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Doug Easton and colleagues report the results of a large-scale genome-wide association study of breast cancer. They discover 15 new susceptibility loci and highlight likely target genes in several of the newly associated regions. 
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Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser - Nature Biotechnology
Large consortia, such as the US National Institutes of Health (NIH) Roadmap Epigenomics Consortium and ENCODE, have generated tens of thousands of sequencing-based genome-wide data sets, creating a useful resource for the scientific community. The WashU Epigenome Browser continues to provide a platform for investigators to effectively engage with this resource in the context of analyzing their own data.
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A package of papers investigates the functional regulatory elements in genomes that have been obtained from human tissue samples and cell lines. The implications of the project are presented here from three viewpoints. See Articles p.317, p.331, p.337 & p.344 and Letters p.350, p.355, p.360 & p.365
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It had never been verified before: unlike other biopolymers, RNA, the long strand that is 'cousin' to DNA, tends not to form knots.
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Steven McCarroll and colleagues report an analysis of multiallelic copy number variants (mCNVs). They characterize mCNVs in 849 whole-genome sequences from the 1000 Genomes Project and find that mCNVs give rise to most gene dosage variation in humans.
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Adam Siepel and colleagues develop a statistical method, fitCons, which combines comparative and functional genomic data to estimate the probability that a point mutation will influence fitness. They generate fitCons scores for three human cell types from ENCODE data sets and demonstrate improved prediction power for cis regulatory elements in comparison to conventional conservation-based scores.
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In this study, the scientists provide insight into the mechanisms by which KATNB1 mutations cause human cerebral cortical malformations, demonstrating its fundamental role during brain development.
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Martin Reincke, Martin Fassnacht and colleagues identify somatic mutations in the USP8 deubiquitinase gene in corticotroph adenomas in Cushing's disease. The mutations enhanced proteolytic cleavage and catalytic activity of USP8, which led to activation of EGF receptor signaling.
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The authors identified ∼10,000 loops which are frequently linked to promoters and enhancers and correlate with gene activation. Loop anchors typically occur at domain boundaries and bind CTCF.
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Cas Simons, Ryan Taft and colleagues report the identification of KCNH1 mutations in six individuals with Temple-Baraitser syndrome (TBS). Electrophysiological measurements of cells expressing mutant KCNH1 channels show decreased activation thresholds and slower deactivation in comparison to wild-type channels, suggesting that these mutations lead to gain of function of KCNH1.
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A new study in mice has shown that the DNA of bacteria that live in the body can pass a trait to offspring in a way similar to the parents' own DNA. According to the authors, the discovery means scientists need to consider a significant new factor -- the DNA of microbes passed from mother to child -- in their efforts to understand how genes influence illness and health.
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Christopher O'Donnell and colleagues report a genome-wide screen for splicing quantitative trait loci (sQTLs) in 5,257 human blood samples. They identify cis sQTLs affecting mRNA isoform variation for over 2,000 genes, 367 of which are linked to trait-associated GWAS SNPs that overlapped with the sQTLs.
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Christina Curtis, Darryl Shibata and colleagues report genomic profiling of 349 individual glands sampled from 15 human colorectal tumors. They observe high within-tumor heterogeneity and mixing of subclones in distant tumor regions, supporting a model whereby tumor growth occurs predominantly as a single expansion, with most detectable subclonal mutations arising during the earliest phases of tumor growth.
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A specific mechanism by which a parent can pass silenced genes to its offspring has been uncovered by researchers for the first time. Importantly, the team found that this silencing could persist for multiple generations -- more than 25, in the case of this study.
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Lusheng Huang, Jun Ren and colleagues report the genome sequences of 69 pigs, representing 11 geographically distinct breeds and 3 wild boar populations, from within China. They identify loci related to high- and low-latitude adaptation and infer a likely ancient introgression event in northern Chinese pigs.
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Arul Chinnaiyan and colleagues report the curation of 7,256 RNA sequencing libraries from tumors, normal tissues and cell lines. They find 58,648 lncRNAs, of which 79% are previously unnannotated.
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Results from a new study defy textbook science, showing for the first time that the building blocks of a protein, called amino acids, can be assembled without blueprints – DNA and an intermediate template called messenger RNA (mRNA). A team of researchers has observed a case in which another protein specifies which amino acids are added.
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A new device for building large tissues from living components of three-dimensional microtissues borrows on ideas from electronics manufacturing. The Bio-Pick, Place, and Perfuse is a step toward someday making whole organs.
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Giuseppe Testa and colleagues report the generation and transcriptional characterization of patient-derived induced pluripotent stem cells (iPSCs) with copy number variants at 7q11.23, which cause syndromes including neurocognitive phenotypes. They find that the dosage of the transcription factor gene GTF2I accounts for 10-20% of the transcriptional dysregulation observed in these cells.
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The authors has discovered that mutations in the GTPBP3 gene cause defects in protein synthesis in mitochondria and are associated with a devastating disease. Identification of mutations in nine unrelated families makes GTPBP3 an important new genetic factor responsible for human mitochondrial disease.
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Understanding the crocodilian genome can help scientists better understand birds. The DNA in alligators, crocodiles and gharials is about 93 percent identical across the genome. By comparison, a human shares about 93 percent of his or her DNA with a macaque.
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Stephanie Debette and colleagues report the results of a genome-wide association study of cervical artery dissection, a major cause of ischemic stroke in young adults. They show that common variation in PHACTR1, previously associated with lower risk of migraine and increased risk of myocardial infarction, is associated with reduced risk of cervical artery dissection.
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