	Amos CI et al.	—	2009	→
European population genetic substructure: further definition of ancestry informative markers for distinguishing among diverse European ethnic groups.	Tian C et al.	—	2009	→
European population substructure is associated with mucocutaneous manifestations and autoantibody production in systemic lupus erythematosus.	Chung SA et al.	—	2009	→
Family-based genome-wide association studies.	Benyamin B et al.	—	2009	→
Fine-scaled human genetic structure revealed by SNP microarrays.	Xing J et al.	—	2009	→
Genetic structure of Europeans: a view from the North-East.	Nelis M et al.	—	2009	→
Genetic structure of the Han Chinese population revealed by genome-wide SNP variation.	Chen J et al.	—	2009	→
Genome-wide association study of determinants of anti-cyclic citrullinated peptide antibody titer in adults with rheumatoid arthritis.	Cui J et al.	—	2009	→
Genome-wide insights into the patterns and determinants of fine-scale population structure in humans.	Biswas S et al.	—	2009	→
Genomic dissection of population substructure of Han Chinese and its implication in association studies.	Xu S et al.	—	2009	→
Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations.	Kopelman NM et al.	—	2009	→
Geographical structure and differential natural selection among North European populations.	McEvoy BP et al.	—	2009	→
High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions.	Barcellos LF et al.	—	2009	→
High differentiation among eight villages in a secluded area of Sardinia revealed by genome-wide high density SNPs analysis.	Pistis G et al.	—	2009	→
IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy.	Suppiah V et al.	—	2009	→
Iterative pruning PCA improves resolution of highly structured populations.	Intarapanich A et al.	—	2009	→
Mapping human genetic diversity in Asia.	HUGO Pan-Asian SNP Consortium et al.	—	2009	→
Power consequences of linkage disequilibrium variation between populations.	Teo YY et al.	—	2009	→
Power of selective genotyping in genome-wide association studies of quantitative traits.	Xing C et al.	—	2009	→
Replication of recently identified associated single-nucleotide polymorphisms from six autoimmune diseases in Genetic Analysis Workshop 16 rheumatoid arthritis data.	Deshmukh H et al.	—	2009	→
Rheumatoid arthritis: a view of the current genetic landscape.	Coenen MJ et al.	—	2009	→
Searching for disease susceptibility variants in structured populations.	Roeder K et al.	—	2009	→
Shared susceptibility variations in autoimmune diseases: a brief perspective on common issues.	Seldin MF et al.	—	2009	→
The chromosome 7q region association with rheumatoid arthritis in females in a British population is not replicated in a North American case-control series.	Korman BD et al.	—	2009	→
The impact of divergence time on the nature of population structure: an example from Iceland.	Price AL et al.	—	2009	→
The TRIB3 Q84R polymorphism and risk of early-onset type 2 diabetes.	Prudente S et al.	—	2009	→
Accounting for ancestry: population substructure and genome-wide association studies.	Tian C et al.	—	2008	→
Analysis of East Asia genetic substructure using genome-wide SNP arrays.	Tian C et al.	—	2008	→
Application of ancestry informative markers to association studies in European Americans.	Seldin MF et al.	—	2008	→
Correlation between genetic and geographic structure in Europe.	Lao O et al.	—	2008	→
Ethnic differences in the serotonin transporter polymorphism (5-HTTLPR) in several European populations.	Noskova T et al.	—	2008	→
Family-based samples can play an important role in genetic association studies.	Lange EM et al.	—	2008	→
Genes mirror geography within Europe.	Novembre J et al.	—	2008	→
Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe.	Salmela E et al.	—	2008	→
Genome-wide association studies for complex traits: consensus, uncertainty and challenges.	McCarthy MI et al.	—	2008	→
Genome-wide association studies: implications for multiethnic samples.	Cooper RS et al.	—	2008	→
Genomic regulation of CTLA4 and multiple sclerosis.	Palacios R et al.	—	2008	→
Investigation of the fine structure of European populations with applications to disease association studies.	Heath SC et al.	—	2008	→
Long-range LD can confound genome scans in admixed populations.	Price AL et al.	—	2008	→
Population substructure and control selection in genome-wide association studies.	Yu K et al.	—	2008	→
Several regions in the major histocompatibility complex confer risk for anti-CCP-antibody positive rheumatoid arthritis, independent of the DRB1 locus.	Lee HS et al.	—	2008	→
The genome-wide patterns of variation expose significant substructure in a founder population.	Jakkula E et al.	—	2008	→
The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research.	Nelson MR et al.	—	2008	→
Tracing sub-structure in the European American population with PCA-informative markers.	Paschou P et al.	—	2008	→
Variation in NPC1, the gene encoding Niemann-Pick C1, a protein involved in intracellular cholesterol transport, is associated with Alzheimer disease and/or aging in the Polish population.	Erickson RP et al.	—	2008	→