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
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 (Weir [1979] Biometrics
35:235–254; S...
FastSKAT: Sequence kernel association tests for very large sets of markers
Genetic Epidemiology - Tập 42 Số 6 - Trang 516-527 - 2018
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 eigenvalues of this
matrix (an m...
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
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 correlated. Ignoring such
correlations ca...
A small-sample multivariate kernel machine test for microbiome association studies
Genetic Epidemiology - Tập 41 Số 3 - Trang 210-220 - 2017
A review of kernel methods for genetic association studies
Genetic Epidemiology - Tập 43 Số 2 - Trang 122-136 - 2019
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 when there is a small
fraction of ...
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
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 of sequencing
technologies, imputa...
A multivariate distance‐based analytic framework for microbial interdependence association test in longitudinal study
Genetic Epidemiology - Tập 41 Số 8 - Trang 769-778 - 2017
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 differences at a single time
point, which d...
Exact variance component tests for longitudinal microbiome studies
Genetic Epidemiology - Tập 43 Số 3 - Trang 250-262 - 2019
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 testing strategies only
apply to mode...
Sequence Kernel Association Test of Multiple Continuous Phenotypes
Genetic Epidemiology - Tập 40 Số 2 - Trang 91-100 - 2016
Small Sample Kernel Association Tests for Human Genetic and Microbiome Association Studies
Genetic Epidemiology - Tập 40 Số 1 - Trang 5-19 - 2016
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 important applications
of KAT. However, ...
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