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Systems genetics approaches to understand complex traits

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TLDR
Systems genetics studies have provided the first global view of the molecular architecture of complex traits and are useful for the identification of genes, pathways and networks that underlie common human diseases.
Abstract
Systems genetics is an approach to understand the flow of biological information that underlies complex traits. It uses a range of experimental and statistical methods to quantitate and integrate intermediate phenotypes, such as transcript, protein or metabolite levels, in populations that vary for traits of interest. Systems genetics studies have provided the first global view of the molecular architecture of complex traits and are useful for the identification of genes, pathways and networks that underlie common human diseases. Given the urgent need to understand how the thousands of loci that have been identified in genome-wide association studies contribute to disease susceptibility, systems genetics is likely to become an increasingly important approach to understanding both biology and disease.

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Multi-omics approaches to disease.

TL;DR: This review provides an overview of omics technologies and methods for their integration across multiple omics layers and offers the opportunity to understand the flow of information that underlies disease.
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The Strategy of the Genes

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Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities

TL;DR: It is found that distinct tissue environments drive divergent programs of gene expression by differentially activating a common enhancer repertoire and by inducing the expression of divergent secondary transcription factors that collaborate with PU.1 to establish tissue-specific enhancers.
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The role of regulatory variation in complex traits and disease

TL;DR: Recent insights into the molecular nature of regulatory variants are reviewed and examples of complete chains of causality that link individual polymorphisms to changes in gene expression, which in turn result in physiological changes and, ultimately, disease risk are presented.
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HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease.

TL;DR: A use case of HaploReg is illustrated for attention deficit hyperactivity disorder (ADHD)-associated SNPs with putative brain regulatory mechanisms, and the number of chromatin state maps to 127 reference epigenomes is greatly expanded.
References
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Book

Introduction to quantitative genetics

TL;DR: The genetic constitution of a population: Hardy-Weinberg equilibrium and changes in gene frequency: migration mutation, changes of variance, and heritability are studied.
Journal ArticleDOI

Molecular portraits of human breast tumours

TL;DR: Variation in gene expression patterns in a set of 65 surgical specimens of human breast tumours from 42 different individuals were characterized using complementary DNA microarrays representing 8,102 human genes, providing a distinctive molecular portrait of each tumour.
MonographDOI

Causality: models, reasoning, and inference

TL;DR: The art and science of cause and effect have been studied in the social sciences for a long time as mentioned in this paper, see, e.g., the theory of inferred causation, causal diagrams and the identification of causal effects.
Journal ArticleDOI

The Genotype-Tissue Expression (GTEx) project

John T. Lonsdale, +129 more
- 29 May 2013 - 
TL;DR: The Genotype-Tissue Expression (GTEx) project is described, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.
Book

Genetics and Analysis of Quantitative Traits

Michael Lynch, +1 more
TL;DR: This book discusses the genetic Basis of Quantitative Variation, Properties of Distributions, Covariance, Regression, and Correlation, and Properties of Single Loci, and Sources of Genetic Variation for Multilocus Traits.
Related Papers (5)

The Genotype-Tissue Expression (GTEx) project

John T. Lonsdale, +129 more
- 29 May 2013 -