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...

Genetic analysis of complex diseases demands novel analytical methods to interpret data collected on thousands of variables by genome-wide association studies. The complexity of such analysis is multiplied when one has to consider interaction effects, be they among the genetic variations (G x G) or with environment risk factors (G x E). Several statistical learning methods seem quite promising ...

Recent groundbreaking work in genetics has identified thousands of small-effect genetic variants throughout the genome that are associated with almost all major diseases. These genome-wide association studies (GWAS) are often proposed as a source of future medical breakthroughs. However, with several notable exceptions, the journey from a small-effect genetic variant to a functional drug has pr...

BACKGROUND Schizophrenia (SCZ) is a very heterogeneous disease that affects approximately 1% of the general population. Recently, the genetic complexity thought to underlie this condition was further supported by three independent studies that identified an increased number of damaging de novo mutations DNM in different SCZ probands. While these three reports support the implication of DNM in t...