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- 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, it can be used to examine changes in heritability over aging and development. It can also be extended to analyse bivariate genetic correlations between traits. There is an ongoing debate about whether GCTA generates reliable or stable estimates of heritability when used on current SNP data. The method is based on the outdated and false dichotomy of genes versus the environment. It also suffers from serious methodological weaknesses, such as susceptibility to population stratification. GCTA heritability estimates are useful because they provide lower bounds for the genetic contributions to traits such as intelligence without relying on the assumptions used in twin studies and other family and pedigree studies, thereby corroborating them and enabling the design of well-powered genome-wide association study (GWAS) designs to find the specific genetic variants involved. For example, a GCTA estimate of 30% SNP heritability is consistent with a larger total genetic heritability of 70%. However, if the GCTA estimate was ~0%, then that would imply one of three things: a) there is no genetic contribution, b) the genetic contribution is entirely in the form of genetic variants not included, or c) the genetic contribution is entirely in the form of non-additive effects such as epistasis/dominance. Running GCTA on individual chromosomes and regressing the estimated proportion of trait variance explained by each chromosome against that chromosome's length can reveal whether the responsible genetic variants cluster or are distributed evenly across the genome or are sex-linked. Chromosomes can of course be replaced by more fine-grained or functionally informed subdivisions. Examining genetic correlations can reveal to what extent observed correlations, such as between intelligence and socioeconomic status, are due to the same genetic traits, and in the case of diseases, can indicate shared causal pathways such as can be inferred from the genetic variation jointly associated with schizophrenia and other mental diseases or reduced intelligence. (en)
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- 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 illustra (en)
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- Genome-wide complex trait analysis (en)
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