Related papers: Genotype-based Case-Control Analysis, Violation of…
Background: By a new concept called "phase diagram", we compare two commonly used genotype-based tests for case-control genetic analysis, one is a Cochran-Armitage trend test (CAT test at $x=0.5$, or CAT0.5) and another (called MAX2) is the…
In genetic studies of complex diseases, the underlying mode of inheritance is often not known. Thus, the most powerful test or other optimal procedure for one model, e.g. recessive, may be quite inefficient if another model, e.g. dominant,…
Although prospective logistic regression is the standard method of analysis for case-control data, it has been recently noted that in genetic epidemiologic studies one can use the ``retrospective'' likelihood to gain major power by…
Since the foundations of Population Genetics the notion of genetic equilibrium (in close analogy to Classical Mechanics) has been associated to the Hardy-Weinberg (HW) Principle and the identification of equilibrium is currently assumed by…
The case-control design is often used to test associations between the case-control status and genetic variants. In addition to this primary phenotype a number of additional traits, known as secondary phenotypes, are routinely recorded and…
Genetic association studies are becoming an important component of medical research. To cite one instance, pharmacogenomics which is gaining prominence as a useful tool for personalized medicine is heavily reliant on results from genetic…
We consider testing equivalence to Hardy-Weinberg Equilibrium in case of multiple alleles. Two different test statistics are proposed for this test problem. The asymptotic distribution of the test statistics is derived. The corresponding…
High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been…
Testing for Hardy-Weinberg equilibrium (HWE) is a fundamental component of genetic data analysis, widely used for quality control and model validation. Although HWE testing is well established for autosomal loci, inference on the X…
Genetic association study is an essential step to discover genetic factors that are associated with a complex trait of interest. In this paper we present a novel generalized quasi-likelihood score (GQLS) test that is suitable for a study…
Clinical end-point traits are often characterized by quantitative or qualitative precursors and it has been argued that it may be statistically a more powerful strategy to analyze these precursor traits to decipher the genetic architecture…
Understanding how genetic variants influence cellular-level processes is an important step towards understanding how they influence important organismal-level traits, or "phenotypes", including human disease susceptibility. To this end…
Fundamental properties of macroscopic gene-mating dynamic evolutionary systems are investigated. We focus on a single locus, any number of alleles in a two-gender dioecious population, for a large class of systems within population…
Because of the high cost of commercial genotyping chip technologies, many investigations have used a two-stage design for genome-wide association studies, using part of the sample for an initial discovery of ``promising'' SNPs at a less…
Statistical methods for testing aggregate rare-variant genetic associations are typically based on either burden or dispersion tests (or a combination of the two). These methods lack statistical power in the presence of diverse genetic…
The vast majority of connections between complex disease and common genetic variants were identified through meta-analysis, a powerful approach that enables large samples sizes while protecting against common artifacts due to population…
The genetic basis of multiple phenotypes such as gene expression, metabolite levels, or imaging features is often investigated by testing a large collection of hypotheses, probing the existence of association between each of the traits and…
The X-chromosome is often excluded from genome-wide association studies because of analytical challenges. Some of the problems, such as the random, skewed or no X-inactivation model uncertainty, have been investigated. Other considerations…
Collection of genotype data in case-control genetic association studies may often be incomplete for reasons related to genes themselves. This non-ignorable missingness structure, if not appropriately accounted for, can result in…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…