Genetic Epidemiology

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Bounds and normalization of the composite linkage disequilibrium coefficient
Genetic Epidemiology - Tập 27 Số 3 - Trang 252-257 - 2004
Dmitri V. Zaykin
AbstractThe composite linkage disequilibrium (LD) measure is often calculated for two‐locus genotypic data, especially when coupling and repulsion double heterozygotes cannot be distinguished. This measure was reported to have good statistical properties and was suggested for routine testing of LD, regardless of Hardy‐Weinberg equilibrium at either of two loci (Wei...... hiện toàn bộ
FastSKAT: Sequence kernel association tests for very large sets of markers
Genetic Epidemiology - Tập 42 Số 6 - Trang 516-527 - 2018
Thomas Lumley, Jennifer A. Brody, Gina M. Peloso, Alanna C. Morrison, Kenneth Rice
AbstractThe sequence kernel association test (SKAT) is widely used to test for associations between a phenotype and a set of genetic variants that are usually rare. Evaluating tail probabilities or quantiles of the null distribution for SKAT requires computing the eigenvalues of a matrix related to the genotype covariance between markers. Extracting the full set of...... hiện toàn bộ
A small‐sample kernel association test for correlated data with application to microbiome association studies
Genetic Epidemiology - Tập 42 Số 8 - Trang 772-782 - 2018
Xiang Zhan, Lingzhou Xue, Haotian Zheng, Anna Plantinga, Michael C. Wu, Daniel J. Schaid, Ni Zhao, Jun Chen
AbstractRecent research has highlighted the importance of the human microbiome in many human disease and health conditions. Most current microbiome association analyses focus on unrelated samples; such methods are not appropriate for analysis of data collected from more advanced study designs such as longitudinal and pedigree studies, where outcomes can be correlat...... hiện toàn bộ
A small-sample multivariate kernel machine test for microbiome association studies
Genetic Epidemiology - Tập 41 Số 3 - Trang 210-220 - 2017
Xiang Zhan, Xingwei Tong, Ni Zhao, Arnab Maity, Michael C. Wu, Jun Chen
A review of kernel methods for genetic association studies
Genetic Epidemiology - Tập 43 Số 2 - Trang 122-136 - 2019
Nicholas B. Larson, Jun Chen, Daniel J. Schaid
ABSTRACTEvaluating the association of multiple genetic variants with a trait of interest by use of kernel‐based methods has made a significant impact on how genetic association analyses are conducted. An advantage of kernel methods is that they tend to be robust when the genetic variants have effects that are a mixture of positive and negative effects, as well as w...... hiện toàn bộ
Combining Family‐ and Population‐Based Imputation Data for Association Analysis of Rare and Common Variants in Large Pedigrees
Genetic Epidemiology - Tập 38 Số 7 - Trang 579-590 - 2014
Mohamad Saad, Ellen M. Wijsman
ABSTRACTIn the last two decades, complex traits have become the main focus of genetic studies. The hypothesis that both rare and common variants are associated with complex traits is increasingly being discussed. Family‐based association studies using relatively large pedigrees are suitable for both rare and common variant identification. Because of the high cost o...... hiện toàn bộ
A multivariate distance‐based analytic framework for microbial interdependence association test in longitudinal study
Genetic Epidemiology - Tập 41 Số 8 - Trang 769-778 - 2017
Yilong Zhang, Sung Won Han, Laura M. Cox, Huilin Li
ABSTRACTHuman microbiome is the collection of microbes living in and on the various parts of our body. The microbes living on our body in nature do not live alone. They act as integrated microbial community with massive competing and cooperating and contribute to our human health in a very important way. Most current analyses focus on examining microbial difference...... hiện toàn bộ
Exact variance component tests for longitudinal microbiome studies
Genetic Epidemiology - Tập 43 Số 3 - Trang 250-262 - 2019
Jing Zhai, Kenneth S. Knox, Homer L. Twigg, Hua Zhou, Jin Zhou
AbstractIn metagenomic studies, testing the association between microbiome composition and clinical outcomes translates to testing the nullity of variance components. Motivated by a lung human immunodeficiency virus (HIV) microbiome project, we study longitudinal microbiome data by using variance component models with more than two variance components. Current test...... hiện toàn bộ
Sequence Kernel Association Test of Multiple Continuous Phenotypes
Genetic Epidemiology - Tập 40 Số 2 - Trang 91-100 - 2016
Baolin Wu, James S. Pankow
Small Sample Kernel Association Tests for Human Genetic and Microbiome Association Studies
Genetic Epidemiology - Tập 40 Số 1 - Trang 5-19 - 2016
Jun Chen, Wenan Chen, Ni Zhao, Michael C. Wu, Daniel J. Schaid
AbstractKernel machine based association tests (KAT) have been increasingly used in testing the association between an outcome and a set of biological measurements due to its power to combine multiple weak signals of complex relationship with the outcome through the specification of a relevant kernel. Human genetic and microbiome association studies are two importa...... hiện toàn bộ
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