solarius: an R interface to SOLAR for variance component analysis in pedigrees

Ziyatdinov, Andrey; Brunel, Héléna; Martinez-Perez, Ángel; Buil, Alfonso; Perera, Alexandre; Soria, José Manuel Nieto

doi:10.1101/035378

Cited by 8 publications

(9 citation statements)

References 4 publications

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“…Heritability of the parcel-wide features was estimated in R 3.6.3 (R Core Team, 2013) using SOLAR-Eclipse 8.4.2 (Kochunov et al, 2015) (http://www.nitrc.org/projects/se_linux; http://solar-eclipse-genetics.org/index.html) via the solarius package (Ziyatdinov et al, 2016) controlling for background variables: age, sex, race, ethnicity, and proxy brain volume. The categorical variables were recoded as dummies, with white or nonhispanic as reference category.…”

Section: Methodsmentioning

confidence: 99%

Heritability of cortical morphology reflects a sensory-fugal plasticity gradient

Vainik

Paquola

Wang

et al. 2020

Preprint

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Human brain plastically adapts to environmental demands. Here, we propose that naturally occuring plasticity in certain brain areas should be reflected by higher environmental influence and therefore lower heritability of the structure of those brain areas. Mesulam's (1998) seminal overview proposed a hierarchy of plasticity, where higher-order multimodal areas should be more plastic than lower-order sensory areas. Using microstructural and functional gradients as proxies for Mesulam's hierarchy, we seek to test whether these gradients predict heritability of brain structure. We test this model simultaneously across multiple measures of cortical structure and microstructure derived from structural magnet resonance imaging. We also account for multiple other explanations of heritability differences, such as signal-to-noise ratio and spatial autocorrelation. We estimated heritability of brain areas using 984 participants from the Human Connectome Project. Multi-level modelling of heritability differences demonstrated that heritability is explained by both signal quality, as well as by the primary microstructural gradient. Namely, sensory areas had higher heritability and limbic/heteromodal areas had lower heritability. Given the increasing availability of genetically informed imaging data, heritability could be a quick method assess brain plasticity.

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Section: Methodsmentioning

confidence: 99%

Heritability of cortical morphology reflects a sensory-fugal plasticity gradient

Vainik

Paquola

Wang

et al. 2020

Preprint

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“…The model provides a vector of fitted values of the phenotype and an estimate of the variance-covariance matrix for each family [28, 29, 30]. …”

Section: Methodsmentioning

confidence: 99%

The Central Role of KNG1 Gene as a Genetic Determinant of Coagulation Pathway-Related Traits: Exploring Metaphenotypes

Brunel¹,

Massanet

Martinez-Perez³

et al. 2016

PLoS ONE

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Traditional genetic studies of single traits may be unable to detect the pleiotropic effects involved in complex diseases. To detect the correlation that exists between several phenotypes involved in the same biological process, we introduce an original methodology to analyze sets of correlated phenotypes involved in the coagulation cascade in genome-wide association studies. The methodology consists of a two-stage process. First, we define new phenotypic meta-variables (linear combinations of the original phenotypes), named metaphenotypes, by applying Independent Component Analysis for the multivariate analysis of correlated phenotypes (i.e. the levels of coagulation pathway–related proteins). The resulting metaphenotypes integrate the information regarding the underlying biological process (i.e. thrombus/clot formation). Secondly, we take advantage of a family based Genome Wide Association Study to identify genetic elements influencing these metaphenotypes and consequently thrombosis risk. Our study utilized data from the GAIT Project (Genetic Analysis of Idiopathic Thrombophilia). We obtained 15 metaphenotypes, which showed significant heritabilities, ranging from 0.2 to 0.7. These results indicate the importance of genetic factors in the variability of these traits. We found 4 metaphenotypes that showed significant associations with SNPs. The most relevant were those mapped in a region near the HRG, FETUB and KNG1 genes. Our results are provocative since they show that the KNG1 locus plays a central role as a genetic determinant of the entire coagulation pathway and thrombus/clot formation. Integrating data from multiple correlated measurements through metaphenotypes is a promising approach to elucidate the hidden genetic mechanisms underlying complex diseases.

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“…We used the SOLARIUS package for R (Ziyatdinov et al, 2016) to assess the following the (a) heritability of within BST‐CeA iFC; (b) co‐heritability of the within BST‐CeA iFC with each of the two principal components; and (c) phenotypic (rho), genetic (rhog), and environmental (rhoe) correlations between BST‐CeA iFC and each of the two principal components. We further ran a post hoc analysis, conducting the same tests but examining BST iFC with the superficial, centromedial, and basolateral amygdala regions.…”

Section: Methodsmentioning

confidence: 99%

Extended‐amygdala intrinsic functional connectivity networks: A population study

Berry

Wise

Lawrence

et al. 2020

Human Brain Mapping

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Pre‐clinical and human neuroimaging research implicates the extended‐amygdala (ExtA) (including the bed nucleus of the stria terminalis [BST] and central nucleus of the amygdala [CeA]) in networks mediating negative emotional states associated with stress and substance‐use behaviours. The extent to which individual ExtA structures form a functionally integrated unit is controversial. We utilised a large sample (n > 1,000 healthy young adult humans) to compare the intrinsic functional connectivity networks (ICNs) of the BST and CeA using task‐free functional magnetic resonance imaging (fMRI) data from the Human Connectome Project. We assessed whether inter‐individual differences within these ICNs were related to two principal components representing negative disposition and alcohol use. Building on recent primate evidence, we tested whether within BST‐CeA intrinsic functional connectivity (iFC) was heritable and further examined co‐heritability with our principal components. We demonstrate the BST and CeA to have discrete, but largely overlapping ICNs similar to previous findings. We found no evidence that within BST—CeA iFC was heritable; however, post hoc analyses found significant BST iFC heritability with the broader superficial and centromedial amygdala regions. There were no significant correlations or co‐heritability associations with our principal components either across the ICNs or for specific BST‐Amygdala iFC. Possible differences in phenotype associations across task‐free, task‐based, and clinical fMRI are discussed, along with suggestions for more causal investigative paradigms that make use of the now well‐established ExtA ICNs.

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solarius: an R interface to SOLAR for variance component analysis in pedigrees

Cited by 8 publications

References 4 publications

Heritability of cortical morphology reflects a sensory-fugal plasticity gradient

Heritability of cortical morphology reflects a sensory-fugal plasticity gradient

The Central Role of KNG1 Gene as a Genetic Determinant of Coagulation Pathway-Related Traits: Exploring Metaphenotypes

Extended‐amygdala intrinsic functional connectivity networks: A population study

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