An important task in the genetic understanding of disease is determining whether there is a significant association between a phenotype and a set of markers. This task is sometimes referred to as a group test in a genome-wide association study. Examples of this task include determining whether a set of rare variants are associated with a phenotype, and whether a set of single nucleotide polymor...

potato virus y (pvy) is one of the most important pathogenic agents that reduce the yield and quality of tobacco (nicotiana tabacum l.). dna-based molecular markers are valuable tools for identifying germplasm in gene banks, assessing kinship ties, and doing marker-assisted selection (mas) for resistance to pests, diseases, and some crop traits of interest. this work presents the results of ass...

Objective(s) Alzheimer’s disease (AD) is a complex disease with multifactorial etiology. Inflammation has been proven to have an important role in the pathogenesis of AD. Both CCR2 and CCR5 genes expression increase in AD patients comparing to control subjects. CCR5 gene encodes a protein which is a member of the beta chemokine receptors family of integral membrane proteins. CCR5-Δ32 is a gene...

Genome-wide association studies (GWAS) have identified many common variants associated with complex traits in human populations. Thus far, most reported variants have relatively small effects and explain only a small proportion of phenotypic variance, leading to the issues of 'missing' heritability and its explanation. Using height as an example, we examined two possible sources of missing heri...

Tinnitus is the perception of a phantom sound that affects between 10 and 15% of the general population. Despite this considerable prevalence, treatments for tinnitus are presently lacking. Tinnitus exhibits a diverse array of recognized risk factors and extreme clinical heterogeneity. Furthermore, it can involve an unknown number of auditory and non-auditory networks and molecular pathways. Th...

Genome-wide association studies (GWAS) have become a preferred method to identify new genetic susceptibility loci. This technique aims to understanding the molecular etiology of common diseases, but in many cases, it has led to the identification of loci with no obvious biological relevance. Herein, we show that previously unrecognized sequence homologies have caused single-nucleotide polymorph...

An approach is described for simulating data sequence, genotype, and phenotype data to study genomic selection and genome-wide association studies (GWAS). The simulation method, implemented in a software package called AlphaDrop, can be used to simulate genomic data and phenotypes with flexibility in terms of the historical population structure, recent pedigree structure, distribution of quanti...

In a genome-wide association study, association between disease trait and hundreds of thousands of genetic markers are tested. Several methods have been proposed to control the false discovery rate in such high-throughput data to adjust for multiple hypotheses testing. For Genetic Analysis Workshop 18, we applied the method of false discovery rate control with p value weighting on family-based ...

Hippocampal volume is a key brain structure for learning ability and memory process, and hippocampal atrophy is a recognized biological marker of Alzheimer's disease. However, the genetic bases of hippocampal volume are still unclear although it is a heritable trait. Genome-wide association studies (GWASs) on hippocampal volume have implicated several significantly associated genetic variants i...

Homologous recombination has been a focus of basic research for over a hundred years [1–3]. The advent of genomics has allowed fine-scale analyses of recombination, including genomewide analysis of global recombination rate [4–6] and hotspot usage (the proportion of recombination that occurs at hotspots) [4,6]. Recently, PLOS Genetics published the work of Ma et al. [7] describing a genome-wide...