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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.
Benjamin Raphael and colleagues report an analysis of altered subnetworks of somatic aberrations in TCGA pan-cancer data sets, including 3,281 samples from 12 cancer types, using a newly developed HotNet2 algorithm. They identify 16 significantly mutated subnetworks and provide a more comprehensive view into altered pathways, including those with known roles in cancer development.
Guido Sauter, Roland Eils, Christoph Plass, Raffaella Santoro and colleagues report that the gene encoding the epigenetic regulator BAZ2A is overexpressed in prostate cancer, where it interacts with EZH2 to induce aberrant gene silencing and cell proliferation. The authors find that BAZ2A levels are predictive of disease recurrence in patients with prostate cancer.
Roland Rad and colleagues report development of a new conditional piggyBac transposition system for performing insertional mutagenesis screens in mice. They apply the system to identify new oncogenic driver pathways for pancreatic cancer.
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.
Emmanouil Dermitzakis, Alfonso Buil and colleagues measure transcriptome-wide expression in a sample of twins to measure the relative contribution of genetic and environmental effects on allele-specific expression and find substantial effects of gene × gene and gene × environment interactions.
Alan Lloyd and colleagues identify a MYB gene in beet that acts as a key regulator of the betalain red pigmentation pathway. They further show that this gene resides at the classical Y pigmentation locus and shares homology with MYB genes that encode positive regulators of the anthocyanin pigmentation pathway in other species.
Stéphanie 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.
Zhong-Jian Liu, Lai-Qiang Huang, Yi-Bo Luo, Hong-Hwa Chen and Yves Van de Peer report the first genome sequence of a crassulacean acid metabolism (CAM) plant, the orchid Phalaenopsis equestris. They identify genes encoding CAM pathway enzymes and find that gene duplication was likely a key process in the evolution of CAM photosynthesis.
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.
Anna-Elina Lehesjoki and colleagues report exome sequencing of 84 cases of progressive myoclonus epilepsy (PME) and targeted resequencing of an additional 28 cases. They identify de novo mutations in KCNC1 in 13 cases and mutations in genes not previously associated with PME, including PRNP, SACS and TBC1D24, in additional cases.
Somasekar Seshagiri, James Brugarolas and colleagues report the mutational landscape of 167 non–clear cell renal cell carcinomas (nccRCCs) from multiple subtypes. They identify subtype-specific driver mutations and gene fusions, including ones involving MITF, which result in expression of the anti-apoptotic protein BIRC7 and might thus indicate candidates for treatment with BIRC7 inhibitors.
Rasmus Marvig and colleagues report the whole-genome sequencing of 474 longitudinally collected clinical isolates of Pseudomonas aeruginosa sampled from 34 children and young patients with cystic fibrosis. They identify evidence of convergent evolution in 52 genes and suggest pathways involved in within-host adaptation and pathogenesis.
Mark Walker and colleagues report the whole-genome sequencing of 132 group A Streptococcus (GAS) isolates of a sequence type that has been associated with scarlet fever. The isolates were obtained from 58 clinical cases of scarlet fever and 83 cases without scarlet fever during the course of a recent epidemic in Hong Kong.
John Lis, Adam Siepel and colleagues map transcription start sites across the genome in two human cell lines using a nuclear run-on protocol called GRO-cap. They find a common architecture of initiation at both promoters and enhancers and that transcript elongation stability provides the strongest distinction between promoters and enhancers.
Erik Larsson and colleagues present an analysis pipeline for identifying likely transcription-altering noncoding somatic mutations in cancer using publicly available data from 505 tumor genomes across 14 cancer types. They find that TERT promoter mutations show strong associations to altered transcriptional levels and identify recurrent promoter mutations in DPH3 and PLEKHS1.
Noah Zaitlen, Alkes Price and colleagues report a new approach to estimate the narrow-sense heritability of complex traits from unrelated individuals in a recently admixed population. They apply this approach to estimate the heritability for 13 quantitative or case-control phenotypes in 21,497 African-American individuals and suggest the inflation of family-based h2 estimates.
Sarah Dunstan, Chiea Chuen Khor and colleagues identify common variants in the HLA-DRB1 region associated with resistance to enteric fever. Individuals carrying the protective variants exhibit roughly five-fold higher resistance against developing this life-threatening infectious disease.
Astrid von Mentzer, Gordon Dougan and colleagues report the whole-genome sequencing of a representative global collection of enterotoxigenic Escherichia coli (ETEC), a major cause of infectious diarrhea, including samples from 20 countries isolated between 1980 and 2011. They find that, although ETEC isolates are widely distributed across the E. coli species and are genetically diverse, there are several discrete lineages that have contributed to overlapping global epidemics.
