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Genome-wide Complex Trait Analysis
Genome-wide complex trait analysis (GCTA) Genome-based restricted maximum likelihood (GREML) is a statistical method for variance component estimation in genetics which quantifies the total narrow-sense (additive) contribution to a trait's heritability of a particular subset of genetic variants (typically limited to SNPs with MAF >1%, hence terms such as "chip heritability"/"SNP heritability"). This is done by directly quantifying the chance genetic similarity of unrelated individuals and comparing it to their measured similarity on a trait; if two unrelated individuals are relatively similar genetically and also have similar trait measurements, then the measured genetics are likely to causally influence that trait, and the correlation can to some degree tell how much. This can be illustrated by plotting the squared pairwise trait differences between individuals against their estimated degree of relatedness. The GCTA framework can be applied in a variety of settings. For example, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Restricted Maximum Likelihood
In statistics, the restricted (or residual, or reduced) maximum likelihood (REML) approach is a particular form of maximum likelihood estimation that does not base estimates on a maximum likelihood fit of all the information, but instead uses a likelihood function calculated from a transformed set of data, so that nuisance parameters have no effect. (see REML) In the case of variance component estimation, the original data set is replaced by a set of contrasts calculated from the data, and the likelihood function is calculated from the probability distribution of these contrasts, according to the model for the complete data set. In particular, REML is used as a method for fitting linear mixed models. In contrast to the earlier maximum likelihood estimation, REML can produce unbiased estimates of variance and covariance parameters. The idea underlying REML estimation was put forward by M. S. Bartlett in 1937. The first description of the approach applied to estimating components of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
External Validity
External validity is the validity of applying the conclusions of a scientific study outside the context of that study. In other words, it is the extent to which the results of a study can be generalized to and across other situations, people, stimuli, and times.Aronson, E., Wilson, T. D., Akert, R. M., & Fehr, B. (2007). Social psychology. (4 ed.). Toronto, ON: Pearson Education. In contrast, internal validity is the validity of conclusions drawn ''within'' the context of a particular study. Because general conclusions are almost always a goal in research, external validity is an important property of any study. Mathematical analysis of external validity concerns a determination of whether generalization across heterogeneous populations is feasible, and devising statistical and computational methods that produce valid generalizations. Threats "A threat to external validity is an explanation of how you might be wrong in making a generalization from the findings of a particular study ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Linkage Disequilibrium
In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is higher or lower than what would be expected if the loci were independent and associated randomly. Linkage disequilibrium is influenced by many factors, including selection, the rate of genetic recombination, mutation rate, genetic drift, the system of mating, population structure, and genetic linkage. As a result, the pattern of linkage disequilibrium in a genome is a powerful signal of the population genetic processes that are structuring it. In spite of its name, linkage disequilibrium may exist between alleles at different loci without any genetic linkage between them and independently of whether or not allele frequencies are in equilibrium (not changing with time). Furthermore, linkage disequilibrium is sometimes referred to as gam ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Linkage Disequilibrium Score Regression
In statistical genetics, linkage disequilibrium score regression (LDSR or LDSC) is a technique that aims to quantify the separate contributions of polygenic effects and various confounding factors, such as population stratification, based on summary statistics from genome-wide association studies (GWASs). The approach involves using regression analysis to examine the relationship between linkage disequilibrium scores and the test statistics of the single-nucleotide polymorphisms (SNPs) from the GWAS. Here, the "linkage disequilibrium score" for a SNP "is the sum of LD ''r2'' measured with all other SNPs". LDSC can be used to produce SNP-based heritability estimates, to partition this heritability into separate categories, and to calculate genetic correlations between separate phenotypes. Because the LDSC approach relies only on summary statistics from an entire GWAS, it can be used efficiently even with very large sample sizes. In LDSC, genetic correlations are calculated based o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Meta-analysis
A meta-analysis is a statistical analysis that combines the results of multiple scientific studies. Meta-analyses can be performed when there are multiple scientific studies addressing the same question, with each individual study reporting measurements that are expected to have some degree of error. The aim then is to use approaches from statistics to derive a pooled estimate closest to the unknown common truth based on how this error is perceived. Meta-analytic results are considered the most trustworthy source of evidence by the evidence-based medicine literature.Herrera Ortiz AF., Cadavid Camacho E, Cubillos Rojas J, Cadavid Camacho T, Zoe Guevara S, Tatiana Rincón Cuenca N, Vásquez Perdomo A, Del Castillo Herazo V, & Giraldo Malo R. A Practical Guide to Perform a Systematic Literature Review and Meta-analysis. Principles and Practice of Clinical Research. 2022;7(4):47–57. https://doi.org/10.21801/ppcrj.2021.74.6 Not only can meta-analyses provide an estimate of the u ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Method Of Moments (statistics)
In statistics, the method of moments is a method of estimation of population parameters. The same principle is used to derive higher moments like skewness and kurtosis. It starts by expressing the population moments (i.e., the expected values of powers of the random variable under consideration) as functions of the parameters of interest. Those expressions are then set equal to the sample moments. The number of such equations is the same as the number of parameters to be estimated. Those equations are then solved for the parameters of interest. The solutions are estimates of those parameters. The method of moments was introduced by Pafnuty Chebyshev in 1887 in the proof of the central limit theorem. The idea of matching empirical moments of a distribution to the population moments dates back at least to Pearson. Method Suppose that the problem is to estimate k unknown parameters \theta_, \theta_2, \dots, \theta_k characterizing the distribution f_W(w; \theta) of the ran ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polygenic
A polygene is a member of a group of non- epistatic genes that interact additively to influence a phenotypic trait, thus contributing to multiple-gene inheritance (polygenic inheritance, multigenic inheritance, quantitative inheritance), a type of non-Mendelian inheritance, as opposed to single-gene inheritance, which is the core notion of Mendelian inheritance. The term "monozygous" is usually used to refer to a hypothetical gene as it is often difficult to distinguish the effect of an individual gene from the effects of other genes and the environment on a particular phenotype. Advances in statistical methodology and high throughput sequencing are, however, allowing researchers to locate candidate genes for the trait. In the case that such a gene is identified, it is referred to as a quantitative trait locus (QTL). These genes are generally pleiotropic as well. The genes that contribute to type 2 diabetes are thought to be mostly polygenes. In July 2016, scientists reported ide ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Design Of Experiments
The design of experiments (DOE, DOX, or experimental design) is the design of any task that aims to describe and explain the variation of information under conditions that are hypothesized to reflect the variation. The term is generally associated with experiments in which the design introduces conditions that directly affect the variation, but may also refer to the design of quasi-experiments, in which natural conditions that influence the variation are selected for observation. In its simplest form, an experiment aims at predicting the outcome by introducing a change of the preconditions, which is represented by one or more independent variables, also referred to as "input variables" or "predictor variables." The change in one or more independent variables is generally hypothesized to result in a change in one or more dependent variables, also referred to as "output variables" or "response variables." The experimental design may also identify control variables that must b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Missing Heritability Problem
The "missing heritability" problem is the fact that single genetic variations cannot account for much of the heritability of diseases, behaviors, and other phenotypes. This is a problem that has significant implications for medicine, since a person's susceptibility to disease may depend more on 'the combined effect of all the genes in the background than on the disease genes in the foreground', or the role of genes may have been severely overestimated. The 'missing heritability' problem was named as such in 2008 (after the " missing baryon problem" in physics). The Human Genome Project led to optimistic forecasts that the large genetic contributions to many traits and diseases (which were identified by quantitative genetics and behavioral genetics in particular) would soon be mapped and pinned down to specific genes and their genetic variants by methods such as candidate-gene studies which used small samples with limited genetic sequencing to focus on specific genes believed to be ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ascertainment Bias
In statistics, sampling bias is a bias in which a sample is collected in such a way that some members of the intended population have a lower or higher sampling probability than others. It results in a biased sample of a population (or non-human factors) in which all individuals, or instances, were not equally likely to have been selected. If this is not accounted for, results can be erroneously attributed to the phenomenon under study rather than to the method of sampling. Medical sources sometimes refer to sampling bias as ascertainment bias. Ascertainment bias has basically the same definition, but is still sometimes classified as a separate type of bias. Distinction from selection bias Sampling bias is usually classified as a subtype of selection bias, sometimes specifically termed sample selection bias, but some classify it as a separate type of bias. A distinction, albeit not universally accepted, of sampling bias is that it undermines the external validity of a test (the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Principal Component Analysis
Principal component analysis (PCA) is a popular technique for analyzing large datasets containing a high number of dimensions/features per observation, increasing the interpretability of data while preserving the maximum amount of information, and enabling the visualization of multidimensional data. Formally, PCA is a statistical technique for reducing the dimensionality of a dataset. This is accomplished by linearly transforming the data into a new coordinate system where (most of) the variation in the data can be described with fewer dimensions than the initial data. Many studies use the first two principal components in order to plot the data in two dimensions and to visually identify clusters of closely related data points. Principal component analysis has applications in many fields such as population genetics, microbiome studies, and atmospheric science. The principal components of a collection of points in a real coordinate space are a sequence of p unit vectors, where the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heritability Of IQ
Research on the heritability of IQ inquires into the degree of variation in IQ within a population that is due to genetic variation between individuals in that population. There has been significant controversy in the academic community about the heritability of IQ since research on the issue began in the late nineteenth century. Intelligence in the normal range is a polygenic trait, meaning that it is influenced by more than one gene, and in the case of intelligence at least 500 genes. Further, explaining the similarity in IQ of closely related persons requires careful study because environmental factors may be correlated with genetic factors. Early twin studies of adult individuals have found a heritability of IQ between 57% and 73%, with some recent studies showing heritability for IQ as high as 80%. IQ goes from being weakly correlated with genetics for children, to being strongly correlated with genetics for late teens and adults. The heritability of IQ increases with the c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
