Population structure can be a source of both false-positive and false-negative findings in a genome-wide association study. This article proposes an approach that helps to reduce the false-positives. It consists of homogenizing the diseased/healthy phenotype ratio across the cohort, by decreasing the statistical weight of selected individuals. After homogenization, the cohort is statistically h...

Intensive efforts have been underway to identify common genetic factors that influence health and disease including cancer using genomewide association studies (GWAS). Our experiences have shown that while it is more advantageous to have large detailed data sets, the amount of information generated by GWAS also present major challenges for statistical analyses. While prospects for the oncoming ...

This article compares baseline, average, and longitudinal data analysis methods for identifying genetic variants in genome-wide association study using the Genetic Analysis Workshop 18 data. We apply methods that include (a) linear mixed models with baseline measures, (b) random intercept linear mixed models with mean measures outcome, and (c) random intercept linear mixed models with longitudi...

We examine improvements to the linear mixed model (LMM) that better correct for population structure and family relatedness in genome-wide association studies (GWAS). LMMs rely on the estimation of a genetic similarity matrix (GSM), which encodes the pairwise similarity between every two individuals in a cohort. These similarities are estimated from single nucleotide polymorphisms (SNPs) or oth...

Tomato volatiles, mainly derived from essential nutrients and health-promoting precursors, affect tomato flavor. Taste volatiles present a major challenge for flavor improvement and quality breeding. In this study, we performed genome-wide association studies (GWAS) to investigate potential chromosome regions associated with the tomato flavor volatiles. We observed significant variation (1200x)...

Apart from the specific findings of this analysis, the authors encourage the use of what they call a nutrientwide association study, analogous to a genome-wide association study (GWAS), to investigate dietary determinants of health outcomes.1 Similar to the agnostic approach used in a GWAS, the features of their approach include the following: (1) the inclusion of all available nutrient exposur...

[This corrects the article DOI: 10.1371/journal.pgen.1007081.].

We conducted a genome-wide association study on the Genetic Analysis Workshop 17 simulated unrelated individuals data using a multilocus score test based on wavelet transformation that we proposed recently. Wavelet transformation is an advanced smoothing technique, whereas the currently popular collapsing methods are the simplest way to smooth multilocus genotypes. The wavelet-based test suppre...

Duke Clinical Research Institute, Duke University Medical Center, Durham, NC 27705, USA Center for Human Genome Variation, Duke University School of Medicine, Durham, NC 27708, USA Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA Dr. John T. Macdonald Foundation Department of Human G...