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High-resolution maps of enhancer–promoter interactions in rare primary human T cell subsets and coronary artery smooth muscle cells link variants associated with autoimmune and cardiovascular diseases to target genes. This represents an important step forward for mapping genes involved in complex diseases.
This study presents a new approach to estimate the tissues contributing to the genetic causality for complex traits and diseases. The method assesses tissue sharing of eQTLs among 44 tissues and then uses these tissue-sharing estimates to infer the tissues where trait-associated variants likely exert their function.
CaVEMaN is a new method that uses whole-genome sequencing and RNA-sequencing data to implicate likely causal variants affecting gene expression. The set of high-confidence causal variants found in multiple tissues is enriched for variants associated with complex traits.
Roger Milne and colleagues conduct a genome-wide association study for estrogen receptor (ER)-negative breast cancer combined with BRCA1 mutation carriers in a large cohort. They identify ten new risk variants and find high genetic correlation between breast cancer risk for BRCA1 mutation carriers and risk of ER-negative breast cancer in the general population.
Covariates for multiphenotype studies (CMS), a new approach for testing for associations from large-scale datasets, leverages genetic and environmental factors shared between correlated variables measured on the same samples. Applying CMS to real and simulated data demonstrates a large increase in power equivalent to that gained by doubling the sample size.
Analysis of a large bread-wheat genomic data set through a quantitative genetic framework designed to study the genetic basis of heterosis shows that hybrids outperform midparents in grain yield by 10%. Genome-wide prediction and association mapping indicate that epistasis plays a significant role in heterosis of grain yield in wheat.
Genetic variants have been associated with myriad molecular phenotypes that provide new insight into the range of mechanisms underlying genetic traits and diseases. Identifying any particular genetic variant's cascade of effects, from molecule to individual, requires assaying multiple layers of molecular complexity. We introduce the Enhancing GTEx (eGTEx) project that extends the GTEx project to combine gene expression with additional intermediate molecular measurements on the same tissues to provide a resource for studying how genetic differences cascade through molecular phenotypes to impact human health.
This large-scale analysis of copy number alterations (CNAs) in patient-derived xenografts (PDXs) across 24 cancer types shows that new CNAs accumulate quickly and that the specific CNAs acquired during passaging differ from those acquired during tumor evolution in patients, suggesting that PDX tumors are under distinct selection pressures from tumors in human hosts.
A genome-wide association analysis using data from Chinese individuals combined with a transethnic meta-analysis of Psychiatry Genomics Consortium data identifies 30 new loci for schizophrenia. These analyses improve the fine-mapping of susceptibility loci and implicate multiple pathways in schizophrenia biology.
Exome sequencing of 2,871 probands with congenital heart disease (CHD) provides new insights into the genetic architecture of these disorders. The results implicate new genes in CHD pathogenesis and highlight striking overlap between genes with damaging de novo mutations in individuals with CHD and autism.
The assembly of the durian genome provides insights into the unique flavor profile of this tropical fruit. Transcriptome and metabolome analyses show that methionine γ-lyase is upregulated and that volatile sulfur compounds are produced during ripening.
Ali Shilatifard and colleagues generate Drosophila lines expressing catalytically deficient Trr, which normally deposits H3K4me1 at enhancers. Trr mutants undergo normal development and show minimal changes in gene expression.
Regulation of epigenetic factors through their recruitment to specific genomic regions is still poorly understood. A recent study demonstrates a global mechanism of tethering Polycomb group (PcG) proteins through sequence-specific DNA-binding factors.
This issue highlights a range of genetic techniques and cell biological models required to begin to understand the levels of long-range regulation of gene expression as it occurs during cell differentiation. Explanations based on the specificity of covalent modifications and binding interactions intersect with evidence for conjectured mechanisms of topological loop creation and maintenance by transcription and motile protein activities.
The functional role of repetitive elements in mammalian genomes is still largely unexplored. A new study provides evidence that LINE-1 retrotransposons regulate chromatin dynamics and are essential for normal embryonic development in mice.