Related papers: Replication in Genome-Wide Association Studies
Reproducibility, the ability to recompute results, and replicability, the chances other experimenters will achieve a consistent result, are two foundational characteristics of successful scientific research. Consistent findings from…
If the prior probability distributions of all possible hypothetical true means and all possible observed means of a continuous variable are conditional on the universal set of all numbers (i.e., before the nature of a study is known and a…
Assessing the statistical power to detect susceptibility variants plays a critical role in GWA studies both from the prospective and retrospective points of view. Power is empirically estimated by simulating phenotypes under a disease model…
Scientific claims gain credibility by replicability, especially if replication under different circumstances and varying designs yields equivalent results. Aggregating results over multiple studies is, however, not straightforward, and when…
In genome-wide association (GWA) studies the goal is to detect associations between genetic markers and a given phenotype. The number of genetic markers can be large and effective methods for control of the overall error rate is a central…
Genome-wide association (GWA) constitutes a prominent portion of studies which have been conducted on personalized medicine and pharmacogenomics. Recently, very few methods have been developed for extracting mutation-diseases associations.…
Presented here is a simple method for cross-validated genome-wide association studies (cvGWAS). Focusing on phenotype prediction, the method is able to reveal a significant amount of missing heritability by properly selecting a small number…
Motivation: Genome-wide association studies (GWASs), which assay more than a million single nucleotide polymorphisms (SNPs) in thousands of individuals, have been widely used to identify genetic risk variants for complex diseases. However,…
It is widely recognized nowadays that complex diseases are caused by, amongst the others, multiple genetic factors. The recent advent of genome-wide association study (GWA) has triggered a wave of research aimed at discovering genetic…
In this paper we have proposed a model for the distribution of allelic probabilities for generating populations as reliably as possible. Our objective was to develop such a model which would allow simulating allelic probabilities with…
This paper develops a method based on model-X knockoffs to find conditional associations that are consistent across diverse environments, controlling the false discovery rate. The motivation for this problem is that large data sets may…
Motivation: Genome-Wide Association Studies (GWAS) seek to identify causal genomic variants associated with rare human diseases. The classical statistical approach for detecting these variants is based on univariate hypothesis testing, with…
Replication studies are essential for assessing the credibility of claims from original studies. A critical aspect of designing replication studies is determining their sample size; a too small sample size may lead to inconclusive studies…
In several large-scale replication projects, statistically non-significant results in both the original and the replication study have been interpreted as a "replication success". Here we discuss the logical problems with this approach:…
In the search for genetic factors that are associated with complex heritable human traits, considerable attention is now being focused on rare variants that individually have small effects. In response, numerous recent papers have proposed…
An ongoing "reproducibility crisis" calls into question scientific discoveries across a variety of disciplines ranging from life to social sciences. Replication studies aim to investigate the validity of findings in published research, and…
Many published research results are false, and controversy continues over the roles of replication and publication policy in improving the reliability of research. Addressing these problems is frustrated by the lack of a formal framework…
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…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
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…