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Population Structure in Genetic Association Studies
Standard genetic association tests using case-control data are based ... types of departure have been called population structure. Each can ... between a test statistic's actual null distribution and the nominal .... Cryptic relatedness occurs when a population consists .... two subpopulations in prevalence of both disease and of.
[ WhittemoreJSM2006.pdf - Read/Download File

Case-control studies of association in structured or admixed
Jul 5, 2001 ... data to enable valid case-control tests of association, even in the presence of population ... A similar effect arises in admixed populations, if the risk of disease depends. 1. Here ... quately reflect the underlying population structure. .... R cases and R controls from a population consisting of K subpopulations.
[ PritchardEtAl01.pdf - Read/Download File

detecting genetic association in case-control studies using similarity
the power of case-control studies, the population stratification issue still needs ... f1 = g1 (i.e., the disease prevalence is different between the two subpopulations), ... from independent markers is utilized to correct for population structures. In the .... Assume the case-control sample consists of nd affected individuals and nc.
[ A12n117.pdf - Read/Download File

The effects of human population structure on large - Don Armstrong
Mar 28, 2004 ... (i) how much underlying structure is there in various human popula- tions and when might this ... correcting for population structure in case-control studies? ... population consists of subpopulations that differ genetically, and if disease ... range of differences in disease prevalence, as these effects also con-.
[ effects_of_structure_on_large_genetic_association_studies_marchini_donnelly_nat_genet_36_5_512_2004_pmid_15052271.pdf - Read/Download File

POPULATION STRATIFICATION: A PROBLEM FOR CASE
Running title: Population stratification and case-control studies ... As another example, numerous studies of the purported association between the ... pressure, often killing people before they reach reproductive age, it is a key factor underlying ... with the subpopulation's variation in their baseline disease rates ( i.e., the rates.
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components analysis corrects for stratification in genome-wide
Jul 23, 2006 ... Population stratification—allele frequency differences between cases and ... control and structured association have proven useful in a variety of ... STRAT, consists of three steps (Fig. ... genetic variation from the allele frequencies of various popula- ... population structure in the context of disease studies.
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The Impact of Divergence Time on the Nature of Population Structure
Jun 5, 2009 ... association statistics in simulated case-control studies [9]. ... studies of Icelandic population structure have focused on Y ... differences between regional subpopulations, our analyses yield ... mixing of ancestry from the different regions of Iceland, ... bias association statistics in disease studies if cases and.
[ 2009_PLoS_Genetics_Price_Iceland_Structure.pdf - Read/Download File

Correcting population stratification in genetic association studies
Jan 22, 2010 ... many diseases, the most practical approach is the population-based design with ... subpopulations in a study due to ancestry difference between study subjects. ... that consists of both discrete and admixed population structures. ..... To test for genetic association for case–control studies, we conduct logistic ...
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Ancestry Estimation and Correction for Population Stratification in
between cases and controls due to systematic differences in ancestry rather ... in background disease rates across the populations being ... stratification in case- control studies, although no true ... up of a mixture of subpopulations with different disease ..... human population structure on large genetic association studies. Nat.
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Correlation of Population Parameters Leading to Power Differences
correlation between disease prevalence and risk allele frequency among subpopulations impacts statistical power. In a model with five subpopulations and moderate population divergence (Fst = 0.01), ... tion on the genetic structure of modern human populations ... for case-control association studies with stratified samples.
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Genome Wide Association Studies
Different methods for detecting association ... between the genotypes at each locus and disease status. ... Allow variable recombination rates in men and women? .... Their high frequency implies that association studies in large population ..... There are 2 general strategies for protecting against structure in case/control ...
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Genomic control, a new approach to genetic-based association
Key Words: population substructure, bias, case-control study, overdispersion, latent class ... individuals drawn from within as opposed to between subpopulations. ... structure for an entirely different subject, the discovery of gene -disease ... highlighted its importance for genetic association studies when disease and marker ...
[ tr749.pdf - Read/Download File

Fine-Scale Patterns of Population Stratification Confound - Plos
Population structure can be a strong confounding factor in association studies ... elevation in or inflation of significance rates as the spurious association ... difficult to control for in association studies. ... sensitive different rare variant association methods are to ... subpopulation, we allowed differences in disease risk between.
[ journal.pone.0065834.PDF - Read/Download File

A randomization test for controlling population stratification in whole
association studies is the confounding effect of population structure. Differences in allele frequencies between cases and controls may be due to systematic ... to subpopulations. ... (up to 1) false positive rates of the other methods. .... The sampling space G is composed of the set of all possible disease vectors whose score ...
[ kimmel-ajhg.pdf - Read/Download File

A tutorial on statistical methods for population association studies
The goal of population association studies is to identify ... between individuals with different disease states and ... Department of Epidemiology ... key methods with a brief discussion of problems (population structure and ... Case. Control. Ancestral mutation. Testing for deviations from HWE can be ... Underlying an individ-.
[ nrg1916.pdf - Read/Download File

Common statistical issues in genome-wide association studies: a
genetic basis of common diseases and complex traits in ... genotyping errors and population structure can introduce misleading signals that ... case–control design for similar statistical power, given the ... of observing an association between the transmission of a .... studies, however, such as different phenotypic definitions,.
[ gwas_review_3.pdf - Read/Download File

(2011) Control of population stratification by correlation-selected
population structure, and have been widely used to control for stratification. ... based on both their eigenvalues and their correlation with the (disease) phenotype. ... a relationship between PCs and the average of the test statis- tics. .... described above apply to case–control studies, with Y = 0 and ... underlying assumptions.
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Centralizing the non-central chi-square: a new - Columbia University
Feb 24, 2006 ... to Correct for Population Stratification in Genetic ... (This quantity d is quite different from Wright's FST and can be large ... cation (PS) in case-control association studies ... of the method consists of a Bayesian clustering ... the program STRUCTURE. .... between disease and marker genotype is spurious.
[ Gorroochurn et al.-Noncentral.pdf - Read/Download File

Analysis of genomic diversity in Mexican Mestizo populations to
May 26, 2009 ... and linkage disequilibrium structure of different populations has made it possible ... differences between Mexican subpopulations that should be consid- ered in the ... diseases are genomewide association studies (GWAS) and admix- ... 80% of the population consists of Mestizos with known differ- ences in ...
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paper 1
May 4, 2006 ... for population-based association mapping, from single-marker tests of association to ... genetic basis of human diseases and other phenotypes.
[ Montana_2006_PopAssocReview.pdf - Read/Download File

International Data Base Population Estimates and - Census.gov
The Census Bureau strives to base the population estimates and projections for each ... In contrast, the de jure population consists of all usual residents, whether or not they .... In evaluating census age-sex structures for base population estimates, .... between its enumerated size and estimated levels of fertility and mortality ...
[ estandproj.pdf - Read/Download File

126 Chapter 6: Genome-wide association study identifies - FTP
... Population stratification. 6.1.3 Case-control association analysis ... 6.2.3 Candidate loci in genes conferring resistance to other antibiotics ... The clonal population structure may be less problematic .... GWAS reports SNPs enriched in the disease population. (case) .... positive rates due to underlying population structure.
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Maista, C; Smith, G; Mamounas, LA; Zhang, R - Coriell Institute for
Oct 15, 2010 ... Failure to control for population stratification due to genetic ancestry ... and different disease prevalence. ... there has been recent admixture between individuals from ... groups show disparities in disease prevalence, morbidity rates , and ... demonstrated a trihybrid ancestral population structure consisting.
[ londin_etal_coriellinstitute_plosone2010_ancestrymarkersfordeterminingcontinentalorigins.pdf - Read/Download File

Population Structure in Cultivated Lettuce and Its Impact on
to avoid spurious associations in lettuce association studies is to assess ... other cultivated plant species is genetic linkage mapping. ... underlying the variation of a trait among elite cultivars, is thus ... structure. Population structure is the presence of subpopulations ... control for false-positive results in association studies.
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Population Structure in Cultivated Lettuce and Its Impact on
to avoid spurious associations in lettuce association studies is to assess ... other cultivated plant species is genetic linkage mapping. ... underlying the variation of a trait among elite cultivars, is thus ... structure. Population structure is the presence of subpopulations ... control for false-positive results in association studies.
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Modelling genes: mathematical and statistical challenges in genomics
We focus here on the challenges within human population genetics, in which data document molecular genetic variation between different people. ... common human diseases. In each case, sophisticated mathematical, statistical, and computa- ..... underlying structure and assign individuals to subpopulations, with the ...
[ icm2006.3.0559.0574.ocr.pdf - Read/Download File

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