Mapping epistatic quantitative trait loci.

Background: How to map quantitative trait loci (QTL) with epistasis efficiently and reliably has been a persistent problem for QTL mapping analysis. There are a number of difficulties for studying epistatic QTL. Linkage can impose a significant challenge for finding epistatic QTL reliably.

Subchondral bone trabecular integrity predicts and changes concurrently with radiographic and magnetic resonance imaging-determined knee osteoarthritis progression.

Objective: To evaluate subchondral bone trabecular integrity (BTI) on radiographs as a predictor of knee osteoarthritis (OA) progression.

Methods: Longitudinal (baseline, 12-month, and 24-month) knee radiographs were available for 60 female subjects with knee OA. OA progression was defined by 12- and 24-month changes in radiographic medial compartment minimal joint space width (JSW) and medial joint space area (JSA), and by medial tibial and femoral cartilage volume on magnetic resonance imaging.

Multiple trait multiple interval mapping of quantitative trait loci from inbred line crosses.

Background: Although many experiments have measurements on multiple traits, most studies performed the analysis of mapping of quantitative trait loci (QTL) for each trait separately using single trait analysis. Single trait analysis does not take advantage of possible genetic and environmental correlations between traits. In this paper, we propose a novel statistical method for multiple trait multiple interval mapping (MTMIM) of QTL for inbred line crosses.

Composite interval mapping and multiple interval mapping: procedures and guidelines for using Windows QTL Cartographer.

Tremendous progress has been made in recent years on developing statistical methods for mapping quantitative trait loci (QTL) from crosses of inbred lines. In this chapter, we provide an introduction of composite interval mapping and multiple interval mapping methods for mapping QTL from inbred line crosses and also detailed instructions to perform the analyses in Windows QTL Cartographer. For each method, we discuss the meaning of each option in the analysis procedures and how to understand and interpret the mapping results through a work-out example.

GWAPower: a statistical power calculation software for genome-wide association studies with quantitative traits.

Background: In designing genome-wide association (GWA) studies it is important to calculate statistical power. General statistical power calculation procedures for quantitative measures often require information concerning summary statistics of distributions such as mean and variance. However, with genetic studies, the effect size of quantitative traits is traditionally expressed as heritability, a quantity defined as the amount of phenotypic variation in the population that can be ascribed to the genetic variants among individuals.

Summarizing and quantifying multilocus linkage disequilibrium patterns with multi-order Markov chain models.

Studies on linkage disequilibrium (LD) are important in mapping disease genes. A novel statistical method, the multi-order Markov chain model has been recently developed to quantify the complexity level of multilocus LD patterns among single nucleotide polymorphism markers (Kim et al., 2008).

Trabecular morphometry by fractal signature analysis is a novel marker of osteoarthritis progression.

Objective: To evaluate the effectiveness of using subchondral bone texture observed on a radiograph taken at baseline to predict progression of knee osteoarthritis (OA) over a 3-year period.

Methods: A total of 138 participants in the Prediction of Osteoarthritis Progression study were evaluated at baseline and after 3 years. Fractal signature analysis (FSA) of the medial subchondral tibial plateau was performed on fixed flexion radiographs of 248 nonreplaced knees, using a commercially available software tool.

Quantitative trait loci mapping and the genetic basis of heterosis in maize and rice.

Despite its importance to agriculture, the genetic basis of heterosis is still not well understood. The main competing hypotheses include dominance, overdominance, and epistasis. NC design III is an experimental design that has been used for estimating the average degree of dominance of quantitative trait loci (QTL) and also for studying heterosis.

Multiple-interval mapping for ordinal traits.

Many statistical methods have been developed to map multiple quantitative trait loci (QTL) in experimental cross populations. Among these methods, multiple-interval mapping (MIM) can map QTL with epistasis simultaneously. However, the previous implementation of MIM is for continuously distributed traits.