... analysis, including gene-based, gene-set and polygenic risk scores, combine the SNP effect sizes in an attempt to boost the power of the analyses. To avoid giving undue weight to SNPs in linkage disequilibrium (LD), the LD needs to be taken into account in these analyses. Objectives: We review methods...

...Jonathan T.L. Kang; Noah A. Rosenberg Background: Many statistics for measuring linkage disequilibrium (LD) take the form of a normalization of the LD coefficient D . Different normalizations produce statistics with different ranges, interpretations, and arguments favoring their use. Methods: Here...

... for G6PD genotyping analysis was performed, and then the linkage disequilibrium blocks of the target SNPs were constructed with Haploview 4.2 software. Results: The prevalence of G6PD deficiency was higher in the Dai ethnic group (8.63%) than in the Jingpo ethnic group (5.91%). The major mutations...

...Mary L. Roop; David E.C. Cole; David C. Hamilton Background: Linkage disequilibrium (LD) is the non-random association between alleles at different loci and remains important for disease mapping studies in humans. A common measure of LD is the sample correlation between indicator variables...

... scan Linkage disequilibrium Statistical genetics Polygenic inheritance Odds ratios GWAS Original Paper Hum Hered 2016;81:173 180 DOI: 10.1159/000454804 Received: August 11, 2016 Accepted: November 21, 2016 Published online: February 8, 2017 How Can We Explain Very Low Odds Ratios in GWAS? I...

... at markers. Methods: For this paper, we performed simulations with known genealogies using different SNP panels with different levels of linkage disequilibrium (LD) to compare several estimators of f , including single-point estimates, methods based on the length of runs of homozygosity (ROHs) and different...

... transplantation. HLA Population genetics European Caucasian Demographic history Genetic diversity Human populations Linkage disequilibrium Multi-allelic loci Natural selection Population data Phenotypic variation HLA haplotypes HLA-NET EUROSTAM © 2014 S. Karger AG, Basel 2014 Copyright...

... the candidate mutations that remain. However, when linkage disequilibrium (LD) is present in the population but ignored in the analysis, unlinked regions with high LD can inflate the type 1 error and thousands of neutral mutations may be mistakenly included in a follow-up resequencing study, which could...

... or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements. Case-parent trio Family-based study Linkage Linkage disequilibrium...

... Imprinting Linkage Linkage disequilibrium Quantitative traits Software KELVIN Statistical evidence National Institutes of Health (NIH) 10.13039/100000002 Hum Hered 2011;72:276 288 DOI: 10.1159/000330634 Published online: December 23, 2011 KELVIN: A Software Package for Rigorous...

..., 2011 PSEUDOMARKER: A Powerful Program for Joint Linkage and/or Linkage Disequilibrium Analysis on Mixtures of Singletons and Related Individuals Tero Hiekkalinnaa, b Alejandro A. Schäfferc Brian Lambertd Petri Norrgranna, b Harald H.H. Göringe Joseph D. Terwilligera, f i aInstitute for Molecular...

...Carlos Zapata Background/Objective: The analysis of linkage disequilibrium is relevant for the exploration of the structure and evolution of genomes and for the gene mapping of quantitative characters and human diseases. The strength of linkage disequilibrium between diallelic loci is commonly...

... interaction tests that are derived from conditional logistic regressions. We found that in the presence of SNP genotype correlation due to population stratification or linkage disequilibrium, tests with incorrectly specified main-genetic-effect models can lead to inflated type I error rates. We also found...

...Brooke L. Fridley; Gregory D. Jenkins Objective: Numerous methods have been proposed to model the association between multiple single nucleotide polymorphisms (SNPs) and a phenotype. Often these methods do not explicitly model the information regarding the linkage disequilibrium (LD) between SNPs...

... Paris Descartes, Necker Medical School, Paris, France; eGenizon BioSciences Inc., Montreal, Que., Canada Key Words Genetic linkage Linkage disequilibrium Conditional allele sharing Abstract Linkage analysis is often followed by association mapping to localize disease variants. In this paper, we...

... are based on comparing genotype scores, e.g. allele frequencies, between the case and control groups. Another class of approaches are motivated to contrast linkage disequilibrium (LD) patterns between the two groups. It is expected that no single test can be uniformly most powerful across all situations...

... case-control scenarios where the risk variant was directly genotyped (direct scenario) or in linkage disequilibrium with the genotyped markers (indirect scenario). Results: The retrospective methods tended to be more powerful for detecting interactions than the prospective methods. In the indirect...

...Momiao Xiong; Ruzong Fan; Li Jin As a dense map of single nucleotide polymorphism (SNP) markers are available, population-based linkage disequilibrium (LD) mapping or association study is becoming one of the major tools for identifying quantitative trait loci (QTL) and for fine gene mapping...

...Céline Bellenguez; Carole Ober; Catherine Bourgain Objective: SNP maps are becoming the gold standard for genetic markers, even for linkage analyses. However, because of the density of SNPs on most high throughput platforms, the resulting significant linkage disequilibrium (LD) can bias classical...

...Andrey Khrunin; Evelin Mihailov; Tiit Nikopensius; Kaarel Krjutškov; Svetlana Limborska; Andres Metspalu Objective: Individual population history is the main reason for the variability of linkage disequilibrium (LD) patterns and haplotype frequencies among populations. Such diversity may influence...